substitution minor allele frequency (MAF) submission details 251 Caucasian population panels 210 non-Caucasian population panels polyphen sift id snp_id gene locuslink id chromosome chromosome coordinate mRNA accession protein accession nucleotide amino acid UCSC strand subsnp_id population id population handle local population id population description total chromosomes genotyped MAF mean MAF stdev chromosomes genotyped number of submissions mean MAF stdev chromosomes genotyped number of submissions update build validation criterion prediction score number sequences aligned prediction score divergence score number sequences aligned grantham MIM number cytogenetic gene description 1 rs328 LPL 4023 8 19864004 NM_000237 NP_000228 C/G S474X plus 3173350 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 112 0.02 0.19 0.19 248 3 0.14 0.02 1546 3 123 "by cluster,freq" Probably damaging Intolerant radical 238600 8p22 lipoprotein lipase 2 rs328 LPL 4023 8 19864004 NM_000237 NP_000228 C/G S474X plus 10467174 1303 SEQUENOM CEPH CEPH (92) 92 0.36 0.19 0.19 248 3 0.14 0.02 1546 3 123 "by cluster,freq" Probably damaging Intolerant radical 238600 8p22 lipoprotein lipase 3 rs328 LPL 4023 8 19864004 NM_000237 NP_000228 C/G S474X plus 24648907 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.27 0.19 0.19 248 3 0.14 0.02 1546 3 123 "by cluster,freq" Probably damaging Intolerant radical 238600 8p22 lipoprotein lipase 4 rs662 PON1 5444 7 94582097 NM_000446 NP_000437 A/G Q192R minus 667 506 NCBI NIHPDR NIHPDR 180 0.48 0.33 0.1 942 7 0.4 0.03 4482 8 123 "by submitter,freq,cluster" Borderline 1.188 47 Tolerant 0.61 2.75 32 conservative 168820 7q21.3 paraoxonase 1 5 rs662 PON1 5444 7 94582097 NM_000446 NP_000437 A/G Q192R minus 4573 491 HU-CHINA CAU "Australian, Belgian, Canadian, English, Finnish, French, German and USA" 460 0.33 0.33 0.1 942 7 0.4 0.03 4482 8 123 "by submitter,freq,cluster" Borderline 1.188 47 Tolerant 0.61 2.75 32 conservative 168820 7q21.3 paraoxonase 1 6 rs662 PON1 5444 7 94582097 NM_000446 NP_000437 A/G Q192R minus 5111592 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.17 0.33 0.1 942 7 0.4 0.03 4482 8 123 "by submitter,freq,cluster" Borderline 1.188 47 Tolerant 0.61 2.75 32 conservative 168820 7q21.3 paraoxonase 1 7 rs662 PON1 5444 7 94582097 NM_000446 NP_000437 A/G Q192R minus 5111592 1303 SEQUENOM CEPH CEPH (92) 92 0.18 0.33 0.1 942 7 0.4 0.03 4482 8 123 "by submitter,freq,cluster" Borderline 1.188 47 Tolerant 0.61 2.75 32 conservative 168820 7q21.3 paraoxonase 1 8 rs662 PON1 5444 7 94582097 NM_000446 NP_000437 A/G Q192R minus 5586846 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.27 0.33 0.1 942 7 0.4 0.03 4482 8 123 "by submitter,freq,cluster" Borderline 1.188 47 Tolerant 0.61 2.75 32 conservative 168820 7q21.3 paraoxonase 1 9 rs662 PON1 5444 7 94582097 NM_000446 NP_000437 A/G Q192R minus 16338591 1120 WIPGA POP-WIPGA-12-05-2003 CORIELL Mixed 56 0.34 0.33 0.1 942 7 0.4 0.03 4482 8 123 "by submitter,freq,cluster" Borderline 1.188 47 Tolerant 0.61 2.75 32 conservative 168820 7q21.3 paraoxonase 1 10 rs662 PON1 5444 7 94582097 NM_000446 NP_000437 A/G Q192R minus 24194186 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.17 0.33 0.1 942 7 0.4 0.03 4482 8 123 "by submitter,freq,cluster" Borderline 1.188 47 Tolerant 0.61 2.75 32 conservative 168820 7q21.3 paraoxonase 1 11 rs671 ALDH2 217 12 110704486 NM_000690 NP_000681 A/G E504K plus 3177110 619 WICVAR MITOGPOP6 CORIELL Mixed 62 0.06 0.06 0 62 1 0.14 0.12 386 4 123 "by cluster,freq" Borderline 1.072 136 Potentially intolerant 0.06 2.82 145 moderately conservative 100650 12q24.2 aldehyde dehydrogenase 2 family (mitochondrial) 12 rs678 ITIH1 3697 3 52796021 NM_002215 NP_002206 A/T E585V plus 21978763 1303 SEQUENOM CEPH CEPH (92) 92 0.38 0.41 0.05 140 2 0.27 0.16 94 2 123 "by cluster,freq" Probably damaging 2.145 19 moderately radical 147270 3p21.2-p21.1 inter-alpha (globulin) inhibitor H1 13 rs678 ITIH1 3697 3 52796021 NM_002215 NP_002206 A/T E585V plus 24349616 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.41 0.05 140 2 0.27 0.16 94 2 123 "by cluster,freq" Probably damaging 2.145 19 moderately radical 147270 3p21.2-p21.1 inter-alpha (globulin) inhibitor H1 14 rs704 VTN 7448 17 23718988 NM_000638 NP_000629 C/T T400M minus 8443 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.48 0.47 0.02 421 4 0.29 0.2 130 2 121 "by doubleHit,freq,cluster" Benign 0.778 11 moderately conservative 193190 17q11 "vitronectin (serum spreading factor, somatomedin B, complement S-protein)" 15 rs704 VTN 7448 17 23718988 NM_000638 NP_000629 C/T T400M minus 1352184 782 TSC-CSHL WICGR6_CAUCASIAN_POOLED WICGR Caucasian (48) 96 0.45 0.47 0.02 421 4 0.29 0.2 130 2 121 "by doubleHit,freq,cluster" Benign 0.778 11 moderately conservative 193190 17q11 "vitronectin (serum spreading factor, somatomedin B, complement S-protein)" 16 rs704 VTN 7448 17 23718988 NM_000638 NP_000629 C/T T400M minus 3172312 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.43 0.47 0.02 421 4 0.29 0.2 130 2 121 "by doubleHit,freq,cluster" Benign 0.778 11 moderately conservative 193190 17q11 "vitronectin (serum spreading factor, somatomedin B, complement S-protein)" 17 rs704 VTN 7448 17 23718988 NM_000638 NP_000629 C/T T400M minus 3172312 1303 SEQUENOM CEPH CEPH (92) 91 0.47 0.47 0.02 421 4 0.29 0.2 130 2 121 "by doubleHit,freq,cluster" Benign 0.778 11 moderately conservative 193190 17q11 "vitronectin (serum spreading factor, somatomedin B, complement S-protein)" 18 rs1208 NAT2 10 8 18302596 NM_000015 NP_000006 A/G R268K plus 2323986 782 TSC-CSHL WICGR6_CAUCASIAN_POOLED WICGR Caucasian (48) 96 0.29 0.34 0.04 434 4 0.29 0.19 412 6 123 "by doubleHit,freq,cluster" Benign 0.474 32 conservative 243400 8p22 N-acetyltransferase 2 (arylamine N-acetyltransferase) 19 rs1208 NAT2 10 8 18302596 NM_000015 NP_000006 A/G R268K plus 2323986 1303 SEQUENOM CEPH CEPH (92) 92 0.35 0.34 0.04 434 4 0.29 0.19 412 6 123 "by doubleHit,freq,cluster" Benign 0.474 32 conservative 243400 8p22 N-acetyltransferase 2 (arylamine N-acetyltransferase) 20 rs1208 NAT2 10 8 18302596 NM_000015 NP_000006 A/G R268K plus 5586793 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.4 0.34 0.04 434 4 0.29 0.19 412 6 123 "by doubleHit,freq,cluster" Benign 0.474 32 conservative 243400 8p22 N-acetyltransferase 2 (arylamine N-acetyltransferase) 21 rs1208 NAT2 10 8 18302596 NM_000015 NP_000006 A/G R268K plus 24796685 1303 SEQUENOM CEPH CEPH (92) 184 0.35 0.34 0.04 434 4 0.29 0.19 412 6 123 "by doubleHit,freq,cluster" Benign 0.474 32 conservative 243400 8p22 N-acetyltransferase 2 (arylamine N-acetyltransferase) 22 rs1258 TAF1L 138474 9 32623119 NM_153809 NP_722516 A/G M820T plus 24810791 1303 SEQUENOM CEPH CEPH (92) 184 0.06 0.06 0 184 1 123 "by cluster,freq" Benign 0.273 13 Tolerant 1 3.03 30 moderately conservative 607798 9p13.3 "TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa" 23 rs1303 SERPINA1 5265 14 93914596 NM_000295 NP_000286 G/T E400D plus 8326 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.3 0.29 0.05 366 4 0.28 0.03 1590 4 123 "by doubleHit,submitter,freq,cluster" Benign 0.079 58 Tolerant 1 2.76 77 conservative 107400 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1" 24 rs1303 SERPINA1 5265 14 93914596 NM_000295 NP_000286 G/T E400D plus 20190 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 38 0.33 0.29 0.05 366 4 0.28 0.03 1590 4 123 "by doubleHit,submitter,freq,cluster" Benign 0.079 58 Tolerant 1 2.76 77 conservative 107400 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1" 25 rs1303 SERPINA1 5265 14 93914596 NM_000295 NP_000286 G/T E400D plus 16651029 1303 SEQUENOM CEPH CEPH (92) 92 0.3 0.29 0.05 366 4 0.28 0.03 1590 4 123 "by doubleHit,submitter,freq,cluster" Benign 0.079 58 Tolerant 1 2.76 77 conservative 107400 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1" 26 rs1303 SERPINA1 5265 14 93914596 NM_000295 NP_000286 G/T E400D plus 24129831 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.29 0.05 366 4 0.28 0.03 1590 4 123 "by doubleHit,submitter,freq,cluster" Benign 0.079 58 Tolerant 1 2.76 77 conservative 107400 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1" 27 rs1716 ITGAE 3682 17 3579585 NM_002208 NP_002199 C/T R950W minus 21376295 1303 SEQUENOM CEPH CEPH (92) 92 0.4 0.4 0 92 1 121 "by submitter,freq,cluster" Benign 0.9 5 Intolerant 0.02 2.83 18 moderately radical 604682 17p13 "integrin, alpha E (antigen CD103, human mucosal lymphocyte antigen 1; alpha polypeptide)" 28 rs1921 G1P2 9636 1 989675 NM_005101 NP_005092 A/G S83N plus 24810939 1303 SEQUENOM CEPH CEPH (92) 184 0.37 0.37 0 184 1 0.2 0 10 1 123 "by cluster,freq" Benign 0.03 5 Potentially intolerant 0.07 2.9 385 conservative 147571 1p36.33 "interferon, alpha-inducible protein (clone IFI-15K)" 29 rs2240 MKI67 4288 10 129797534 NM_002417 NP_002408 C/G L854V plus 2960666 1303 SEQUENOM CEPH CEPH (92) 92 0.25 0.24 0.03 140 2 0.28 0.05 104 3 123 "by doubleHit,freq,cluster" conservative 176741 10q25-qter antigen identified by monoclonal antibody Ki-67 30 rs2240 MKI67 4288 10 129797534 NM_002417 NP_002408 C/G L854V plus 23644026 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.24 0.03 140 2 0.28 0.05 104 3 123 "by doubleHit,freq,cluster" conservative 176741 10q25-qter antigen identified by monoclonal antibody Ki-67 31 rs2347 POLR3E 55718 16 22227018 NM_018119 NP_060589 A/C S46A minus 2375 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.08 0.08 0.02 260 3 123 "HapMap,submitter,freq" Borderline 1.163 11 Tolerant 0.58 2.85 24 moderately conservative 16p12.3 polymerase (RNA) III (DNA directed) polypeptide E (80kD) 32 rs2347 POLR3E 55718 16 22227018 NM_018119 NP_060589 A/C S46A minus 2375 1303 SEQUENOM CEPH CEPH (92) 92 0.09 0.08 0.02 260 3 123 "HapMap,submitter,freq" Borderline 1.163 11 Tolerant 0.58 2.85 24 moderately conservative 16p12.3 polymerase (RNA) III (DNA directed) polypeptide E (80kD) 33 rs2347 POLR3E 55718 16 22227018 NM_018119 NP_060589 A/C S46A minus 24569247 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.08 0.02 260 3 123 "HapMap,submitter,freq" Borderline 1.163 11 Tolerant 0.58 2.85 24 moderately conservative 16p12.3 polymerase (RNA) III (DNA directed) polypeptide E (80kD) 34 rs2640 HRI 27102 7 5839691 NM_014413 NP_055228 C/T K558R plus 2670 885 TSC-CSHL HapMap-CEPH-30-trios 110 0.03 0.08 0.04 916 6 0.33 0.04 4106 4 123 "HapMap,freq,cluster" Borderline 1.047 8 Tolerant 0.27 2.99 11 conservative 7p22 heme-regulated initiation factor 2-alpha kinase 35 rs2640 HRI 27102 7 5839691 NM_014413 NP_055228 C/T K558R plus 2670 1303 SEQUENOM CEPH CEPH (92) 92 0.09 0.08 0.04 916 6 0.33 0.04 4106 4 123 "HapMap,freq,cluster" Borderline 1.047 8 Tolerant 0.27 2.99 11 conservative 7p22 heme-regulated initiation factor 2-alpha kinase 36 rs2640 HRI 27102 7 5839691 NM_014413 NP_055228 C/T K558R plus 4551 491 HU-CHINA CAU "Australian, Belgian, Canadian, English, Finnish, French, German and USA" 460 0.11 0.08 0.04 916 6 0.33 0.04 4106 4 123 "HapMap,freq,cluster" Borderline 1.047 8 Tolerant 0.27 2.99 11 conservative 7p22 heme-regulated initiation factor 2-alpha kinase 37 rs2640 HRI 27102 7 5839691 NM_014413 NP_055228 C/T K558R plus 16336055 902 AFFY Caucasian 22 0.09 0.08 0.04 916 6 0.33 0.04 4106 4 123 "HapMap,freq,cluster" Borderline 1.047 8 Tolerant 0.27 2.99 11 conservative 7p22 heme-regulated initiation factor 2-alpha kinase 38 rs2640 HRI 27102 7 5839691 NM_014413 NP_055228 C/T K558R plus 23989050 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.08 0.04 916 6 0.33 0.04 4106 4 123 "HapMap,freq,cluster" Borderline 1.047 8 Tolerant 0.27 2.99 11 conservative 7p22 heme-regulated initiation factor 2-alpha kinase 39 rs2640 HRI 27102 7 5839691 NM_014413 NP_055228 C/T K558R plus 24796328 1303 SEQUENOM CEPH CEPH (92) 184 0.04 0.08 0.04 916 6 0.33 0.04 4106 4 123 "HapMap,freq,cluster" Borderline 1.047 8 Tolerant 0.27 2.99 11 conservative 7p22 heme-regulated initiation factor 2-alpha kinase 40 rs2759 MPO 4353 17 53703105 NM_000250 NP_000241 A/G I717V minus 16338615 1120 WIPGA POP-WIPGA-12-05-2003 CORIELL Mixed 16 0.06 0.03 0.02 64 2 0.04 0 46 1 123 "by cluster,freq" Benign 0.293 19 Tolerant 1 2.78 29 conservative 606989 17q23.1 myeloperoxidase 41 rs2759 MPO 4353 17 53703105 NM_000250 NP_000241 A/G I717V minus 23791841 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.03 0.02 64 2 0.04 0 46 1 123 "by cluster,freq" Benign 0.293 19 Tolerant 1 2.78 29 conservative 606989 17q23.1 myeloperoxidase 42 rs2791 TRAP1 10131 16 3648171 NM_016292 NP_057376 C/T R692H plus 2821 1303 SEQUENOM CEPH CEPH (92) 92 0.09 0.08 0.02 140 2 123 "by cluster,freq" Potentially damaging 1.355 6 Intolerant 0.01 2.85 27 conservative 606219 16p13.3 heat shock protein 75 43 rs2791 TRAP1 10131 16 3648171 NM_016292 NP_057376 C/T R692H plus 24709278 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.08 0.02 140 2 123 "by cluster,freq" Potentially damaging 1.355 6 Intolerant 0.01 2.85 27 conservative 606219 16p13.3 heat shock protein 75 44 rs2941 GRM1 2911 6 146796825 NM_000838 NP_000829 A/G V929I plus 2972 549 KYUGEN CP CEPH (78) 156 0.11 0.09 0.02 432 3 123 "by cluster,freq" Benign 0.238 16 conservative 604473 6q24 "glutamate receptor, metabotropic 1" 45 rs2941 GRM1 2911 6 146796825 NM_000838 NP_000829 A/G V929I plus 14796794 1303 SEQUENOM CEPH CEPH (92) 92 0.07 0.09 0.02 432 3 123 "by cluster,freq" Benign 0.238 16 conservative 604473 6q24 "glutamate receptor, metabotropic 1" 46 rs2941 GRM1 2911 6 146796825 NM_000838 NP_000829 A/G V929I plus 24796320 1303 SEQUENOM CEPH CEPH (92) 184 0.09 0.09 0.02 432 3 123 "by cluster,freq" Benign 0.238 16 conservative 604473 6q24 "glutamate receptor, metabotropic 1" 47 rs3501 PAXIP1L 22976 7 154176057 NM_007349 NP_031375 A/G M979V minus 3536 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.26 0.26 0 212 2 0.4 0 10 1 100 "HapMap,submitter,freq,cluster" conservative 608254 7q36 PAX transcription activation domain interacting protein 1 like 48 rs3501 PAXIP1L 22976 7 154176057 NM_007349 NP_031375 A/G M979V minus 3536 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.26 0 212 2 0.4 0 10 1 100 "HapMap,submitter,freq,cluster" conservative 608254 7q36 PAX transcription activation domain interacting protein 1 like 49 rs3575 LDHB 3945 12 21679867 NM_002300 NP_002291 C/T C294Y plus 24811306 1303 SEQUENOM CEPH CEPH (92) 184 0.41 0.41 0 184 1 123 "by cluster,freq" Probably damaging 3.442 150 Intolerant 0 2.84 161 radical 150100 12p12.2-p12.1 lactate dehydrogenase B 50 rs4530 ADORA2A 135 22 23154075 NM_000675 NP_000666 C/T A50V plus 7888 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 74 0.03 0.03 0 74 1 0.05 0.01 126 2 123 "HapMap,freq,cluster" Benign 0.173 9 Tolerant 1 2.77 49 moderately conservative 102776 22q11.23 adenosine A2a receptor 51 rs4531 DBH 1621 9 133538924 NM_000787 NP_000778 G/T A304S plus 7897 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 70 0.1 0.09 0.01 162 2 0.07 0.02 574 3 121 "by cluster,freq" Borderline 1.07 11 Tolerant 0.9 2.81 27 moderately conservative 223360 9q34 dopamine beta-hydroxylase (dopamine beta-monooxygenase) 52 rs4531 DBH 1621 9 133538924 NM_000787 NP_000778 G/T A304S plus 22887000 1303 SEQUENOM CEPH CEPH (92) 92 0.09 0.09 0.01 162 2 0.07 0.02 574 3 121 "by cluster,freq" Borderline 1.07 11 Tolerant 0.9 2.81 27 moderately conservative 223360 9q34 dopamine beta-hydroxylase (dopamine beta-monooxygenase) 53 rs4534 CYP11B1 1584 8 143958104 NM_000497 NP_000488 A/G R43Q minus 8040 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.1 0.1 0 86 1 0.4 0.13 1448 4 123 "by doubleHit,freq,cluster" conservative 202010 8q21 "cytochrome P450, family 11, subfamily B, polypeptide 1" 54 rs4539 CYP11B2 1585 8 143993541 NM_000498 NP_000489 A/G K173R minus 8079 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.33 0.33 0 86 1 0.3 0 148 1 52 "by cluster,freq" Tolerant 0.55 2.81 33 conservative 124080 8q21-q22 "cytochrome P450, family 11, subfamily B, polypeptide 2" 55 rs4541 CYP11B1 1584 8 143953695 NM_000497 NP_000488 C/T A386V minus 8047 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.33 0.33 0 172 2 0.1 0 68 1 120 "by doubleHit,freq,cluster" Possibly damaging 1.505 36 moderately conservative 202010 8q21 "cytochrome P450, family 11, subfamily B, polypeptide 1" 56 rs4541 CYP11B1 1584 8 143953695 NM_000497 NP_000488 C/T A386V minus 8084 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.33 0.33 0 172 2 0.1 0 68 1 120 "by doubleHit,freq,cluster" Possibly damaging 1.505 36 moderately conservative 202010 8q21 "cytochrome P450, family 11, subfamily B, polypeptide 1" 57 rs4544 CYP11B2 1585 8 143991808 NM_000498 NP_000489 C/T I339T minus 8088 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 80 0.33 0.33 0 80 1 0.45 0.07 82 2 123 "by cluster,freq" Benign 0.225 36 Tolerant 0.52 2.81 33 moderately conservative 124080 8q21-q22 "cytochrome P450, family 11, subfamily B, polypeptide 2" 58 rs4545 CYP11B2 1585 8 143991043 NM_000498 NP_000489 A/G G435S minus 8089 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 82 0.33 0.33 0 82 1 0.05 0 68 1 120 "by doubleHit,freq,cluster" Potentially damaging 1.38 17 Tolerant 0.66 2.84 27 moderately conservative 124080 8q21-q22 "cytochrome P450, family 11, subfamily B, polypeptide 2" 59 rs4562 CLDN7 1366 17 7104463 NM_001307 NP_001298 A/G V197A plus 8465 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.32 0.32 0 280 2 120 "by doubleHit,freq,cluster" Benign 0.847 27 moderately conservative 17p13 claudin 7 60 rs4562 CLDN7 1366 17 7104463 NM_001307 NP_001298 A/G V197A plus 606039 1303 SEQUENOM CEPH CEPH (92) 92 0.32 0.32 0 280 2 120 "by doubleHit,freq,cluster" Benign 0.847 27 moderately conservative 17p13 claudin 7 61 rs4588 GC 2638 4 72983358 NM_000583 NP_000574 A/C T436K minus 8817 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.3 0.33 0.07 524 4 0.22 0.04 344 4 123 "by cluster,freq" Benign 0.198 9 Borderline 0.16 2.75 20 moderately conservative 139200 4q12-q13 group-specific component (vitamin D binding protein) 62 rs4588 GC 2638 4 72983358 NM_000583 NP_000574 A/C T436K minus 6903803 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.23 0.33 0.07 524 4 0.22 0.04 344 4 123 "by cluster,freq" Benign 0.198 9 Borderline 0.16 2.75 20 moderately conservative 139200 4q12-q13 group-specific component (vitamin D binding protein) 63 rs4588 GC 2638 4 72983358 NM_000583 NP_000574 A/C T436K minus 6903803 1303 SEQUENOM CEPH CEPH (92) 92 0.3 0.33 0.07 524 4 0.22 0.04 344 4 123 "by cluster,freq" Benign 0.198 9 Borderline 0.16 2.75 20 moderately conservative 139200 4q12-q13 group-specific component (vitamin D binding protein) 64 rs4588 GC 2638 4 72983358 NM_000583 NP_000574 A/C T436K minus 24796216 1303 SEQUENOM CEPH CEPH (92) 184 0.4 0.33 0.07 524 4 0.22 0.04 344 4 123 "by cluster,freq" Benign 0.198 9 Borderline 0.16 2.75 20 moderately conservative 139200 4q12-q13 group-specific component (vitamin D binding protein) 65 rs4602 KRT19 3880 17 36937847 NM_002276 NP_002267 C/G A60G minus 8962 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.37 0.34 0.06 324 3 0.15 0.17 86 2 123 "by doubleHit,freq" Tolerant 0.65 2.87 65 moderately conservative 148020 17q21.2 keratin 19 66 rs4602 KRT19 3880 17 36937847 NM_002276 NP_002267 C/G A60G minus 8962 1303 SEQUENOM CEPH CEPH (92) 92 0.34 0.34 0.06 324 3 0.15 0.17 86 2 123 "by doubleHit,freq" Tolerant 0.65 2.87 65 moderately conservative 148020 17q21.2 keratin 19 67 rs4602 KRT19 3880 17 36937847 NM_002276 NP_002267 C/G A60G minus 23597995 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.23 0.34 0.06 324 3 0.15 0.17 86 2 123 "by doubleHit,freq" Tolerant 0.65 2.87 65 moderately conservative 148020 17q21.2 keratin 19 68 rs4619 IGFBP1 3484 7 45705909 NM_000596 NP_000587 A/G I253M plus 9319 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.36 0.34 0.03 628 5 0.4 0.08 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.88 12 Borderline 0.2 2.8 26 conservative 146730 7p13-p12 insulin-like growth factor binding protein 1 69 rs4619 IGFBP1 3484 7 45705909 NM_000596 NP_000587 A/G I253M plus 2965913 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.3 0.34 0.03 628 5 0.4 0.08 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.88 12 Borderline 0.2 2.8 26 conservative 146730 7p13-p12 insulin-like growth factor binding protein 1 70 rs4619 IGFBP1 3484 7 45705909 NM_000596 NP_000587 A/G I253M plus 2965913 1303 SEQUENOM CEPH CEPH (92) 92 0.36 0.34 0.03 628 5 0.4 0.08 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.88 12 Borderline 0.2 2.8 26 conservative 146730 7p13-p12 insulin-like growth factor binding protein 1 71 rs4619 IGFBP1 3484 7 45705909 NM_000596 NP_000587 A/G I253M plus 13452540 693 EGP_SNPS PDR90 NIHPDR 180 0.35 0.34 0.03 628 5 0.4 0.08 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.88 12 Borderline 0.2 2.8 26 conservative 146730 7p13-p12 insulin-like growth factor binding protein 1 72 rs4619 IGFBP1 3484 7 45705909 NM_000596 NP_000587 A/G I253M plus 23455231 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.34 0.03 628 5 0.4 0.08 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.88 12 Borderline 0.2 2.8 26 conservative 146730 7p13-p12 insulin-like growth factor binding protein 1 73 rs4644 LGALS3 3958 14 54674688 NM_002306 NP_002297 A/C P64H plus 9801 1303 SEQUENOM CEPH CEPH (92) 92 0.08 0.21 0.25 138 2 0.22 0.11 86 2 123 "by cluster,freq" moderately conservative 153619 14q21-q22 "lectin, galactoside-binding, soluble, 3 (galectin 3)" 74 rs4644 LGALS3 3958 14 54674688 NM_002306 NP_002297 A/C P64H plus 24615984 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.46 0.21 0.25 138 2 0.22 0.11 86 2 123 "by cluster,freq" moderately conservative 153619 14q21-q22 "lectin, galactoside-binding, soluble, 3 (galectin 3)" 75 rs4652 LGALS3 3958 14 54674789 NM_002306 NP_002297 A/C T98P plus 10155 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.45 0.46 0.03 280 2 120 "by doubleHit,freq,cluster" conservative 153619 14q21-q22 "lectin, galactoside-binding, soluble, 3 (galectin 3)" 76 rs4652 LGALS3 3958 14 54674789 NM_002306 NP_002297 A/C T98P plus 10741054 1303 SEQUENOM CEPH CEPH (92) 92 0.49 0.46 0.03 280 2 120 "by doubleHit,freq,cluster" conservative 153619 14q21-q22 "lectin, galactoside-binding, soluble, 3 (galectin 3)" 77 rs4660 SPP1 6696 4 89261184 NM_000582 NP_000573 A/G R287H plus 10351 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.13 0.13 0 280 2 0.17 0 46 1 123 by freq Possibly damaging 1.979 20 conservative 166490 4q21-q25 "secreted phosphoprotein 1 (osteopontin, bone sialoprotein I, early T-lymphocyte activation 1)" 78 rs4660 SPP1 6696 4 89261184 NM_000582 NP_000573 A/G R287H plus 10351 1303 SEQUENOM CEPH CEPH (92) 92 0.13 0.13 0 280 2 0.17 0 46 1 123 by freq Possibly damaging 1.979 20 conservative 166490 4q21-q25 "secreted phosphoprotein 1 (osteopontin, bone sialoprotein I, early T-lymphocyte activation 1)" 79 rs4673 CYBA 1535 16 87240737 NM_000101 NP_000092 C/T Y72H minus 9045 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.5 0.42 0.09 506 6 0.13 0.11 1918 7 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.704 16 moderately conservative 608508 16q24 "cytochrome b-245, alpha polypeptide" 80 rs4673 CYBA 1535 16 87240737 NM_000101 NP_000092 C/T Y72H minus 3173156 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 44 0.43 0.42 0.09 506 6 0.13 0.11 1918 7 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.704 16 moderately conservative 608508 16q24 "cytochrome b-245, alpha polypeptide" 81 rs4673 CYBA 1535 16 87240737 NM_000101 NP_000092 C/T Y72H minus 6598678 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.34 0.42 0.09 506 6 0.13 0.11 1918 7 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.704 16 moderately conservative 608508 16q24 "cytochrome b-245, alpha polypeptide" 82 rs4673 CYBA 1535 16 87240737 NM_000101 NP_000092 C/T Y72H minus 6598678 1303 SEQUENOM CEPH CEPH (92) 46 0.5 0.42 0.09 506 6 0.13 0.11 1918 7 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.704 16 moderately conservative 608508 16q24 "cytochrome b-245, alpha polypeptide" 83 rs4673 CYBA 1535 16 87240737 NM_000101 NP_000092 C/T Y72H minus 6903734 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.32 0.42 0.09 506 6 0.13 0.11 1918 7 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.704 16 moderately conservative 608508 16q24 "cytochrome b-245, alpha polypeptide" 84 rs4673 CYBA 1535 16 87240737 NM_000101 NP_000092 C/T Y72H minus 23779281 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.42 0.09 506 6 0.13 0.11 1918 7 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.704 16 moderately conservative 608508 16q24 "cytochrome b-245, alpha polypeptide" 85 rs4740 EBI3 10148 19 4187996 NM_005755 NP_005746 A/G V201I plus 13009 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.41 0.35 0.07 556 6 0.31 0.03 136 4 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 1 2.84 19 conservative 605816 19p13.3 Epstein-Barr virus induced gene 3 86 rs4740 EBI3 10148 19 4187996 NM_005755 NP_005746 A/G V201I plus 88814 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 20 0.25 0.35 0.07 556 6 0.31 0.03 136 4 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 1 2.84 19 conservative 605816 19p13.3 Epstein-Barr virus induced gene 3 87 rs4740 EBI3 10148 19 4187996 NM_005755 NP_005746 A/G V201I plus 88814 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 88 0.28 0.35 0.07 556 6 0.31 0.03 136 4 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 1 2.84 19 conservative 605816 19p13.3 Epstein-Barr virus induced gene 3 88 rs4740 EBI3 10148 19 4187996 NM_005755 NP_005746 A/G V201I plus 1968400 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.3 0.35 0.07 556 6 0.31 0.03 136 4 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 1 2.84 19 conservative 605816 19p13.3 Epstein-Barr virus induced gene 3 89 rs4740 EBI3 10148 19 4187996 NM_005755 NP_005746 A/G V201I plus 1968400 1303 SEQUENOM CEPH CEPH (92) 92 0.41 0.35 0.07 556 6 0.31 0.03 136 4 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 1 2.84 19 conservative 605816 19p13.3 Epstein-Barr virus induced gene 3 90 rs4740 EBI3 10148 19 4187996 NM_005755 NP_005746 A/G V201I plus 24191234 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.35 0.07 556 6 0.31 0.03 136 4 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 1 2.84 19 conservative 605816 19p13.3 Epstein-Barr virus induced gene 3 91 rs4760 PLAUR 5329 19 48844940 NM_002659 NP_002650 C/T L317P minus 10984 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.11 0.13 0.03 510 4 0.02 0 46 1 121 "by doubleHit,freq,cluster" Possibly damaging 1.947 9 moderately conservative 173391 19q13 "plasminogen activator, urokinase receptor" 92 rs4760 PLAUR 5329 19 48844940 NM_002659 NP_002650 C/T L317P minus 13784 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.16 0.13 0.03 510 4 0.02 0 46 1 121 "by doubleHit,freq,cluster" Possibly damaging 1.947 9 moderately conservative 173391 19q13 "plasminogen activator, urokinase receptor" 93 rs4760 PLAUR 5329 19 48844940 NM_002659 NP_002650 C/T L317P minus 5607654 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 42 0.12 0.13 0.03 510 4 0.02 0 46 1 121 "by doubleHit,freq,cluster" Possibly damaging 1.947 9 moderately conservative 173391 19q13 "plasminogen activator, urokinase receptor" 94 rs4760 PLAUR 5329 19 48844940 NM_002659 NP_002650 C/T L317P minus 21508716 1303 SEQUENOM CEPH CEPH (92) 92 0.14 0.13 0.03 510 4 0.02 0 46 1 121 "by doubleHit,freq,cluster" Possibly damaging 1.947 9 moderately conservative 173391 19q13 "plasminogen activator, urokinase receptor" 95 rs4774 MHC2TA 4261 16 10908349 NM_000246 NP_000237 C/G G500A plus 11869 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.36 0.33 0.04 698 6 0.18 0.11 94 2 123 "HapMap,doubleHit,freq,cluster" Borderline 1.227 9 moderately conservative 600005 16p13 MHC class II transactivator 96 rs4774 MHC2TA 4261 16 10908349 NM_000246 NP_000237 C/G G500A plus 14168 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.31 0.33 0.04 698 6 0.18 0.11 94 2 123 "HapMap,doubleHit,freq,cluster" Borderline 1.227 9 moderately conservative 600005 16p13 MHC class II transactivator 97 rs4774 MHC2TA 4261 16 10908349 NM_000246 NP_000237 C/G G500A plus 3172899 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 62 0.39 0.33 0.04 698 6 0.18 0.11 94 2 123 "HapMap,doubleHit,freq,cluster" Borderline 1.227 9 moderately conservative 600005 16p13 MHC class II transactivator 98 rs4774 MHC2TA 4261 16 10908349 NM_000246 NP_000237 C/G G500A plus 6596713 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.32 0.33 0.04 698 6 0.18 0.11 94 2 123 "HapMap,doubleHit,freq,cluster" Borderline 1.227 9 moderately conservative 600005 16p13 MHC class II transactivator 99 rs4774 MHC2TA 4261 16 10908349 NM_000246 NP_000237 C/G G500A plus 6596713 1303 SEQUENOM CEPH CEPH (92) 92 0.36 0.33 0.04 698 6 0.18 0.11 94 2 123 "HapMap,doubleHit,freq,cluster" Borderline 1.227 9 moderately conservative 600005 16p13 MHC class II transactivator 100 rs4774 MHC2TA 4261 16 10908349 NM_000246 NP_000237 C/G G500A plus 23587538 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.33 0.04 698 6 0.18 0.11 94 2 123 "HapMap,doubleHit,freq,cluster" Borderline 1.227 9 moderately conservative 600005 16p13 MHC class II transactivator 101 rs4807 TXNDC7 10130 2 10881501 NM_005742 NP_005733 A/G K214R minus 15613 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.22 0.22 0 328 3 0.31 0.04 1586 3 123 "by doubleHit,freq,cluster" Potentially damaging 1.393 14 Borderline 0.19 2.9 29 conservative 2p25.1 thioredoxin domain containing 7 (protein disulfide isomerase) 102 rs4807 TXNDC7 10130 2 10881501 NM_005742 NP_005733 A/G K214R minus 2427777 1303 SEQUENOM CEPH CEPH (92) 92 0.22 0.22 0 328 3 0.31 0.04 1586 3 123 "by doubleHit,freq,cluster" Potentially damaging 1.393 14 Borderline 0.19 2.9 29 conservative 2p25.1 thioredoxin domain containing 7 (protein disulfide isomerase) 103 rs4807 TXNDC7 10130 2 10881501 NM_005742 NP_005733 A/G K214R minus 24162907 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.22 0 328 3 0.31 0.04 1586 3 123 "by doubleHit,freq,cluster" Potentially damaging 1.393 14 Borderline 0.19 2.9 29 conservative 2p25.1 thioredoxin domain containing 7 (protein disulfide isomerase) 104 rs4814 SRP14 6727 15 38115849 NM_003134 NP_003125 A/G T130A minus 15331 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.24 0.31 0.1 376 2 52 by freq moderately conservative 600708 15q22 signal recognition particle 14kDa (homologous Alu RNA binding protein) 105 rs4814 SRP14 6727 15 38115849 NM_003134 NP_003125 A/G T130A minus 15862 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.38 0.31 0.1 376 2 52 by freq moderately conservative 600708 15q22 signal recognition particle 14kDa (homologous Alu RNA binding protein) 106 rs4816 PCMT1 5110 6 150206859 NM_005389 NP_005380 A/G V120I plus 15904 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.37 0.37 0 188 1 108 by freq Benign 0.304 16 Tolerant 1 2.86 29 conservative 176851 6q24-q25 protein-L-isoaspartate (D-aspartate) O-methyltransferase 107 rs4870 TNFRSF14 8764 1 2528567 NM_003820 NP_003811 A/G K17R minus 16359043 693 EGP_SNPS PDR90 NIHPDR 172 0.42 0.42 0 172 1 120 "by doubleHit,freq,cluster" conservative 602746 1p36.3-p36.2 "tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)" 108 rs4907 PSMB3 5691 17 34163025 NM_002795 NP_002786 A/T M34L plus 6616906 1303 SEQUENOM CEPH CEPH (92) 92 0.03 0.03 0 92 1 123 by freq Borderline 1.14 39 Intolerant 0.05 2.88 38 conservative 602176 17q12 "proteasome (prosome, macropain) subunit, beta type, 3" 109 rs4925 GSTO1 9446 10 106012779 NM_004832 NP_004823 A/C A140D plus 4926470 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.34 0.35 0.01 260 3 0.13 0.02 1620 4 123 "HapMap,submitter,freq,cluster" Benign 0.184 19 Borderline 0.16 2.93 23 moderately radical 605482 10q25.1 glutathione S-transferase omega 1 110 rs4925 GSTO1 9446 10 106012779 NM_004832 NP_004823 A/C A140D plus 20723413 1303 SEQUENOM CEPH CEPH (92) 92 0.36 0.35 0.01 260 3 0.13 0.02 1620 4 123 "HapMap,submitter,freq,cluster" Benign 0.184 19 Borderline 0.16 2.93 23 moderately radical 605482 10q25.1 glutathione S-transferase omega 1 111 rs4925 GSTO1 9446 10 106012779 NM_004832 NP_004823 A/C A140D plus 24502881 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.35 0.01 260 3 0.13 0.02 1620 4 123 "HapMap,submitter,freq,cluster" Benign 0.184 19 Borderline 0.16 2.93 23 moderately radical 605482 10q25.1 glutathione S-transferase omega 1 112 rs4945 MFGE8 4240 15 87257548 NM_005928 NP_005919 A/C R3S minus 5471 1303 SEQUENOM CEPH CEPH (92) 92 0.4 0.4 0 92 1 123 by freq moderately radical 602281 15q25 milk fat globule-EGF factor 8 protein 113 rs5054 AKR1B1 231 7 133601027 NM_001628 NP_001619 A/T I15F minus 6498 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.01 0 92 1 0.1 0 68 1 52 HapMap Possibly damaging 1.697 67 Intolerant 0.01 2.76 118 conservative 103880 7q35 "aldo-keto reductase family 1, member B1 (aldose reductase)" 114 rs5056 AKR1B1 231 7 133593702 NM_001628 NP_001619 A/T H42L minus 6500 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.01 0 92 1 0.05 0 80 1 52 by freq Probably damaging 3.801 71 Intolerant 0 2.77 123 moderately conservative 103880 7q35 "aldo-keto reductase family 1, member B1 (aldose reductase)" 115 rs5167 APOC4 346 19 50140305 NM_001646 NP_001637 G/T L96R plus 16797417 1303 SEQUENOM CEPH CEPH (92) 92 0.23 0.38 0.12 322 3 0.4 0.06 450 5 123 "by doubleHit,submitter,freq,cluster" moderately radical 600745 19q13.2 apolipoprotein C-IV 116 rs5167 APOC4 346 19 50140305 NM_001646 NP_001637 G/T L96R plus 24106807 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.39 0.38 0.12 322 3 0.4 0.06 450 5 123 "by doubleHit,submitter,freq,cluster" moderately radical 600745 19q13.2 apolipoprotein C-IV 117 rs5167 APOC4 346 19 50140305 NM_001646 NP_001637 G/T L96R plus 24795972 1303 SEQUENOM CEPH CEPH (92) 184 0.45 0.38 0.12 322 3 0.4 0.06 450 5 123 "by doubleHit,submitter,freq,cluster" moderately radical 600745 19q13.2 apolipoprotein C-IV 118 rs5273 PTGS2 5743 1 183375425 NM_000963 NP_000954 C/T V511A minus 4479801 506 NCBI NIHPDR NIHPDR 160 0.01 0.01 0 330 2 0.05 0.06 380 5 113 "by cluster,freq" Benign 0.282 62 Tolerant 0.54 2.88 54 moderately conservative 600262 1q25.2-q25.3 prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase) 119 rs5273 PTGS2 5743 1 183375425 NM_000963 NP_000954 C/T V511A minus 6396201 693 EGP_SNPS PDR90 NIHPDR 170 0.01 0.01 0 330 2 0.05 0.06 380 5 113 "by cluster,freq" Benign 0.282 62 Tolerant 0.54 2.88 54 moderately conservative 600262 1q25.2-q25.3 prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase) 120 rs5294 CYP11B1 1584 8 143953458 NM_000497 NP_000488 C/T Y439H minus 24796366 1303 SEQUENOM CEPH CEPH (92) 184 0.36 0.36 0 184 1 0.05 0 68 1 123 "by cluster,freq" Borderline 0.16 2.77 40 moderately conservative 202010 8q21 "cytochrome P450, family 11, subfamily B, polypeptide 1" 121 rs5320 DBH 1621 9 133537027 NM_000787 NP_000778 A/G A197T plus 6782 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.02 0.04 0.04 210 2 0.1 0 148 1 121 "HapMap,freq,cluster" Borderline 1.041 11 Tolerant 0.44 2.87 24 moderately conservative 223360 9q34 dopamine beta-hydroxylase (dopamine beta-monooxygenase) 122 rs5320 DBH 1621 9 133537027 NM_000787 NP_000778 A/G A197T plus 22886995 1303 SEQUENOM CEPH CEPH (92) 92 0.07 0.04 0.04 210 2 0.1 0 148 1 121 "HapMap,freq,cluster" Borderline 1.041 11 Tolerant 0.44 2.87 24 moderately conservative 223360 9q34 dopamine beta-hydroxylase (dopamine beta-monooxygenase) 123 rs5324 DBH 1621 9 133538212 NM_000787 NP_000778 A/G D276N plus 6786 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.1 0.1 0 120 1 0.06 0.01 126 2 123 "HapMap,submitter,freq,cluster" Borderline 1.029 11 Tolerant 0.22 2.81 27 conservative 223360 9q34 dopamine beta-hydroxylase (dopamine beta-monooxygenase) 124 rs5355 SELE 6401 1 166427528 NM_000450 NP_000441 C/T L575F minus 5111468 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 42 0.05 0.07 0.03 182 3 0.08 0.04 116 2 123 "by cluster,freq" Intolerant 0.04 3.13 23 conservative 131210 1q22-q25 selectin E (endothelial adhesion molecule 1) 125 rs5355 SELE 6401 1 166427528 NM_000450 NP_000441 C/T L575F minus 5111468 1303 SEQUENOM CEPH CEPH (92) 92 0.1 0.07 0.03 182 3 0.08 0.04 116 2 123 "by cluster,freq" Intolerant 0.04 3.13 23 conservative 131210 1q22-q25 selectin E (endothelial adhesion molecule 1) 126 rs5355 SELE 6401 1 166427528 NM_000450 NP_000441 C/T L575F minus 24266318 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.07 0.03 182 3 0.08 0.04 116 2 123 "by cluster,freq" Intolerant 0.04 3.13 23 conservative 131210 1q22-q25 selectin E (endothelial adhesion molecule 1) 127 rs5361 SELE 6401 1 166432718 NM_000450 NP_000441 A/C S149R minus 5111403 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 44 0.09 0.08 0.07 194 3 0.06 0.02 538 6 123 "by cluster,freq" Possibly damaging 1.548 8 Intolerant 0 2.8 52 moderately radical 131210 1q22-q25 selectin E (endothelial adhesion molecule 1) 128 rs5361 SELE 6401 1 166432718 NM_000450 NP_000441 A/C S149R minus 5111403 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.08 0.07 194 3 0.06 0.02 538 6 123 "by cluster,freq" Possibly damaging 1.548 8 Intolerant 0 2.8 52 moderately radical 131210 1q22-q25 selectin E (endothelial adhesion molecule 1) 129 rs5361 SELE 6401 1 166432718 NM_000450 NP_000441 A/C S149R minus 6903932 775 SNP500CANCER CAUC1 Caucasian (31) 58 0.16 0.08 0.07 194 3 0.06 0.02 538 6 123 "by cluster,freq" Possibly damaging 1.548 8 Intolerant 0 2.8 52 moderately radical 131210 1q22-q25 selectin E (endothelial adhesion molecule 1) 130 rs5368 SELE 6401 1 166428604 NM_000450 NP_000441 C/T H468Y minus 5111428 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 44 0.02 0.03 0.01 184 3 0.18 0.05 1768 5 123 "by submitter,freq,cluster" Probably damaging 2.116 8 moderately conservative 131210 1q22-q25 selectin E (endothelial adhesion molecule 1) 131 rs5368 SELE 6401 1 166428604 NM_000450 NP_000441 C/T H468Y minus 5111428 1303 SEQUENOM CEPH CEPH (92) 92 0.03 0.03 0.01 184 3 0.18 0.05 1768 5 123 "by submitter,freq,cluster" Probably damaging 2.116 8 moderately conservative 131210 1q22-q25 selectin E (endothelial adhesion molecule 1) 132 rs5368 SELE 6401 1 166428604 NM_000450 NP_000441 C/T H468Y minus 23860569 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.03 0.01 184 3 0.18 0.05 1768 5 123 "by submitter,freq,cluster" Probably damaging 2.116 8 moderately conservative 131210 1q22-q25 selectin E (endothelial adhesion molecule 1) 133 rs5370 EDN1 1906 6 12404241 NM_001955 NP_001946 G/T K198N plus 3176606 619 WICVAR MITOGPOP6 CORIELL Mixed 54 0.2 0.28 0.06 812 6 0.27 0.07 1972 6 123 "by doubleHit,freq,cluster" Benign 0.225 10 moderately conservative 131240 6p24.1 endothelin 1 134 rs5370 EDN1 1906 6 12404241 NM_001955 NP_001946 G/T K198N plus 8819730 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.29 0.28 0.06 812 6 0.27 0.07 1972 6 123 "by doubleHit,freq,cluster" Benign 0.225 10 moderately conservative 131240 6p24.1 endothelin 1 135 rs5370 EDN1 1906 6 12404241 NM_001955 NP_001946 G/T K198N plus 14857936 693 EGP_SNPS PDR90 NIHPDR 144 0.23 0.28 0.06 812 6 0.27 0.07 1972 6 123 "by doubleHit,freq,cluster" Benign 0.225 10 moderately conservative 131240 6p24.1 endothelin 1 136 rs5370 EDN1 1906 6 12404241 NM_001955 NP_001946 G/T K198N plus 24787768 1303 SEQUENOM CEPH CEPH (92) 184 0.3 0.28 0.06 812 6 0.27 0.07 1972 6 123 "by doubleHit,freq,cluster" Benign 0.225 10 moderately conservative 131240 6p24.1 endothelin 1 137 rs5370 EDN1 1906 6 12404241 NM_001955 NP_001946 G/T K198N plus 24796004 1303 SEQUENOM CEPH CEPH (92) 184 0.24 0.28 0.06 812 6 0.27 0.07 1972 6 123 "by doubleHit,freq,cluster" Benign 0.225 10 moderately conservative 131240 6p24.1 endothelin 1 138 rs5370 EDN1 1906 6 12404241 NM_001955 NP_001946 G/T K198N plus 24796238 1303 SEQUENOM CEPH CEPH (92) 184 0.36 0.28 0.06 812 6 0.27 0.07 1972 6 123 "by doubleHit,freq,cluster" Benign 0.225 10 moderately conservative 131240 6p24.1 endothelin 1 139 rs5491 ICAM1 3383 19 10246540 NM_000201 NP_000192 A/T K56M plus 5586604 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.02 0.02 0 62 1 0.16 0.14 564 8 123 "HapMap,submitter,freq,cluster" Benign 0.892 12 Potentially intolerant 0.1 2.77 25 moderately conservative 147840 19p13.3-p13.2 "intercellular adhesion molecule 1 (CD54), human rhinovirus receptor" 140 rs5498 ICAM1 3383 19 10256683 NM_000201 NP_000192 A/G K469E plus 3172763 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 62 0.34 0.39 0.06 420 5 0.26 0.1 196 2 123 "by cluster,freq" Potentially damaging 1.464 13 moderately conservative 147840 19p13.3-p13.2 "intercellular adhesion molecule 1 (CD54), human rhinovirus receptor" 141 rs5498 ICAM1 3383 19 10256683 NM_000201 NP_000192 A/G K469E plus 4328201 649 FHCRC POPU1 USA (20) 40 0.33 0.39 0.06 420 5 0.26 0.1 196 2 123 "by cluster,freq" Potentially damaging 1.464 13 moderately conservative 147840 19p13.3-p13.2 "intercellular adhesion molecule 1 (CD54), human rhinovirus receptor" 142 rs5498 ICAM1 3383 19 10256683 NM_000201 NP_000192 A/G K469E plus 7985472 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 42 0.36 0.39 0.06 420 5 0.26 0.1 196 2 123 "by cluster,freq" Potentially damaging 1.464 13 moderately conservative 147840 19p13.3-p13.2 "intercellular adhesion molecule 1 (CD54), human rhinovirus receptor" 143 rs5498 ICAM1 3383 19 10256683 NM_000201 NP_000192 A/G K469E plus 7985472 1303 SEQUENOM CEPH CEPH (92) 92 0.48 0.39 0.06 420 5 0.26 0.1 196 2 123 "by cluster,freq" Potentially damaging 1.464 13 moderately conservative 147840 19p13.3-p13.2 "intercellular adhesion molecule 1 (CD54), human rhinovirus receptor" 144 rs5498 ICAM1 3383 19 10256683 NM_000201 NP_000192 A/G K469E plus 24796638 1303 SEQUENOM CEPH CEPH (92) 184 0.39 0.39 0.06 420 5 0.26 0.1 196 2 123 "by cluster,freq" Potentially damaging 1.464 13 moderately conservative 147840 19p13.3-p13.2 "intercellular adhesion molecule 1 (CD54), human rhinovirus receptor" 145 rs5503 ICAM2 3384 17 59436418 NM_000873 NP_000864 A/G A37T minus 3178070 619 WICVAR MITOGPOP6 CORIELL Mixed 42 0.05 0.05 0 42 1 0.05 0 80 1 102 "by submitter,freq,cluster" Benign 0.909 5 Intolerant 0.04 2.82 26 moderately conservative 146630 17q23-q25 intercellular adhesion molecule 2 146 rs5522 NR3C2 4306 4 149715080 NM_000901 NP_000892 A/G V180I minus 10110564 902 AFFY Caucasian 24 0.08 0.16 0.09 162 3 0.16 0.05 306 6 123 "by submitter,freq,cluster" Benign 0.093 6 conservative 600983 4q31.1 "nuclear receptor subfamily 3, group C, member 2" 147 rs5522 NR3C2 4306 4 149715080 NM_000901 NP_000892 A/G V180I minus 22887609 1303 SEQUENOM CEPH CEPH (92) 92 0.22 0.16 0.09 162 3 0.16 0.05 306 6 123 "by submitter,freq,cluster" Benign 0.093 6 conservative 600983 4q31.1 "nuclear receptor subfamily 3, group C, member 2" 148 rs5522 NR3C2 4306 4 149715080 NM_000901 NP_000892 A/G V180I minus 23731817 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.07 0.16 0.09 162 3 0.16 0.05 306 6 123 "by submitter,freq,cluster" Benign 0.093 6 conservative 600983 4q31.1 "nuclear receptor subfamily 3, group C, member 2" 149 rs5856 NOL5A 10528 20 2586882 NM_006392 NP_006383 C/T V576A plus 8464 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.35 0.35 0 280 2 0.24 0 750 1 121 "by doubleHit,freq,cluster" moderately conservative 20p13 nucleolar protein 5A (56kDa with KKE/D repeat) 150 rs5856 NOL5A 10528 20 2586882 NM_006392 NP_006383 C/T V576A plus 5420265 1303 SEQUENOM CEPH CEPH (92) 92 0.35 0.35 0 280 2 0.24 0 750 1 121 "by doubleHit,freq,cluster" moderately conservative 20p13 nucleolar protein 5A (56kDa with KKE/D repeat) 151 rs5880 CETP 1071 16 55572592 NM_000078 NP_000069 C/G A390P plus 7482 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 114 0.1 0.07 0.04 252 3 0.01 0 328 3 123 "by cluster,freq" Intolerant 0.05 2.82 15 conservative 118470 16q21 "cholesteryl ester transfer protein, plasma" 152 rs5880 CETP 1071 16 55572592 NM_000078 NP_000069 C/G A390P plus 20419188 1303 SEQUENOM CEPH CEPH (92) 92 0.06 0.07 0.04 252 3 0.01 0 328 3 123 "by cluster,freq" Intolerant 0.05 2.82 15 conservative 118470 16q21 "cholesteryl ester transfer protein, plasma" 153 rs5880 CETP 1071 16 55572592 NM_000078 NP_000069 C/G A390P plus 23418077 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.02 0.07 0.04 252 3 0.01 0 328 3 123 "by cluster,freq" Intolerant 0.05 2.82 15 conservative 118470 16q21 "cholesteryl ester transfer protein, plasma" 154 rs5881 CETP 1071 16 55569513 NM_000078 NP_000069 A/G G331S plus 7483 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 114 0.03 0.03 0 114 1 52 HapMap Tolerant 0.73 2.88 14 moderately conservative 118470 16q21 "cholesteryl ester transfer protein, plasma" 155 rs5882 CETP 1071 16 55573593 NM_000078 NP_000069 A/G V422I plus 7484 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 114 0.33 0.32 0.01 162 2 0.43 0.03 378 4 123 "by doubleHit,submitter,freq,cluster" conservative 118470 16q21 "cholesteryl ester transfer protein, plasma" 156 rs5882 CETP 1071 16 55573593 NM_000078 NP_000069 A/G V422I plus 23991710 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.32 0.01 162 2 0.43 0.03 378 4 123 "by doubleHit,submitter,freq,cluster" conservative 118470 16q21 "cholesteryl ester transfer protein, plasma" 157 rs5887 CETP 1071 16 55575053 NM_000078 NP_000069 A/G V486M plus 7489 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 114 0.03 0.03 0 114 1 123 by freq conservative 118470 16q21 "cholesteryl ester transfer protein, plasma" 158 rs5893 F2R 2149 5 76064302 NM_001992 NP_001983 A/G S166G plus 7495 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.03 0.03 0 106 1 52 by freq Borderline 1.142 8 Potentially intolerant 0.07 2.79 25 moderately conservative 187930 5q13 coagulation factor II (thrombin) receptor 159 rs5896 F2 2147 11 46701579 NM_000506 NP_000497 C/T T165M plus 7498 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 126 0.1 0.11 0.08 432 5 0.16 0.23 138 3 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.602 10 Potentially intolerant 0.1 2.9 26 moderately conservative 176930 11p11-q12 coagulation factor II (thrombin) 160 rs5896 F2 2147 11 46701579 NM_000506 NP_000497 C/T T165M plus 4384736 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.07 0.11 0.08 432 5 0.16 0.23 138 3 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.602 10 Potentially intolerant 0.1 2.9 26 moderately conservative 176930 11p11-q12 coagulation factor II (thrombin) 161 rs5896 F2 2147 11 46701579 NM_000506 NP_000497 C/T T165M plus 4384736 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.05 0.11 0.08 432 5 0.16 0.23 138 3 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.602 10 Potentially intolerant 0.1 2.9 26 moderately conservative 176930 11p11-q12 coagulation factor II (thrombin) 162 rs5896 F2 2147 11 46701579 NM_000506 NP_000497 C/T T165M plus 4384736 1303 SEQUENOM CEPH CEPH (92) 92 0.24 0.11 0.08 432 5 0.16 0.23 138 3 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.602 10 Potentially intolerant 0.1 2.9 26 moderately conservative 176930 11p11-q12 coagulation factor II (thrombin) 163 rs5896 F2 2147 11 46701579 NM_000506 NP_000497 C/T T165M plus 24181221 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.11 0.08 432 5 0.16 0.23 138 3 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.602 10 Potentially intolerant 0.1 2.9 26 moderately conservative 176930 11p11-q12 coagulation factor II (thrombin) 164 rs5897 F2 2147 11 46706147 NM_000506 NP_000497 A/C P386T plus 7499 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 128 0.03 0.03 0 128 1 52 HapMap Probably damaging 2.396 10 Tolerant 0.41 2.8 35 conservative 176930 11p11-q12 coagulation factor II (thrombin) 165 rs5901 F3 2152 1 94710771 NM_001993 NP_001984 C/T R163W minus 7503 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.03 0.03 0 86 1 121 "by cluster,freq" Benign 0.737 19 Borderline 0.11 2.87 16 moderately radical 134390 1p22-p21 "coagulation factor III (thromboplastin, tissue factor)" 166 rs5911 ITGA2B 3674 17 39808591 NM_000419 NP_000410 A/C I874S plus 7514 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 112 0.1 0.2 0.14 230 2 0.43 0 1498 1 121 "HapMap,doubleHit,freq,cluster" Benign 0.003 13 Tolerant 0.45 2.82 20 moderately radical 607759 17q21.32 "integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41B)" 167 rs5911 ITGA2B 3674 17 39808591 NM_000419 NP_000410 A/C I874S plus 2394254 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.3 0.2 0.14 230 2 0.43 0 1498 1 121 "HapMap,doubleHit,freq,cluster" Benign 0.003 13 Tolerant 0.45 2.82 20 moderately radical 607759 17q21.32 "integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41B)" 168 rs5914 ITGA2B 3674 17 39807594 NM_000419 NP_000410 A/T Y968N minus 7517 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 112 0.03 0.03 0 112 1 52 by freq Probably damaging 2.407 11 Intolerant 0.01 2.77 23 moderately radical 607759 17q21.32 "integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41B)" 169 rs5915 ITGA2B 3674 17 39822249 NM_000419 NP_000410 C/T T40I minus 7518 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 112 0.03 0.03 0 112 1 52 HapMap Possibly damaging 1.749 8 Intolerant 0.01 2.76 22 moderately conservative 607759 17q21.32 "integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41B)" 170 rs5917 ITGB3 3690 17 42716952 NM_000212 NP_000203 A/G R169Q plus 7520 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.03 0.03 0 106 1 121 "by cluster,freq" Possibly damaging 1.527 28 Borderline 0.12 2.87 51 conservative 173470 17q21.32 "integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)" 171 rs5918 ITGB3 3690 17 42715729 NM_000212 NP_000203 C/T L59P plus 7521 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 98 0.1 0.1 0 98 1 52 by freq Benign 0.984 18 Tolerant 0.31 2.95 44 moderately conservative 173470 17q21.32 "integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)" 172 rs5921 ITGB3 3690 17 42724600 NM_000212 NP_000203 A/G V453I plus 7526 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.03 0.03 0 106 1 52 by freq Benign 0.031 28 Tolerant 0.56 2.87 52 conservative 173470 17q21.32 "integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)" 173 rs5928 LDLR 3949 19 11101240 NM_000527 NP_000518 A/G R814Q plus 7533 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 126 0.03 0.03 0 126 1 52 by freq Benign 0.115 34 Tolerant 0.81 2.94 40 conservative 606945 19p13.3 low density lipoprotein receptor (familial hypercholesterolemia) 174 rs5931 LDLR 3949 19 11061228 NM_000527 NP_000518 C/G G2R plus 7537 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 126 0.03 0.03 0 126 1 52 HapMap moderately radical 606945 19p13.3 low density lipoprotein receptor (familial hypercholesterolemia) 175 rs5938 PTAFR 5724 1 28161004 NM_000952 NP_000943 A/C A224D minus 7545 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 114 0.03 0.03 0 114 1 0.1 0 1548 2 123 "by cluster,freq" Potentially damaging 1.329 11 Potentially intolerant 0.08 2.78 33 moderately radical 173393 1p35-p34.3 platelet-activating factor receptor 176 rs5939 PTAFR 5724 1 28160662 NM_000952 NP_000943 A/G N338S minus 7546 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 114 0.03 0.03 0 114 1 0.09 0 46 1 123 "by submitter,freq,cluster" Borderline 1.242 7 conservative 173393 1p35-p34.3 platelet-activating factor receptor 177 rs5954 APOD 347 3 529568 NM_001647 NP_001638 C/T S115L minus 7564 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 108 0.03 0.03 0 108 1 52 by freq Possibly damaging 1.675 8 Tolerant 0.46 2.76 16 moderately radical 107740 3q26.2-qter apolipoprotein D 178 rs5961 F10 2159 13 112831786 NM_000504 NP_000495 C/G Q30H plus 7571 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 108 0.03 0.02 0.01 200 2 0.04 0 46 1 123 "by cluster,freq" Borderline 1.24 10 Borderline 0.12 2.8 24 conservative 227600 13q34 coagulation factor X 179 rs5961 F10 2159 13 112831786 NM_000504 NP_000495 C/G Q30H plus 7571 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.02 0.01 200 2 0.04 0 46 1 123 "by cluster,freq" Borderline 1.24 10 Borderline 0.12 2.8 24 conservative 227600 13q34 coagulation factor X 180 rs5963 F10 2159 13 112825189 NM_000504 NP_000495 A/C L7I plus 7573 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 108 0.03 0.03 0 108 1 52 by freq Intolerant 0.05 3.09 11 conservative 227600 13q34 coagulation factor X 181 rs5968 F11 2160 4 187568053 NM_000128 NP_000119 C/T P66L plus 7578 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 108 0.03 0.03 0 108 1 52 by freq Possibly damaging 1.74 10 moderately conservative 264900 4q35 coagulation factor XI (plasma thromboplastin antecedent) 182 rs5969 F11 2160 4 187572669 NM_000128 NP_000119 A/G Q244R plus 7579 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 104 0.03 0.03 0 104 1 52 by freq Potentially damaging 1.359 14 conservative 264900 4q35 coagulation factor XI (plasma thromboplastin antecedent) 183 rs5972 F11 2160 4 187576582 NM_000128 NP_000119 A/T I308F plus 7582 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 108 0.03 0.03 0 108 1 52 by freq Possibly damaging 1.564 14 Intolerant 0.01 2.87 54 conservative 264900 4q35 coagulation factor XI (plasma thromboplastin antecedent) 184 rs5982 F13A1 2162 6 6119865 NM_000129 NP_000120 C/T P565L minus 7592 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.1 0.18 0.11 198 3 0.13 0.04 132 3 123 "by doubleHit,freq,cluster" Potentially intolerant 0.1 2.78 18 moderately conservative 134570 6p25.3-p24.3 "coagulation factor XIII, A1 polypeptide" 185 rs5982 F13A1 2162 6 6119865 NM_000129 NP_000120 C/T P565L minus 4250318 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 44 0.27 0.18 0.11 198 3 0.13 0.04 132 3 123 "by doubleHit,freq,cluster" Potentially intolerant 0.1 2.78 18 moderately conservative 134570 6p25.3-p24.3 "coagulation factor XIII, A1 polypeptide" 186 rs5982 F13A1 2162 6 6119865 NM_000129 NP_000120 C/T P565L minus 24334604 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.18 0.11 198 3 0.13 0.04 132 3 123 "by doubleHit,freq,cluster" Potentially intolerant 0.1 2.78 18 moderately conservative 134570 6p25.3-p24.3 "coagulation factor XIII, A1 polypeptide" 187 rs5983 F13A1 2162 6 6112832 NM_000129 NP_000120 A/T L589Q minus 7593 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.03 0.03 0 106 1 52 by freq Tolerant 0.56 2.78 18 moderately radical 134570 6p25.3-p24.3 "coagulation factor XIII, A1 polypeptide" 188 rs5984 F13A1 2162 6 6119907 NM_000129 NP_000120 C/T T551I minus 7594 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 108 0.03 0.03 0 108 1 123 by freq Tolerant 0.34 2.78 18 moderately conservative 134570 6p25.3-p24.3 "coagulation factor XIII, A1 polypeptide" 189 rs5985 F13A1 2162 6 6263794 NM_000129 NP_000120 G/T V35L minus 7595 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 108 0.03 0.2 0.2 242 3 0.2 0 44 1 120 "by doubleHit,freq,cluster" Tolerant 0.49 2.92 14 conservative 134570 6p25.3-p24.3 "coagulation factor XIII, A1 polypeptide" 190 rs5985 F13A1 2162 6 6263794 NM_000129 NP_000120 G/T V35L minus 4250177 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 42 0.24 0.2 0.2 242 3 0.2 0 44 1 120 "by doubleHit,freq,cluster" Tolerant 0.49 2.92 14 conservative 134570 6p25.3-p24.3 "coagulation factor XIII, A1 polypeptide" 191 rs5985 F13A1 2162 6 6263794 NM_000129 NP_000120 G/T V35L minus 19693415 1303 SEQUENOM CEPH CEPH (92) 92 0.39 0.2 0.2 242 3 0.2 0 44 1 120 "by doubleHit,freq,cluster" Tolerant 0.49 2.92 14 conservative 134570 6p25.3-p24.3 "coagulation factor XIII, A1 polypeptide" 192 rs5987 F13A1 2162 6 6097139 NM_000129 NP_000120 A/G V651I minus 7597 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 108 0.1 0.11 0.01 246 3 0.04 0 46 1 121 "by cluster,freq" Tolerant 1 2.78 18 conservative 134570 6p25.3-p24.3 "coagulation factor XIII, A1 polypeptide" 193 rs5987 F13A1 2162 6 6097139 NM_000129 NP_000120 A/G V651I minus 4250337 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.09 0.11 0.01 246 3 0.04 0 46 1 121 "by cluster,freq" Tolerant 1 2.78 18 conservative 134570 6p25.3-p24.3 "coagulation factor XIII, A1 polypeptide" 194 rs5987 F13A1 2162 6 6097139 NM_000129 NP_000120 A/G V651I minus 4250337 1303 SEQUENOM CEPH CEPH (92) 92 0.12 0.11 0.01 246 3 0.04 0 46 1 121 "by cluster,freq" Tolerant 1 2.78 18 conservative 134570 6p25.3-p24.3 "coagulation factor XIII, A1 polypeptide" 195 rs5988 F13A1 2162 6 6097136 NM_000129 NP_000120 C/G E652Q minus 7598 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.33 0.27 0.07 244 3 0.17 0 46 1 123 "by cluster,freq" conservative 134570 6p25.3-p24.3 "coagulation factor XIII, A1 polypeptide" 196 rs5988 F13A1 2162 6 6097136 NM_000129 NP_000120 C/G E652Q minus 4250338 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.28 0.27 0.07 244 3 0.17 0 46 1 123 "by cluster,freq" conservative 134570 6p25.3-p24.3 "coagulation factor XIII, A1 polypeptide" 197 rs5988 F13A1 2162 6 6097136 NM_000129 NP_000120 C/G E652Q minus 4250338 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.27 0.07 244 3 0.17 0 46 1 123 "by cluster,freq" conservative 134570 6p25.3-p24.3 "coagulation factor XIII, A1 polypeptide" 198 rs6065 GP1BA 2811 17 4777161 NM_000173 NP_000164 C/T T161M plus 3199559 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.02 0.04 0.02 138 2 0.17 0 48 1 121 "by cluster,freq" Potentially damaging 1.35 8 Borderline 0.11 2.86 260 moderately conservative 606672 17pter-p12 "glycoprotein Ib (platelet), alpha polypeptide" 199 rs6065 GP1BA 2811 17 4777161 NM_000173 NP_000164 C/T T161M plus 3199559 1303 SEQUENOM CEPH CEPH (92) 92 0.05 0.04 0.02 138 2 0.17 0 48 1 121 "by cluster,freq" Potentially damaging 1.35 8 Borderline 0.11 2.86 260 moderately conservative 606672 17pter-p12 "glycoprotein Ib (platelet), alpha polypeptide" 200 rs6068 GP1BA 2811 17 4776894 NM_000173 NP_000164 A/G R72H plus 7685 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 98 0.03 0.03 0 98 1 52 by freq Borderline 1.125 8 Tolerant 1 2.79 246 conservative 606672 17pter-p12 "glycoprotein Ib (platelet), alpha polypeptide" 201 rs6078 LIPC 3990 15 56621285 NM_000236 NP_000227 A/G V95M plus 7695 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 102 0.1 0.06 0.04 266 3 0.15 0.18 94 2 123 "HapMap,freq" Potentially damaging 1.334 8 Tolerant 0.76 2.8 41 conservative 151670 15q21-q23 "lipase, hepatic" 202 rs6078 LIPC 3990 15 56621285 NM_000236 NP_000227 A/G V95M plus 7695 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.03 0.06 0.04 266 3 0.15 0.18 94 2 123 "HapMap,freq" Potentially damaging 1.334 8 Tolerant 0.76 2.8 41 conservative 151670 15q21-q23 "lipase, hepatic" 203 rs6078 LIPC 3990 15 56621285 NM_000236 NP_000227 A/G V95M plus 24224736 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.06 0.04 266 3 0.15 0.18 94 2 123 "HapMap,freq" Potentially damaging 1.334 8 Tolerant 0.76 2.8 41 conservative 151670 15q21-q23 "lipase, hepatic" 204 rs6079 LIPC 3990 15 56643145 NM_000236 NP_000227 A/G S440N plus 7696 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.03 0.03 0 106 1 52 HapMap Benign 0 8 Tolerant 0.6 2.97 39 conservative 151670 15q21-q23 "lipase, hepatic" 205 rs6083 LIPC 3990 15 56625302 NM_000236 NP_000227 A/G N215S plus 7700 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 104 0.33 0.38 0.02 1283 5 0.29 0.11 94 2 123 "HapMap,doubleHit,freq,cluster" Potentially damaging 1.386 8 Potentially intolerant 0.06 2.8 45 conservative 151670 15q21-q23 "lipase, hepatic" 206 rs6083 LIPC 3990 15 56625302 NM_000236 NP_000227 A/G N215S plus 6587908 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.42 0.38 0.02 1283 5 0.29 0.11 94 2 123 "HapMap,doubleHit,freq,cluster" Potentially damaging 1.386 8 Potentially intolerant 0.06 2.8 45 conservative 151670 15q21-q23 "lipase, hepatic" 207 rs6083 LIPC 3990 15 56625302 NM_000236 NP_000227 A/G N215S plus 6587908 1303 SEQUENOM CEPH CEPH (92) 92 0.36 0.38 0.02 1283 5 0.29 0.11 94 2 123 "HapMap,doubleHit,freq,cluster" Potentially damaging 1.386 8 Potentially intolerant 0.06 2.8 45 conservative 151670 15q21-q23 "lipase, hepatic" 208 rs6083 LIPC 3990 15 56625302 NM_000236 NP_000227 A/G N215S plus 12587368 928 IBARROSO ELY UK (Ely region of East Anglia) 921 0.38 0.38 0.02 1283 5 0.29 0.11 94 2 123 "HapMap,doubleHit,freq,cluster" Potentially damaging 1.386 8 Potentially intolerant 0.06 2.8 45 conservative 151670 15q21-q23 "lipase, hepatic" 209 rs6083 LIPC 3990 15 56625302 NM_000236 NP_000227 A/G N215S plus 24718495 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.41 0.38 0.02 1283 5 0.29 0.11 94 2 123 "HapMap,doubleHit,freq,cluster" Potentially damaging 1.386 8 Potentially intolerant 0.06 2.8 45 conservative 151670 15q21-q23 "lipase, hepatic" 210 rs6087 MPL 4352 1 43472956 NM_005373 NP_005364 C/T A58V plus 7704 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 104 0.03 0.03 0 104 1 52 by freq Borderline 1.227 7 Tolerant 0.32 2.8 19 moderately conservative 159530 1p34 myeloproliferative leukemia virus oncogene 211 rs6088 MPL 4352 1 43474145 NM_005373 NP_005364 A/G E168K plus 7705 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 102 0.03 0.03 0 102 1 52 by freq Potentially damaging 1.267 6 Potentially intolerant 0.08 2.87 19 moderately conservative 159530 1p34 myeloproliferative leukemia virus oncogene 212 rs6090 SERPINE1 5054 7 100365158 NM_000602 NP_000593 A/G V17I plus 7707 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.03 0.03 0.01 154 2 0.12 0.06 225 4 123 "by submitter,freq,cluster" Benign 0.106 6 Borderline 0.19 3.23 11 conservative 173360 7q21.3-q22 "serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1" 213 rs6090 SERPINE1 5054 7 100365158 NM_000602 NP_000593 A/G V17I plus 23411103 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.03 0.01 154 2 0.12 0.06 225 4 123 "by submitter,freq,cluster" Benign 0.106 6 Borderline 0.19 3.23 11 conservative 173360 7q21.3-q22 "serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1" 214 rs6092 SERPINE1 5054 7 100365152 NM_000602 NP_000593 A/G A15T plus 7709 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.1 0.12 0.04 250 4 0.13 0.01 125 2 123 "by cluster,freq" Benign 0.937 6 Potentially intolerant 0.08 3.23 11 moderately conservative 173360 7q21.3-q22 "serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1" 215 rs6092 SERPINE1 5054 7 100365152 NM_000602 NP_000593 A/G A15T plus 3172290 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 4 0.25 0.12 0.04 250 4 0.13 0.01 125 2 123 "by cluster,freq" Benign 0.937 6 Potentially intolerant 0.08 3.23 11 moderately conservative 173360 7q21.3-q22 "serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1" 216 rs6092 SERPINE1 5054 7 100365152 NM_000602 NP_000593 A/G A15T plus 3172290 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.12 0.04 250 4 0.13 0.01 125 2 123 "by cluster,freq" Benign 0.937 6 Potentially intolerant 0.08 3.23 11 moderately conservative 173360 7q21.3-q22 "serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1" 217 rs6092 SERPINE1 5054 7 100365152 NM_000602 NP_000593 A/G A15T plus 23987545 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.12 0.04 250 4 0.13 0.01 125 2 123 "by cluster,freq" Benign 0.937 6 Potentially intolerant 0.08 3.23 11 moderately conservative 173360 7q21.3-q22 "serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1" 218 rs6098 SERPINB2 5055 18 59715374 NM_002575 NP_002566 A/G N120D plus 7715 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 104 0.33 0.24 0.07 364 4 0.41 0.09 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.97 2.83 59 conservative 173390 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2" 219 rs6098 SERPINB2 5055 18 59715374 NM_002575 NP_002566 A/G N120D plus 3094604 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.23 0.24 0.07 364 4 0.41 0.09 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.97 2.83 59 conservative 173390 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2" 220 rs6098 SERPINB2 5055 18 59715374 NM_002575 NP_002566 A/G N120D plus 3094604 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.24 0.07 364 4 0.41 0.09 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.97 2.83 59 conservative 173390 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2" 221 rs6098 SERPINB2 5055 18 59715374 NM_002575 NP_002566 A/G N120D plus 23531315 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.24 0.07 364 4 0.41 0.09 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.97 2.83 59 conservative 173390 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2" 222 rs6100 SERPINB2 5055 18 59720625 NM_002575 NP_002566 A/G R229H plus 7717 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 96 0.03 0.03 0 96 1 52 HapMap Potentially intolerant 0.06 2.83 59 conservative 173390 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2" 223 rs6103 SERPINB2 5055 18 59721483 NM_002575 NP_002566 C/G N404K plus 7720 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.33 0.25 0.06 310 5 0.38 0.08 166 5 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.31 2.83 59 moderately conservative 173390 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2" 224 rs6103 SERPINB2 5055 18 59721483 NM_002575 NP_002566 C/G N404K plus 7720 902 AFFY Caucasian 24 0.17 0.25 0.06 310 5 0.38 0.08 166 5 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.31 2.83 59 moderately conservative 173390 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2" 225 rs6103 SERPINB2 5055 18 59721483 NM_002575 NP_002566 C/G N404K plus 7720 904 AFFY CEPH 12 0.17 0.25 0.06 310 5 0.38 0.08 166 5 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.31 2.83 59 moderately conservative 173390 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2" 226 rs6103 SERPINB2 5055 18 59721483 NM_002575 NP_002566 C/G N404K plus 14303771 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.23 0.25 0.06 310 5 0.38 0.08 166 5 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.31 2.83 59 moderately conservative 173390 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2" 227 rs6103 SERPINB2 5055 18 59721483 NM_002575 NP_002566 C/G N404K plus 23531504 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.25 0.06 310 5 0.38 0.08 166 5 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.31 2.83 59 moderately conservative 173390 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2" 228 rs6104 SERPINB2 5055 18 59721509 NM_002575 NP_002566 C/G S413C plus 7721 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.33 0.29 0.08 154 2 0.41 0.09 94 2 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.29 2.83 59 moderately radical 173390 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2" 229 rs6104 SERPINB2 5055 18 59721509 NM_002575 NP_002566 C/G S413C plus 23531513 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.29 0.08 154 2 0.41 0.09 94 2 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.29 2.83 59 moderately radical 173390 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2" 230 rs6114 SERPINA5 5104 14 94126160 NM_000624 NP_000615 C/G G217R plus 7731 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.03 0.03 0 106 1 0.07 0 92 2 123 "by submitter,freq,cluster" Potentially damaging 1.273 8 Tolerant 0.3 2.76 79 moderately radical 601841 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5" 231 rs6115 SERPINA5 5104 14 94123643 NM_000624 NP_000615 A/G S64N plus 7732 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 102 0.1 0.2 0.12 240 3 0.11 0 46 1 120 "by doubleHit,freq,cluster" Potentially damaging 1.494 7 conservative 601841 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5" 232 rs6115 SERPINA5 5104 14 94123643 NM_000624 NP_000615 A/G S64N plus 1382288 1303 SEQUENOM CEPH CEPH (92) 92 0.23 0.2 0.12 240 3 0.11 0 46 1 120 "by doubleHit,freq,cluster" Potentially damaging 1.494 7 conservative 601841 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5" 233 rs6115 SERPINA5 5104 14 94123643 NM_000624 NP_000615 A/G S64N plus 2982120 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.37 0.2 0.12 240 3 0.11 0 46 1 120 "by doubleHit,freq,cluster" Potentially damaging 1.494 7 conservative 601841 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5" 234 rs6118 SERPINA5 5104 14 94123616 NM_000624 NP_000615 C/T A55V plus 7735 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 102 0.1 0.08 0.03 288 4 0.33 0.14 140 3 123 "by cluster,freq" Borderline 1.227 7 Tolerant 0.31 2.75 77 moderately conservative 601841 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5" 235 rs6118 SERPINA5 5104 14 94123616 NM_000624 NP_000615 C/T A55V plus 1372189 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.08 0.03 288 4 0.33 0.14 140 3 123 "by cluster,freq" Borderline 1.227 7 Tolerant 0.31 2.75 77 moderately conservative 601841 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5" 236 rs6118 SERPINA5 5104 14 94123616 NM_000624 NP_000615 C/T A55V plus 2982119 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.09 0.08 0.03 288 4 0.33 0.14 140 3 123 "by cluster,freq" Borderline 1.227 7 Tolerant 0.31 2.75 77 moderately conservative 601841 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5" 237 rs6118 SERPINA5 5104 14 94123616 NM_000624 NP_000615 C/T A55V plus 23648710 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0.03 288 4 0.33 0.14 140 3 123 "by cluster,freq" Borderline 1.227 7 Tolerant 0.31 2.75 77 moderately conservative 601841 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5" 238 rs6119 SERPINA5 5104 14 94123765 NM_000624 NP_000615 A/G K105E plus 7736 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 102 0.03 0.12 0.11 284 4 0.33 0.16 132 3 123 "by doubleHit,freq,cluster" Benign 0.075 7 Tolerant 0.38 2.76 79 moderately conservative 601841 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5" 239 rs6119 SERPINA5 5104 14 94123765 NM_000624 NP_000615 A/G K105E plus 2982123 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 44 0.09 0.12 0.11 284 4 0.33 0.16 132 3 123 "by doubleHit,freq,cluster" Benign 0.075 7 Tolerant 0.38 2.76 79 moderately conservative 601841 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5" 240 rs6119 SERPINA5 5104 14 94123765 NM_000624 NP_000615 A/G K105E plus 12279178 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.12 0.11 284 4 0.33 0.16 132 3 123 "by doubleHit,freq,cluster" Benign 0.075 7 Tolerant 0.38 2.76 79 moderately conservative 601841 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5" 241 rs6119 SERPINA5 5104 14 94123765 NM_000624 NP_000615 A/G K105E plus 23648718 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.09 0.12 0.11 284 4 0.33 0.16 132 3 123 "by doubleHit,freq,cluster" Benign 0.075 7 Tolerant 0.38 2.76 79 moderately conservative 601841 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5" 242 rs6120 SERPINA5 5104 14 94123813 NM_000624 NP_000615 C/G P121A plus 7737 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 102 0.03 0.03 0 102 1 52 by freq Probably damaging 2.1 7 Intolerant 0.01 2.76 79 conservative 601841 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5" 243 rs6125 SELP 6403 1 166313975 NM_003005 NP_002996 A/G V209M minus 5111836 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.02 0.02 0 46 1 0.05 0 42 1 108 "by cluster,freq" Intolerant 0.04 2.84 42 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 244 rs6127 SELP 6403 1 166297971 NM_003005 NP_002996 A/G D603N minus 7744 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 102 0.33 0.34 0.1 698 5 0.24 0 46 1 123 "by doubleHit,freq,cluster" Potentially damaging 1.494 5 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 245 rs6127 SELP 6403 1 166297971 NM_003005 NP_002996 A/G D603N minus 5111936 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 44 0.45 0.34 0.1 698 5 0.24 0 46 1 123 "by doubleHit,freq,cluster" Potentially damaging 1.494 5 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 246 rs6127 SELP 6403 1 166297971 NM_003005 NP_002996 A/G D603N minus 24796122 1303 SEQUENOM CEPH CEPH (92) 184 0.31 0.34 0.1 698 5 0.24 0 46 1 123 "by doubleHit,freq,cluster" Potentially damaging 1.494 5 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 247 rs6127 SELP 6403 1 166297971 NM_003005 NP_002996 A/G D603N minus 24811825 1303 SEQUENOM CEPH CEPH (92) 184 0.47 0.34 0.1 698 5 0.24 0 46 1 123 "by doubleHit,freq,cluster" Potentially damaging 1.494 5 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 248 rs6127 SELP 6403 1 166297971 NM_003005 NP_002996 A/G D603N minus 24811973 1303 SEQUENOM CEPH CEPH (92) 184 0.23 0.34 0.1 698 5 0.24 0 46 1 123 "by doubleHit,freq,cluster" Potentially damaging 1.494 5 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 249 rs6130 SELP 6403 1 166307865 NM_003005 NP_002996 C/T S500F minus 7747 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.03 0.03 0 106 1 52 by freq Benign 0.675 5 Borderline 0.11 2.93 37 radical 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 250 rs6131 SELP 6403 1 166312543 NM_003005 NP_002996 A/G S331N minus 7748 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.1 0.13 0.03 292 4 0.23 0.03 142 3 123 "by doubleHit,freq,cluster" Benign 0.126 5 Tolerant 0.48 3.14 35 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 251 rs6131 SELP 6403 1 166312543 NM_003005 NP_002996 A/G S331N minus 5111846 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.13 0.13 0.03 292 4 0.23 0.03 142 3 123 "by doubleHit,freq,cluster" Benign 0.126 5 Tolerant 0.48 3.14 35 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 252 rs6131 SELP 6403 1 166312543 NM_003005 NP_002996 A/G S331N minus 5111846 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.13 0.03 292 4 0.23 0.03 142 3 123 "by doubleHit,freq,cluster" Benign 0.126 5 Tolerant 0.48 3.14 35 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 253 rs6131 SELP 6403 1 166312543 NM_003005 NP_002996 A/G S331N minus 23188337 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0.03 292 4 0.23 0.03 142 3 123 "by doubleHit,freq,cluster" Benign 0.126 5 Tolerant 0.48 3.14 35 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 254 rs6133 SELP 6403 1 166297004 NM_003005 NP_002996 G/T V640L minus 7750 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 104 0.33 0.16 0.15 290 4 0.46 0 94 2 123 "by doubleHit,freq,cluster" Benign 0.31 5 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 255 rs6133 SELP 6403 1 166297004 NM_003005 NP_002996 G/T V640L minus 5111948 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.04 0.16 0.15 290 4 0.46 0 94 2 123 "by doubleHit,freq,cluster" Benign 0.31 5 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 256 rs6133 SELP 6403 1 166297004 NM_003005 NP_002996 G/T V640L minus 5111948 1303 SEQUENOM CEPH CEPH (92) 92 0.09 0.16 0.15 290 4 0.46 0 94 2 123 "by doubleHit,freq,cluster" Benign 0.31 5 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 257 rs6133 SELP 6403 1 166297004 NM_003005 NP_002996 G/T V640L minus 23161353 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.16 0.15 290 4 0.46 0 94 2 123 "by doubleHit,freq,cluster" Benign 0.31 5 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 258 rs6134 SELP 6403 1 166312442 NM_003005 NP_002996 A/G M365V minus 7751 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.03 0.03 0 106 1 52 by freq Benign 0.98 5 Tolerant 1 3.14 35 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 259 rs6136 SELP 6403 1 166295609 NM_003005 NP_002996 A/C T756P minus 7753 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.1 0.1 0.03 290 4 0.02 0 90 2 123 "by submitter,freq,cluster" Potentially damaging 1.357 5 Borderline 0.15 3.11 24 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 260 rs6136 SELP 6403 1 166295609 NM_003005 NP_002996 A/C T756P minus 5111969 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 44 0.14 0.1 0.03 290 4 0.02 0 90 2 123 "by submitter,freq,cluster" Potentially damaging 1.357 5 Borderline 0.15 3.11 24 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 261 rs6136 SELP 6403 1 166295609 NM_003005 NP_002996 A/C T756P minus 5111969 1303 SEQUENOM CEPH CEPH (92) 92 0.06 0.1 0.03 290 4 0.02 0 90 2 123 "by submitter,freq,cluster" Potentially damaging 1.357 5 Borderline 0.15 3.11 24 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 262 rs6136 SELP 6403 1 166295609 NM_003005 NP_002996 A/C T756P minus 24265196 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.1 0.03 290 4 0.02 0 90 2 123 "by submitter,freq,cluster" Potentially damaging 1.357 5 Borderline 0.15 3.11 24 conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 263 rs6149 VLDLR 7436 9 2625545 NM_003383 NP_003374 A/G V59I plus 7770 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 106 0.03 0.02 0.01 226 2 0.22 0 46 1 123 "HapMap,freq,cluster" Benign 0.143 9 Tolerant 0.22 2.91 37 conservative 192977 9p24 very low density lipoprotein receptor 264 rs6149 VLDLR 7436 9 2625545 NM_003383 NP_003374 A/G V59I plus 7770 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.01 0.02 0.01 226 2 0.22 0 46 1 123 "HapMap,freq,cluster" Benign 0.143 9 Tolerant 0.22 2.91 37 conservative 192977 9p24 very low density lipoprotein receptor 265 rs6180 GHR 2690 5 42754996 NM_000163 NP_000154 A/C I544L plus 7802 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.33 0.43 0.06 392 6 0.43 0.03 480 8 123 "by doubleHit,freq,cluster" Potentially damaging 1.362 25 Borderline 0.15 2.87 221 conservative 600946 5p13-p12 growth hormone receptor 266 rs6180 GHR 2690 5 42754996 NM_000163 NP_000154 A/C I544L plus 2123222 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 12 0.5 0.43 0.06 392 6 0.43 0.03 480 8 123 "by doubleHit,freq,cluster" Potentially damaging 1.362 25 Borderline 0.15 2.87 221 conservative 600946 5p13-p12 growth hormone receptor 267 rs6180 GHR 2690 5 42754996 NM_000163 NP_000154 A/C I544L plus 2123222 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 92 0.47 0.43 0.06 392 6 0.43 0.03 480 8 123 "by doubleHit,freq,cluster" Potentially damaging 1.362 25 Borderline 0.15 2.87 221 conservative 600946 5p13-p12 growth hormone receptor 268 rs6180 GHR 2690 5 42754996 NM_000163 NP_000154 A/C I544L plus 2123222 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.43 0.06 392 6 0.43 0.03 480 8 123 "by doubleHit,freq,cluster" Potentially damaging 1.362 25 Borderline 0.15 2.87 221 conservative 600946 5p13-p12 growth hormone receptor 269 rs6180 GHR 2690 5 42754996 NM_000163 NP_000154 A/C I544L plus 6903813 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.42 0.43 0.06 392 6 0.43 0.03 480 8 123 "by doubleHit,freq,cluster" Potentially damaging 1.362 25 Borderline 0.15 2.87 221 conservative 600946 5p13-p12 growth hormone receptor 270 rs6180 GHR 2690 5 42754996 NM_000163 NP_000154 A/C I544L plus 24423132 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.43 0.06 392 6 0.43 0.03 480 8 123 "by doubleHit,freq,cluster" Potentially damaging 1.362 25 Borderline 0.15 2.87 221 conservative 600946 5p13-p12 growth hormone receptor 271 rs6181 GHR 2690 5 42735779 NM_000163 NP_000154 A/G R179H plus 7803 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.03 0.03 0 86 1 116 "HapMap,cluster" Potentially damaging 1.4 25 Borderline 0.13 2.84 53 conservative 600946 5p13-p12 growth hormone receptor 272 rs6182 GHR 2690 5 42754685 NM_000163 NP_000154 G/T C440F plus 7804 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.1 0.1 0 86 1 0.17 0 48 1 123 "by submitter,freq,cluster" Probably damaging 2.191 25 Potentially intolerant 0.08 3.05 174 radical 600946 5p13-p12 growth hormone receptor 273 rs6183 GHR 2690 5 42754849 NM_000163 NP_000154 A/C P495T plus 7805 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.03 0.03 0 86 1 52 by freq Probably damaging 2.248 25 Intolerant 0 2.84 222 conservative 600946 5p13-p12 growth hormone receptor 274 rs6184 GHR 2690 5 42755101 NM_000163 NP_000154 A/C P579T plus 7806 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.1 0.1 0 86 1 0.08 0.09 252 2 116 "by cluster,freq" Potentially damaging 1.473 25 Tolerant 0.29 2.87 211 conservative 600946 5p13-p12 growth hormone receptor 275 rs6185 GNRH1 2796 8 25336717 NM_000825 NP_000816 C/G W16S minus 7807 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.33 0.25 0.07 406 5 0.43 0.12 1912 7 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.365 6 radical 152760 8p21-p11.2 gonadotropin-releasing hormone 1 (leutinizing-releasing hormone) 276 rs6185 GNRH1 2796 8 25336717 NM_000825 NP_000816 C/G W16S minus 5586544 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.3 0.25 0.07 406 5 0.43 0.12 1912 7 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.365 6 radical 152760 8p21-p11.2 gonadotropin-releasing hormone 1 (leutinizing-releasing hormone) 277 rs6185 GNRH1 2796 8 25336717 NM_000825 NP_000816 C/G W16S minus 6731916 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.23 0.25 0.07 406 5 0.43 0.12 1912 7 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.365 6 radical 152760 8p21-p11.2 gonadotropin-releasing hormone 1 (leutinizing-releasing hormone) 278 rs6185 GNRH1 2796 8 25336717 NM_000825 NP_000816 C/G W16S minus 6731916 1303 SEQUENOM CEPH CEPH (92) 92 0.19 0.25 0.07 406 5 0.43 0.12 1912 7 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.365 6 radical 152760 8p21-p11.2 gonadotropin-releasing hormone 1 (leutinizing-releasing hormone) 279 rs6185 GNRH1 2796 8 25336717 NM_000825 NP_000816 C/G W16S minus 24053467 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.25 0.07 406 5 0.43 0.12 1912 7 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.365 6 radical 152760 8p21-p11.2 gonadotropin-releasing hormone 1 (leutinizing-releasing hormone) 280 rs6190 NR3C1 2908 5 142760530 NM_000176 NP_000167 A/G R23K minus 14865729 693 EGP_SNPS PDR90 NIHPDR 152 0.01 0.01 0 152 1 119 "by cluster,freq" Potentially damaging 1.293 19 conservative 138040 5q31 "nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)" 281 rs6192 NR3C1 2908 5 142760405 NM_000176 NP_000167 G/T F65V minus 7814 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.03 0.02 0.01 238 2 119 "HapMap,cluster" Probably damaging 1.999 22 conservative 138040 5q31 "nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)" 282 rs6192 NR3C1 2908 5 142760405 NM_000176 NP_000167 G/T F65V minus 14865730 693 EGP_SNPS PDR90 NIHPDR 152 0.01 0.02 0.01 238 2 119 "HapMap,cluster" Probably damaging 1.999 22 conservative 138040 5q31 "nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)" 283 rs6195 NR3C1 2908 5 142759510 NM_000176 NP_000167 A/G N363S minus 7817 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.03 0.03 0.02 230 3 0.02 0 646 2 120 "HapMap,freq,cluster" Potentially damaging 1.493 23 Tolerant 0.89 2.84 57 conservative 138040 5q31 "nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)" 284 rs6195 NR3C1 2908 5 142759510 NM_000176 NP_000167 A/G N363S minus 7817 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.02 0.03 0.02 230 3 0.02 0 646 2 120 "HapMap,freq,cluster" Potentially damaging 1.493 23 Tolerant 0.89 2.84 57 conservative 138040 5q31 "nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)" 285 rs6195 NR3C1 2908 5 142759510 NM_000176 NP_000167 A/G N363S minus 7817 902 AFFY Caucasian 24 0.08 0.03 0.02 230 3 0.02 0 646 2 120 "HapMap,freq,cluster" Potentially damaging 1.493 23 Tolerant 0.89 2.84 57 conservative 138040 5q31 "nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)" 286 rs6201 HSD3B1 3283 1 119766257 NM_000862 NP_000853 A/G I79V plus 24811836 1303 SEQUENOM CEPH CEPH (92) 184 0.47 0.47 0 184 1 0.12 0.08 338 4 123 "by cluster,freq" Benign 0.16 29 Tolerant 1 2.84 40 conservative 109715 1p13.1 "hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1" 287 rs6205 HSD3B1 3283 1 119769044 NM_000862 NP_000853 C/T F286L plus 7827 1303 SEQUENOM CEPH CEPH (92) 92 0.07 0.07 0 92 1 123 by freq Potentially damaging 1.441 30 Tolerant 1 2.85 39 conservative 109715 1p13.1 "hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1" 288 rs6211 HSD3B2 3284 1 119674220 NM_000198 NP_000189 C/G E94Q plus 7833 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.03 0.11 0.11 178 2 0.02 0.02 250 2 113 "by cluster,freq" Benign 0.634 30 Tolerant 1 2.91 40 conservative 201810 1p13.1 "hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 2" 289 rs6211 HSD3B2 3284 1 119674220 NM_000198 NP_000189 C/G E94Q plus 5586599 1303 SEQUENOM CEPH CEPH (92) 92 0.18 0.11 0.11 178 2 0.02 0.02 250 2 113 "by cluster,freq" Benign 0.634 30 Tolerant 1 2.91 40 conservative 201810 1p13.1 "hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 2" 290 rs6232 PCSK1 5122 5 95777541 NM_000439 NP_000430 A/G N221D minus 7854 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.03 0.09 0.09 344 4 123 "HapMap,freq" Benign 0.371 10 Tolerant 0.23 2.78 108 conservative 162150 5q15-q21 proprotein convertase subtilisin/kexin type 1 291 rs6232 PCSK1 5122 5 95777541 NM_000439 NP_000430 A/G N221D minus 7854 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.04 0.09 0.09 344 4 123 "HapMap,freq" Benign 0.371 10 Tolerant 0.23 2.78 108 conservative 162150 5q15-q21 proprotein convertase subtilisin/kexin type 1 292 rs6232 PCSK1 5122 5 95777541 NM_000439 NP_000430 A/G N221D minus 7854 1303 SEQUENOM CEPH CEPH (92) 92 0.22 0.09 0.09 344 4 123 "HapMap,freq" Benign 0.371 10 Tolerant 0.23 2.78 108 conservative 162150 5q15-q21 proprotein convertase subtilisin/kexin type 1 293 rs6232 PCSK1 5122 5 95777541 NM_000439 NP_000430 A/G N221D minus 24445734 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.09 0.09 344 4 123 "HapMap,freq" Benign 0.371 10 Tolerant 0.23 2.78 108 conservative 162150 5q15-q21 proprotein convertase subtilisin/kexin type 1 294 rs6234 PCSK1 5122 5 95754730 NM_000439 NP_000430 C/G Q665E minus 7856 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 84 0.33 0.3 0.07 224 3 0.21 0.14 94 2 123 "by cluster,freq" Benign 0 9 conservative 162150 5q15-q21 proprotein convertase subtilisin/kexin type 1 295 rs6234 PCSK1 5122 5 95754730 NM_000439 NP_000430 C/G Q665E minus 7856 1303 SEQUENOM CEPH CEPH (92) 92 0.33 0.3 0.07 224 3 0.21 0.14 94 2 123 "by cluster,freq" Benign 0 9 conservative 162150 5q15-q21 proprotein convertase subtilisin/kexin type 1 296 rs6234 PCSK1 5122 5 95754730 NM_000439 NP_000430 C/G Q665E minus 24001977 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.3 0.07 224 3 0.21 0.14 94 2 123 "by cluster,freq" Benign 0 9 conservative 162150 5q15-q21 proprotein convertase subtilisin/kexin type 1 297 rs6235 PCSK1 5122 5 95754654 NM_000439 NP_000430 C/G S690T minus 7857 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.1 0.25 0.13 346 4 0.21 0.14 94 2 123 "HapMap,submitter,freq,cluster" Borderline 1.19 7 moderately conservative 162150 5q15-q21 proprotein convertase subtilisin/kexin type 1 298 rs6235 PCSK1 5122 5 95754654 NM_000439 NP_000430 C/G S690T minus 7857 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.27 0.25 0.13 346 4 0.21 0.14 94 2 123 "HapMap,submitter,freq,cluster" Borderline 1.19 7 moderately conservative 162150 5q15-q21 proprotein convertase subtilisin/kexin type 1 299 rs6235 PCSK1 5122 5 95754654 NM_000439 NP_000430 C/G S690T minus 7857 1303 SEQUENOM CEPH CEPH (92) 92 0.4 0.25 0.13 346 4 0.21 0.14 94 2 123 "HapMap,submitter,freq,cluster" Borderline 1.19 7 moderately conservative 162150 5q15-q21 proprotein convertase subtilisin/kexin type 1 300 rs6235 PCSK1 5122 5 95754654 NM_000439 NP_000430 C/G S690T minus 24001971 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.25 0.13 346 4 0.21 0.14 94 2 123 "HapMap,submitter,freq,cluster" Borderline 1.19 7 moderately conservative 162150 5q15-q21 proprotein convertase subtilisin/kexin type 1 301 rs6259 SHBG 6462 17 7477252 NM_001040 NP_001031 A/G D356N plus 5586913 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.1 0.2 0.11 152 2 0.08 0.02 340 4 123 "by cluster,freq" Benign 0.164 11 Tolerant 0.46 2.75 16 conservative 182205 17p13-p12 sex hormone-binding globulin 302 rs6259 SHBG 6462 17 7477252 NM_001040 NP_001031 A/G D356N plus 5586913 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.2 0.11 152 2 0.08 0.02 340 4 123 "by cluster,freq" Benign 0.164 11 Tolerant 0.46 2.75 16 conservative 182205 17p13-p12 sex hormone-binding globulin 303 rs6260 SHBG 6462 17 7474289 NM_001040 NP_001031 A/G R25H plus 7883 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.1 0.1 0 86 1 0.06 0.07 252 2 118 "HapMap,freq,cluster" Probably damaging 2.284 6 conservative 182205 17p13-p12 sex hormone-binding globulin 304 rs6262 DDC 1644 7 50370129 NM_000790 NP_000781 C/T P210L minus 16361341 693 EGP_SNPS PDR90 NIHPDR 180 0.01 0.01 0 180 1 121 "HapMap,freq,cluster" Probably damaging 2.224 106 Intolerant 0.01 2.82 229 moderately conservative 107930 7p11 dopa decarboxylase (aromatic L-amino acid decarboxylase) 305 rs6263 DDC 1644 7 50370109 NM_000790 NP_000781 A/G M217V minus 16361342 693 EGP_SNPS PDR90 NIHPDR 180 0.03 0.03 0.01 294 2 121 "HapMap,freq,cluster" Borderline 1.014 106 Potentially intolerant 0.06 2.82 229 conservative 107930 7p11 dopa decarboxylase (aromatic L-amino acid decarboxylase) 306 rs6263 DDC 1644 7 50370109 NM_000790 NP_000781 A/G M217V minus 16361342 885 TSC-CSHL HapMap-CEPH-30-trios 114 0.04 0.03 0.01 294 2 121 "HapMap,freq,cluster" Borderline 1.014 106 Potentially intolerant 0.06 2.82 229 conservative 107930 7p11 dopa decarboxylase (aromatic L-amino acid decarboxylase) 307 rs6266 CNTF 1270 11 58148513 NM_000614 NP_000605 A/G H182R plus 7890 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 74 0.03 0.03 0 74 1 52 by freq Probably damaging 2.24 7 Tolerant 0.45 3 16 conservative 118945 11q12.2 ciliary neurotrophic factor 308 rs6270 COMT 1312 22 18324704 NM_000754 NP_000745 C/G C34S plus 7895 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 70 0.33 0.33 0 70 1 113 "HapMap,cluster" Benign 0.027 5 moderately radical 116790 22q11.21 catechol-O-methyltransferase 309 rs6271 DBH 1621 9 133551828 NM_000787 NP_000778 C/T R535C plus 7898 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 74 0.1 0.07 0.04 166 2 123 "by submitter,freq,cluster" Probably damaging 2.278 11 Intolerant 0.05 2.81 26 radical 223360 9q34 dopamine beta-hydroxylase (dopamine beta-monooxygenase) 310 rs6271 DBH 1621 9 133551828 NM_000787 NP_000778 C/T R535C plus 7898 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.07 0.04 166 2 123 "by submitter,freq,cluster" Probably damaging 2.278 11 Intolerant 0.05 2.81 26 radical 223360 9q34 dopamine beta-hydroxylase (dopamine beta-monooxygenase) 311 rs6330 NGFB 4803 1 115541355 NM_002506 NP_002497 C/T A35V minus 7958 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 74 0.33 0.42 0.07 332 5 0.17 0.02 968 2 120 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.034 30 moderately conservative 162030 1p13.1 "nerve growth factor, beta polypeptide" 312 rs6330 NGFB 4803 1 115541355 NM_002506 NP_002497 C/T A35V minus 4044499 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.48 0.42 0.07 332 5 0.17 0.02 968 2 120 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.034 30 moderately conservative 162030 1p13.1 "nerve growth factor, beta polypeptide" 313 rs6330 NGFB 4803 1 115541355 NM_002506 NP_002497 C/T A35V minus 4044499 1303 SEQUENOM CEPH CEPH (92) 92 0.4 0.42 0.07 332 5 0.17 0.02 968 2 120 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.034 30 moderately conservative 162030 1p13.1 "nerve growth factor, beta polypeptide" 314 rs6330 NGFB 4803 1 115541355 NM_002506 NP_002497 C/T A35V minus 15356259 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.45 0.42 0.07 332 5 0.17 0.02 968 2 120 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.034 30 moderately conservative 162030 1p13.1 "nerve growth factor, beta polypeptide" 315 rs6330 NGFB 4803 1 115541355 NM_002506 NP_002497 C/T A35V minus 15356259 848 IIPGA-WEISS-MARTINEZ E-1 CEPH 6 0.33 0.42 0.07 332 5 0.17 0.02 968 2 120 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.034 30 moderately conservative 162030 1p13.1 "nerve growth factor, beta polypeptide" 316 rs6336 NTRK1 4914 1 153661991 NM_002529 NP_002520 C/T H604Y plus 7964 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 74 0.03 0.05 0.03 348 3 123 by freq Possibly damaging 1.834 7 Intolerant 0.01 2.92 33 moderately conservative 191315 1q21-q22 "neurotrophic tyrosine kinase, receptor, type 1" 317 rs6336 NTRK1 4914 1 153661991 NM_002529 NP_002520 C/T H604Y plus 6416724 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.05 0.03 348 3 123 by freq Possibly damaging 1.834 7 Intolerant 0.01 2.92 33 moderately conservative 191315 1q21-q22 "neurotrophic tyrosine kinase, receptor, type 1" 318 rs6336 NTRK1 4914 1 153661991 NM_002529 NP_002520 C/T H604Y plus 28447275 914 HG_BONN_CNS_SNPS EURO96 European 182 0.07 0.05 0.03 348 3 123 by freq Possibly damaging 1.834 7 Intolerant 0.01 2.92 33 moderately conservative 191315 1q21-q22 "neurotrophic tyrosine kinase, receptor, type 1" 319 rs6339 NTRK1 4914 1 153662019 NM_002529 NP_002520 G/T G613V plus 7967 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 74 0.03 0.06 0.03 256 2 123 by freq Possibly damaging 1.497 7 Potentially intolerant 0.1 2.98 25 moderately radical 191315 1q21-q22 "neurotrophic tyrosine kinase, receptor, type 1" 320 rs6339 NTRK1 4914 1 153662019 NM_002529 NP_002520 G/T G613V plus 28447276 914 HG_BONN_CNS_SNPS EURO96 European 182 0.07 0.06 0.03 256 2 123 by freq Possibly damaging 1.497 7 Potentially intolerant 0.1 2.98 25 moderately radical 191315 1q21-q22 "neurotrophic tyrosine kinase, receptor, type 1" 321 rs6405 CYP11B1 1584 8 143958203 NM_000497 NP_000488 A/G C10Y minus 8043 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.03 0.03 0 86 1 52 by freq Tolerant 1 3.16 26 radical 202010 8q21 "cytochrome P450, family 11, subfamily B, polypeptide 1" 322 rs6407 CYP11B1 1584 8 143954209 NM_000497 NP_000488 A/G A348T minus 8046 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.03 0.03 0 86 1 52 by freq Borderline 1.168 36 Borderline 0.15 2.77 41 moderately conservative 202010 8q21 "cytochrome P450, family 11, subfamily B, polypeptide 1" 323 rs6438 CYP11B2 1585 8 143996174 NM_000498 NP_000489 A/G A29T minus 8081 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 84 0.03 0.03 0 84 1 0.04 0 46 1 123 "by cluster,freq" Benign 0.221 36 Tolerant 0.71 2.9 29 moderately conservative 124080 8q21-q22 "cytochrome P450, family 11, subfamily B, polypeptide 2" 324 rs6472 CYP21A2 1589 6 32115828 NM_000500 NP_000491 C/G S269T plus 8123 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.33 0.22 0.13 362 3 0.1 0 1478 1 123 "by cluster,freq" Borderline 1.001 23 Potentially intolerant 0.1 2.79 33 moderately conservative 201910 6p21.3 "cytochrome P450, family 21, subfamily A, polypeptide 2" 325 rs6472 CYP21A2 1589 6 32115828 NM_000500 NP_000491 C/G S269T plus 13097014 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.22 0.13 362 3 0.1 0 1478 1 123 "by cluster,freq" Borderline 1.001 23 Potentially intolerant 0.1 2.79 33 moderately conservative 201910 6p21.3 "cytochrome P450, family 21, subfamily A, polypeptide 2" 326 rs6472 CYP21A2 1589 6 32115828 NM_000500 NP_000491 C/G S269T plus 24796289 1303 SEQUENOM CEPH CEPH (92) 184 0.25 0.22 0.13 362 3 0.1 0 1478 1 123 "by cluster,freq" Borderline 1.001 23 Potentially intolerant 0.1 2.79 33 moderately conservative 201910 6p21.3 "cytochrome P450, family 21, subfamily A, polypeptide 2" 327 rs6474 CYP21A2 1589 6 32114865 NM_000500 NP_000491 A/G R103K plus 8125 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 84 0.33 0.33 0 84 1 113 "by doubleHit,freq,cluster" Benign 0.118 14 Tolerant 0.63 2.81 27 conservative 201910 6p21.3 "cytochrome P450, family 21, subfamily A, polypeptide 2" 328 rs6476 CYP21A2 1589 6 32115572 NM_000500 NP_000491 A/T M240K plus 8127 504 WIAF-CSNP WIAF-CSNP-POP1 "European (30), Asians (14) African Americans (10) and African Pygmies (7)" 86 0.03 0.03 0 86 1 120 "by doubleHit,freq,cluster" Benign 0.284 23 Tolerant 1 2.79 33 moderately conservative 201910 6p21.3 "cytochrome P450, family 21, subfamily A, polypeptide 2" 329 rs6525 BMP8A 353500 1 39657177 NM_181809 NP_861525 A/G R293H plus 8185 508 WIAF-CSNP WIAF-CSNP-MITOGPOP1 "Europeans (20), Asians (10) and African-Americans (10)" 38 0.33 0.31 0.01 318 3 121 "by doubleHit,freq,cluster" conservative 1p34.2 bone morphogenetic protein 8a 330 rs6525 BMP8A 353500 1 39657177 NM_181809 NP_861525 A/G R293H plus 17934 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.31 0.31 0.01 318 3 121 "by doubleHit,freq,cluster" conservative 1p34.2 bone morphogenetic protein 8a 331 rs6525 BMP8A 353500 1 39657177 NM_181809 NP_861525 A/G R293H plus 20433475 1303 SEQUENOM CEPH CEPH (92) 92 0.31 0.31 0.01 318 3 121 "by doubleHit,freq,cluster" conservative 1p34.2 bone morphogenetic protein 8a 332 rs6577 GSTA2 2939 6 52723374 NM_000846 NP_000837 A/C E210A minus 869782 506 NCBI NIHPDR NIHPDR 78 0.29 0.18 0.15 170 2 120 "by doubleHit,submitter,freq,cluster" Benign 0.802 61 Tolerant 0.21 2.86 64 moderately radical 138360 6p12.1 glutathione S-transferase A2 333 rs6577 GSTA2 2939 6 52723374 NM_000846 NP_000837 A/C E210A minus 3671245 1303 SEQUENOM CEPH CEPH (92) 92 0.08 0.18 0.15 170 2 120 "by doubleHit,submitter,freq,cluster" Benign 0.802 61 Tolerant 0.21 2.86 64 moderately radical 138360 6p12.1 glutathione S-transferase A2 334 rs6647 SERPINA1 5265 14 93917168 NM_000295 NP_000286 C/T V237A minus 20192 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 38 0.33 0.28 0.03 178 3 0.27 0.3 94 2 123 "by doubleHit,freq,cluster" Tolerant 0.48 2.75 79 moderately conservative 107400 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1" 335 rs6647 SERPINA1 5265 14 93917168 NM_000295 NP_000286 C/T V237A minus 1875346 1303 SEQUENOM CEPH CEPH (92) 92 0.27 0.28 0.03 178 3 0.27 0.3 94 2 123 "by doubleHit,freq,cluster" Tolerant 0.48 2.75 79 moderately conservative 107400 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1" 336 rs6647 SERPINA1 5265 14 93917168 NM_000295 NP_000286 C/T V237A minus 23648078 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.28 0.03 178 3 0.27 0.3 94 2 123 "by doubleHit,freq,cluster" Tolerant 0.48 2.75 79 moderately conservative 107400 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1" 337 rs6791 STXBP2 6813 19 7618277 NM_006949 NP_008880 A/G I526V plus 8516 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.26 0.28 0.05 324 3 0.18 0.04 88 2 123 "by doubleHit,freq,cluster" Benign 0.106 26 conservative 601717 19p13.3-p13.2 syntaxin binding protein 2 338 rs6791 STXBP2 6813 19 7618277 NM_006949 NP_008880 A/G I526V plus 1414714 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.28 0.05 324 3 0.18 0.04 88 2 123 "by doubleHit,freq,cluster" Benign 0.106 26 conservative 601717 19p13.3-p13.2 syntaxin binding protein 2 339 rs6791 STXBP2 6813 19 7618277 NM_006949 NP_008880 A/G I526V plus 24417641 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.39 0.28 0.05 324 3 0.18 0.04 88 2 123 "by doubleHit,freq,cluster" Benign 0.106 26 conservative 601717 19p13.3-p13.2 syntaxin binding protein 2 340 rs6794 EXOSC7 23016 3 45027779 NM_015004 NP_055819 C/G V274L plus 8519 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.5 0.49 0.01 354 3 0.12 0 1474 1 120 "HapMap,doubleHit,freq,cluster" Borderline 1.21 6 conservative 606488 3p21.32 exosome component 7 341 rs6794 EXOSC7 23016 3 45027779 NM_015004 NP_055819 C/G V274L plus 10058733 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.48 0.49 0.01 354 3 0.12 0 1474 1 120 "HapMap,doubleHit,freq,cluster" Borderline 1.21 6 conservative 606488 3p21.32 exosome component 7 342 rs6794 EXOSC7 23016 3 45027779 NM_015004 NP_055819 C/G V274L plus 10058733 1303 SEQUENOM CEPH CEPH (92) 46 0.5 0.49 0.01 354 3 0.12 0 1474 1 120 "HapMap,doubleHit,freq,cluster" Borderline 1.21 6 conservative 606488 3p21.32 exosome component 7 343 rs6834 KARS 3735 16 74219304 NM_005548 NP_005539 C/G T595S minus 12357600 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.05 0.03 0.03 212 2 0.33 0 84 1 120 "HapMap,doubleHit,freq,cluster" Borderline 1.107 9 moderately conservative 601421 16q23-q24 lysyl-tRNA synthetase 344 rs6834 KARS 3735 16 74219304 NM_005548 NP_005539 C/G T595S minus 12357600 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.03 0.03 212 2 0.33 0 84 1 120 "HapMap,doubleHit,freq,cluster" Borderline 1.107 9 moderately conservative 601421 16q23-q24 lysyl-tRNA synthetase 345 rs6901 PITRM1 10531 10 3170227 NM_014889 NP_055704 A/G Q1037R minus 8650 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.28 0.3 0.05 389 4 0.25 0.02 1692 5 123 "by doubleHit,freq,cluster" Potentially damaging 1.355 8 conservative 10p15.3 pitrilysin metalloproteinase 1 346 rs6901 PITRM1 10531 10 3170227 NM_014889 NP_055704 A/G Q1037R minus 3349913 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 60 0.33 0.3 0.05 389 4 0.25 0.02 1692 5 123 "by doubleHit,freq,cluster" Potentially damaging 1.355 8 conservative 10p15.3 pitrilysin metalloproteinase 1 347 rs6901 PITRM1 10531 10 3170227 NM_014889 NP_055704 A/G Q1037R minus 3349913 1303 SEQUENOM CEPH CEPH (92) 93 0.28 0.3 0.05 389 4 0.25 0.02 1692 5 123 "by doubleHit,freq,cluster" Potentially damaging 1.355 8 conservative 10p15.3 pitrilysin metalloproteinase 1 348 rs6901 PITRM1 10531 10 3170227 NM_014889 NP_055704 A/G Q1037R minus 24294922 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.3 0.05 389 4 0.25 0.02 1692 5 123 "by doubleHit,freq,cluster" Potentially damaging 1.355 8 conservative 10p15.3 pitrilysin metalloproteinase 1 349 rs6940 IFI16 3428 1 155837741 NM_005531 NP_005522 A/T T723S plus 3127046 1303 SEQUENOM CEPH CEPH (92) 92 0.1 0.1 0 92 1 120 "by doubleHit,freq,cluster" moderately conservative 147586 1q22 "interferon, gamma-inducible protein 16" 350 rs6972 BZRP 706 22 41883470 NM_000714 NP_000705 A/G R162H plus 8733 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.33 0.27 0.09 544 5 0.14 0.08 652 7 120 "by doubleHit,freq,cluster" Benign 0.32 10 conservative 109610 22q13.31 benzodiazapine receptor (peripheral) 351 rs6972 BZRP 706 22 41883470 NM_000714 NP_000705 A/G R162H plus 3176163 619 WICVAR MITOGPOP6 CORIELL Mixed 34 0.03 0.27 0.09 544 5 0.14 0.08 652 7 120 "by doubleHit,freq,cluster" Benign 0.32 10 conservative 109610 22q13.31 benzodiazapine receptor (peripheral) 352 rs6972 BZRP 706 22 41883470 NM_000714 NP_000705 A/G R162H plus 5169438 1303 SEQUENOM CEPH CEPH (92) 92 0.33 0.27 0.09 544 5 0.14 0.08 652 7 120 "by doubleHit,freq,cluster" Benign 0.32 10 conservative 109610 22q13.31 benzodiazapine receptor (peripheral) 353 rs6972 BZRP 706 22 41883470 NM_000714 NP_000705 A/G R162H plus 7986212 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.18 0.27 0.09 544 5 0.14 0.08 652 7 120 "by doubleHit,freq,cluster" Benign 0.32 10 conservative 109610 22q13.31 benzodiazapine receptor (peripheral) 354 rs6972 BZRP 706 22 41883470 NM_000714 NP_000705 A/G R162H plus 12704282 693 EGP_SNPS PDR90 NIHPDR 170 0.24 0.27 0.09 544 5 0.14 0.08 652 7 120 "by doubleHit,freq,cluster" Benign 0.32 10 conservative 109610 22q13.31 benzodiazapine receptor (peripheral) 355 rs7041 GC 2638 4 72983369 NM_000583 NP_000574 G/T D432E minus 6903804 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.42 0.42 0.02 1073 3 0.34 0.1 344 4 121 "by doubleHit,submitter,freq,cluster" Benign 0.113 9 Tolerant 1 2.75 20 conservative 139200 4q12-q13 group-specific component (vitamin D binding protein) 356 rs7041 GC 2638 4 72983369 NM_000583 NP_000574 G/T D432E minus 6903804 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.42 0.02 1073 3 0.34 0.1 344 4 121 "by doubleHit,submitter,freq,cluster" Benign 0.113 9 Tolerant 1 2.75 20 conservative 139200 4q12-q13 group-specific component (vitamin D binding protein) 357 rs7041 GC 2638 4 72983369 NM_000583 NP_000574 G/T D432E minus 12587289 928 IBARROSO ELY UK (Ely region of East Anglia) 921 0.41 0.42 0.02 1073 3 0.34 0.1 344 4 121 "by doubleHit,submitter,freq,cluster" Benign 0.113 9 Tolerant 1 2.75 20 conservative 139200 4q12-q13 group-specific component (vitamin D binding protein) 358 rs7185 FARSLB 10056 2 223262112 NM_005687 NP_005678 C/T V585I plus 14504693 1303 SEQUENOM CEPH CEPH (92) 92 0.07 0.09 0.04 140 2 0.03 0.05 1552 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.012 13 conservative 2q36.1-q36.2 "phenylalanine-tRNA synthetase-like, beta subunit" 359 rs7185 FARSLB 10056 2 223262112 NM_005687 NP_005678 C/T V585I plus 23326076 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.09 0.04 140 2 0.03 0.05 1552 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.012 13 conservative 2q36.1-q36.2 "phenylalanine-tRNA synthetase-like, beta subunit" 360 rs7251 IRF3 3661 19 54854721 NM_001571 NP_001562 C/G S427T minus 9071 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.31 0.33 0.05 342 3 123 "by doubleHit,freq,cluster" moderately conservative 603734 19q13.3-q13.4 interferon regulatory factor 3 361 rs7251 IRF3 3661 19 54854721 NM_001571 NP_001562 C/G S427T minus 1321615 1303 SEQUENOM CEPH CEPH (92) 92 0.31 0.33 0.05 342 3 123 "by doubleHit,freq,cluster" moderately conservative 603734 19q13.3-q13.4 interferon regulatory factor 3 362 rs7251 IRF3 3661 19 54854721 NM_001571 NP_001562 C/G S427T minus 3177824 619 WICVAR MITOGPOP6 CORIELL Mixed 62 0.42 0.33 0.05 342 3 123 "by doubleHit,freq,cluster" moderately conservative 603734 19q13.3-q13.4 interferon regulatory factor 3 363 rs7412 APOE 348 19 50103919 NM_000041 NP_000032 C/T R176C plus 870165 563 DEBNICK MDECODE-1 European-Americans 48 0.19 0.1 0.05 1970 4 0.04 0 48 1 120 "by doubleHit,freq,cluster" Benign 0.035 29 Intolerant 0.02 2.79 33 radical 107741 19q13.2 apolipoprotein E 364 rs7412 APOE 348 19 50103919 NM_000041 NP_000032 C/T R176C plus 870165 564 DEBNICK MDECODE-2 Finnish 48 0.04 0.1 0.05 1970 4 0.04 0 48 1 120 "by doubleHit,freq,cluster" Benign 0.035 29 Intolerant 0.02 2.79 33 radical 107741 19q13.2 apolipoprotein E 365 rs7412 APOE 348 19 50103919 NM_000041 NP_000032 C/T R176C plus 12568612 887 CUORCGL AMERICAN CAUCASIANS American Caucasians 1782 0.09 0.1 0.05 1970 4 0.04 0 48 1 120 "by doubleHit,freq,cluster" Benign 0.035 29 Intolerant 0.02 2.79 33 radical 107741 19q13.2 apolipoprotein E 366 rs7412 APOE 348 19 50103919 NM_000041 NP_000032 C/T R176C plus 15840556 1303 SEQUENOM CEPH CEPH (92) 92 0.28 0.1 0.05 1970 4 0.04 0 48 1 120 "by doubleHit,freq,cluster" Benign 0.035 29 Intolerant 0.02 2.79 33 radical 107741 19q13.2 apolipoprotein E 367 rs7483 GSTM3 2947 1 109991743 NM_000849 NP_000840 A/G V224I minus 9353 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.26 0.29 0.06 458 5 0.33 0.13 436 6 123 "by doubleHit,freq,cluster" conservative 138390 1p13.3 glutathione S-transferase M3 (brain) 368 rs7483 GSTM3 2947 1 109991743 NM_000849 NP_000840 A/G V224I minus 2378699 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.29 0.06 458 5 0.33 0.13 436 6 123 "by doubleHit,freq,cluster" conservative 138390 1p13.3 glutathione S-transferase M3 (brain) 369 rs7483 GSTM3 2947 1 109991743 NM_000849 NP_000840 A/G V224I minus 3172582 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 68 0.41 0.29 0.06 458 5 0.33 0.13 436 6 123 "by doubleHit,freq,cluster" conservative 138390 1p13.3 glutathione S-transferase M3 (brain) 370 rs7483 GSTM3 2947 1 109991743 NM_000849 NP_000840 A/G V224I minus 6903821 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.34 0.29 0.06 458 5 0.33 0.13 436 6 123 "by doubleHit,freq,cluster" conservative 138390 1p13.3 glutathione S-transferase M3 (brain) 371 rs7483 GSTM3 2947 1 109991743 NM_000849 NP_000840 A/G V224I minus 23868204 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.29 0.06 458 5 0.33 0.13 436 6 123 "by doubleHit,freq,cluster" conservative 138390 1p13.3 glutathione S-transferase M3 (brain) 372 rs7535 SRP14 6727 15 38115867 NM_003134 NP_003125 C/G P124A minus 3177688 619 WICVAR MITOGPOP6 CORIELL Mixed 44 0.23 0.09 0.12 162 2 0.28 0 1482 1 121 "HapMap,doubleHit,freq,cluster" conservative 600708 15q22 signal recognition particle 14kDa (homologous Alu RNA binding protein) 373 rs7535 SRP14 6727 15 38115867 NM_003134 NP_003125 C/G P124A minus 4092989 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.04 0.09 0.12 162 2 0.28 0 1482 1 121 "HapMap,doubleHit,freq,cluster" conservative 600708 15q22 signal recognition particle 14kDa (homologous Alu RNA binding protein) 374 rs7571 ADPRTL1 143 13 23898617 NM_006437 NP_006428 C/G A1656P minus 6903629 775 SNP500CANCER CAUC1 Caucasian (31) 58 0.48 0.48 0 58 1 0.46 0.05 342 4 119 "by doubleHit,freq,cluster" conservative 607519 13q11 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1 375 rs7799 ELF1 1997 13 40431052 NM_172373 NP_758961 A/G N58S minus 9720 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.32 0.32 0 280 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.575 5 Borderline 0.16 2.97 21 conservative 189973 13q13 E74-like factor 1 (ets domain transcription factor) 376 rs7799 ELF1 1997 13 40431052 NM_172373 NP_758961 A/G N58S minus 2934168 1303 SEQUENOM CEPH CEPH (92) 92 0.32 0.32 0 280 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.575 5 Borderline 0.16 2.97 21 conservative 189973 13q13 E74-like factor 1 (ets domain transcription factor) 377 rs7825 OVGP1 5016 1 111669139 NM_002557 NP_002548 C/G E676Q plus 9747 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.4 0.4 0.07 364 5 0.23 0.05 1639 6 123 "by doubleHit,submitter,freq,cluster" conservative 603578 1p13 "oviductal glycoprotein 1, 120kDa (mucin 9, oviductin)" 378 rs7825 OVGP1 5016 1 111669139 NM_002557 NP_002548 C/G E676Q plus 2620723 1303 SEQUENOM CEPH CEPH (92) 92 0.4 0.4 0.07 364 5 0.23 0.05 1639 6 123 "by doubleHit,submitter,freq,cluster" conservative 603578 1p13 "oviductal glycoprotein 1, 120kDa (mucin 9, oviductin)" 379 rs7825 OVGP1 5016 1 111669139 NM_002557 NP_002548 C/G E676Q plus 16333801 902 AFFY Caucasian 24 0.42 0.4 0.07 364 5 0.23 0.05 1639 6 123 "by doubleHit,submitter,freq,cluster" conservative 603578 1p13 "oviductal glycoprotein 1, 120kDa (mucin 9, oviductin)" 380 rs7825 OVGP1 5016 1 111669139 NM_002557 NP_002548 C/G E676Q plus 16333801 904 AFFY CEPH 12 0.08 0.4 0.07 364 5 0.23 0.05 1639 6 123 "by doubleHit,submitter,freq,cluster" conservative 603578 1p13 "oviductal glycoprotein 1, 120kDa (mucin 9, oviductin)" 381 rs7825 OVGP1 5016 1 111669139 NM_002557 NP_002548 C/G E676Q plus 24266714 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.4 0.07 364 5 0.23 0.05 1639 6 123 "by doubleHit,submitter,freq,cluster" conservative 603578 1p13 "oviductal glycoprotein 1, 120kDa (mucin 9, oviductin)" 382 rs8012 GCDH 2639 19 12871520 NM_013976 NP_039663 A/G Q417R plus 9953 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.26 0.26 0 280 2 121 "by doubleHit,freq,cluster" Potentially intolerant 0.08 2.93 57 conservative 608801 19p13.2 glutaryl-Coenzyme A dehydrogenase 383 rs8012 GCDH 2639 19 12871520 NM_013976 NP_039663 A/G Q417R plus 17615281 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.26 0 280 2 121 "by doubleHit,freq,cluster" Potentially intolerant 0.08 2.93 57 conservative 608801 19p13.2 glutaryl-Coenzyme A dehydrogenase 384 rs8017 TCEB2 6923 16 2761574 NM_207013 NP_996896 C/T S129N plus 3287771 1303 SEQUENOM CEPH CEPH (92) 46 0.5 0.5 0 46 1 123 "by doubleHit,freq,cluster" conservative 600787 16p12.3 "transcription elongation factor B (SIII), polypeptide 2 (18kDa, elongin B)" 385 rs8207 PPIG 9360 2 170319370 NM_004792 NP_004783 A/G N699D plus 10166 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.2 0.21 0.01 398 3 121 "HapMap,doubleHit,freq,cluster" conservative 606093 2q31.1 peptidyl-prolyl isomerase G (cyclophilin G) 386 rs8207 PPIG 9360 2 170319370 NM_004792 NP_004783 A/G N699D plus 10007638 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.22 0.21 0.01 398 3 121 "HapMap,doubleHit,freq,cluster" conservative 606093 2q31.1 peptidyl-prolyl isomerase G (cyclophilin G) 387 rs8207 PPIG 9360 2 170319370 NM_004792 NP_004783 A/G N699D plus 10007638 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.21 0.01 398 3 121 "HapMap,doubleHit,freq,cluster" conservative 606093 2q31.1 peptidyl-prolyl isomerase G (cyclophilin G) 388 rs8289 M6PRBP1 10226 19 4810937 NM_005817 NP_005808 A/G I56V minus 10262 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.43 0.4 0.1 324 3 0.4 0.01 1582 3 123 "by doubleHit,freq,cluster" Benign 0.089 6 Tolerant 0.61 2.95 37 conservative 602702 19p13.3 mannose-6-phosphate receptor binding protein 1 389 rs8289 M6PRBP1 10226 19 4810937 NM_005817 NP_005808 A/G I56V minus 3747046 1303 SEQUENOM CEPH CEPH (92) 92 0.43 0.4 0.1 324 3 0.4 0.01 1582 3 123 "by doubleHit,freq,cluster" Benign 0.089 6 Tolerant 0.61 2.95 37 conservative 602702 19p13.3 mannose-6-phosphate receptor binding protein 1 390 rs8289 M6PRBP1 10226 19 4810937 NM_005817 NP_005808 A/G I56V minus 24082489 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.18 0.4 0.1 324 3 0.4 0.01 1582 3 123 "by doubleHit,freq,cluster" Benign 0.089 6 Tolerant 0.61 2.95 37 conservative 602702 19p13.3 mannose-6-phosphate receptor binding protein 1 391 rs8305 POLI 11201 18 50074803 NM_007195 NP_009126 A/G A706T plus 4480077 506 NCBI NIHPDR NIHPDR 122 0.26 0.28 0.06 560 5 0.17 0.08 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.9 5 moderately conservative 605252 18q21.1 polymerase (DNA directed) iota 392 rs8305 POLI 11201 18 50074803 NM_007195 NP_009126 A/G A706T plus 4916789 693 EGP_SNPS PDR90 NIHPDR 178 0.24 0.28 0.06 560 5 0.17 0.08 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.9 5 moderately conservative 605252 18q21.1 polymerase (DNA directed) iota 393 rs8305 POLI 11201 18 50074803 NM_007195 NP_009126 A/G A706T plus 4916789 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.26 0.28 0.06 560 5 0.17 0.08 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.9 5 moderately conservative 605252 18q21.1 polymerase (DNA directed) iota 394 rs8305 POLI 11201 18 50074803 NM_007195 NP_009126 A/G A706T plus 4916789 1303 SEQUENOM CEPH CEPH (92) 92 0.38 0.28 0.06 560 5 0.17 0.08 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.9 5 moderately conservative 605252 18q21.1 polymerase (DNA directed) iota 395 rs8305 POLI 11201 18 50074803 NM_007195 NP_009126 A/G A706T plus 24531273 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.28 0.06 560 5 0.17 0.08 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.9 5 moderately conservative 605252 18q21.1 polymerase (DNA directed) iota 396 rs8337 UBD 10537 6 29631655 NM_006398 NP_006389 C/G C160S minus 10314 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.28 0.24 0.07 604 4 0.08 0.03 84 2 123 "by doubleHit,freq,cluster" moderately radical 606050 6p21.3 ubiquitin D 397 rs8337 UBD 10537 6 29631655 NM_006398 NP_006389 C/G C160S minus 24341481 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.24 0.07 604 4 0.08 0.03 84 2 123 "by doubleHit,freq,cluster" moderately radical 606050 6p21.3 ubiquitin D 398 rs8337 UBD 10537 6 29631655 NM_006398 NP_006389 C/G C160S minus 24790044 1303 SEQUENOM CEPH CEPH (92) 184 0.28 0.24 0.07 604 4 0.08 0.03 84 2 123 "by doubleHit,freq,cluster" moderately radical 606050 6p21.3 ubiquitin D 399 rs8337 UBD 10537 6 29631655 NM_006398 NP_006389 C/G C160S minus 24796241 1303 SEQUENOM CEPH CEPH (92) 184 0.15 0.24 0.07 604 4 0.08 0.03 84 2 123 "by doubleHit,freq,cluster" moderately radical 606050 6p21.3 ubiquitin D 400 rs8455 LXN 56925 3 159871482 NM_020169 NP_064554 C/T H53R plus 14195380 1303 SEQUENOM CEPH CEPH (92) 92 0.45 0.42 0.07 140 2 0.23 0.06 94 2 123 by freq conservative 3q25.32 latexin 401 rs8455 LXN 56925 3 159871482 NM_020169 NP_064554 C/T H53R plus 24381862 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.42 0.07 140 2 0.23 0.06 94 2 123 by freq conservative 3q25.32 latexin 402 rs8473 MKI67 4288 10 129789568 NM_002417 NP_002408 A/G K3217E minus 10462 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.3 0.35 0.09 448 4 0.44 0.03 1588 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 176741 10q25-qter antigen identified by monoclonal antibody Ki-67 403 rs8473 MKI67 4288 10 129789568 NM_002417 NP_002408 A/G K3217E minus 10624698 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.47 0.35 0.09 448 4 0.44 0.03 1588 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 176741 10q25-qter antigen identified by monoclonal antibody Ki-67 404 rs8473 MKI67 4288 10 129789568 NM_002417 NP_002408 A/G K3217E minus 10624698 1303 SEQUENOM CEPH CEPH (92) 92 0.3 0.35 0.09 448 4 0.44 0.03 1588 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 176741 10q25-qter antigen identified by monoclonal antibody Ki-67 405 rs8473 MKI67 4288 10 129789568 NM_002417 NP_002408 A/G K3217E minus 23643988 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.35 0.09 448 4 0.44 0.03 1588 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 176741 10q25-qter antigen identified by monoclonal antibody Ki-67 406 rs8572 OXA1L 5018 14 22306364 NM_005015 NP_005006 A/G A104V minus 1487347 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 80 0.2 0.14 0.08 338 5 0.3 0.15 212 4 121 "by doubleHit,freq,cluster" Benign 0.173 8 moderately conservative 601066 14q11.2 oxidase (cytochrome c) assembly 1-like 407 rs8572 OXA1L 5018 14 22306364 NM_005015 NP_005006 A/G A104V minus 1487347 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.14 0.14 0.08 338 5 0.3 0.15 212 4 121 "by doubleHit,freq,cluster" Benign 0.173 8 moderately conservative 601066 14q11.2 oxidase (cytochrome c) assembly 1-like 408 rs8572 OXA1L 5018 14 22306364 NM_005015 NP_005006 A/G A104V minus 1487347 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 94 0.21 0.14 0.08 338 5 0.3 0.15 212 4 121 "by doubleHit,freq,cluster" Benign 0.173 8 moderately conservative 601066 14q11.2 oxidase (cytochrome c) assembly 1-like 409 rs8572 OXA1L 5018 14 22306364 NM_005015 NP_005006 A/G A104V minus 1487347 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.14 0.08 338 5 0.3 0.15 212 4 121 "by doubleHit,freq,cluster" Benign 0.173 8 moderately conservative 601066 14q11.2 oxidase (cytochrome c) assembly 1-like 410 rs8572 OXA1L 5018 14 22306364 NM_005015 NP_005006 A/G A104V minus 3173367 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 58 0.1 0.14 0.08 338 5 0.3 0.15 212 4 121 "by doubleHit,freq,cluster" Benign 0.173 8 moderately conservative 601066 14q11.2 oxidase (cytochrome c) assembly 1-like 411 rs8821 FLII 2314 17 18089259 NM_002018 NP_002009 A/G R1243H minus 10850 1303 SEQUENOM CEPH CEPH (92) 92 0.05 0.05 0 92 1 120 by freq Potentially damaging 1.308 8 Tolerant 0.54 2.76 78 conservative 600362 17p11.2 flightless I homolog (Drosophila) 412 rs8875 NDUFC2 4718 11 77468303 NM_004549 NP_004540 C/G L46V plus 793572 1303 SEQUENOM CEPH CEPH (92) 92 0.23 0.23 0 92 1 123 by freq Benign 0.761 6 conservative 603845 11q13.4 "NADH dehydrogenase (ubiquinone) 1, subcomplex unknown, 2, 14.5kDa" 413 rs8923 MTHFS 10588 15 77924615 NM_006441 NP_006432 A/G T202A minus 10798867 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.08 0.07 0.02 260 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 604197 15q24.3 "5,10-methenyltetrahydrofolate synthetase (5-formyltetrahydrofolate cyclo-ligase)" 414 rs8923 MTHFS 10588 15 77924615 NM_006441 NP_006432 A/G T202A minus 10798867 1303 SEQUENOM CEPH CEPH (92) 92 0.06 0.07 0.02 260 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 604197 15q24.3 "5,10-methenyltetrahydrofolate synthetase (5-formyltetrahydrofolate cyclo-ligase)" 415 rs8923 MTHFS 10588 15 77924615 NM_006441 NP_006432 A/G T202A minus 24521262 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.07 0.02 260 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 604197 15q24.3 "5,10-methenyltetrahydrofolate synthetase (5-formyltetrahydrofolate cyclo-ligase)" 416 rs8971 GART 2618 21 33805488 NM_000819 NP_000810 A/G D752G minus 11013 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.18 0.18 0 418 3 0.13 0.01 1576 3 123 "by cluster,freq" Possibly damaging 1.64 25 Tolerant 0.39 2.98 192 moderately conservative 138440 21q22.11 "phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase" 417 rs8971 GART 2618 21 33805488 NM_000819 NP_000810 A/G D752G minus 24546261 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.17 0.18 0 418 3 0.13 0.01 1576 3 123 "by cluster,freq" Possibly damaging 1.64 25 Tolerant 0.39 2.98 192 moderately conservative 138440 21q22.11 "phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase" 418 rs8971 GART 2618 21 33805488 NM_000819 NP_000810 A/G D752G minus 24796624 1303 SEQUENOM CEPH CEPH (92) 184 0.18 0.18 0 418 3 0.13 0.01 1576 3 123 "by cluster,freq" Possibly damaging 1.64 25 Tolerant 0.39 2.98 192 moderately conservative 138440 21q22.11 "phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase" 419 rs8999 TTF1 7270 9 132306895 NM_007344 NP_031370 G/T A290S minus 11043 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.08 0.07 0.01 212 2 0.26 0 1500 1 120 "HapMap,freq,cluster" moderately conservative 600777 9q34.3 "transcription termination factor, RNA polymerase I" 420 rs8999 TTF1 7270 9 132306895 NM_007344 NP_031370 G/T A290S minus 11043 1303 SEQUENOM CEPH CEPH (92) 92 0.06 0.07 0.01 212 2 0.26 0 1500 1 120 "HapMap,freq,cluster" moderately conservative 600777 9q34.3 "transcription termination factor, RNA polymerase I" 421 rs9002 GPR125 166647 4 22066436 XM_291111 XP_291111 A/G V1043M minus 6469754 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.27 0.16 0.18 212 2 123 "HapMap,doubleHit,freq" Borderline 0.17 2.78 34 conservative 4p15.32-p15.31 G protein-coupled receptor 125 422 rs9002 GPR125 166647 4 22066436 XM_291111 XP_291111 A/G V1043M minus 6469754 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.16 0.18 212 2 123 "HapMap,doubleHit,freq" Borderline 0.17 2.78 34 conservative 4p15.32-p15.31 G protein-coupled receptor 125 423 rs9250 SENP6 26054 6 76482008 NM_015571 NP_056386 A/G Y1106C plus 11320 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.25 0.3 0.06 522 5 0.02 0 44 1 123 "HapMap,doubleHit,submitter,freq,cluster" radical 605003 6q13-q14.3 SUMO1/sentrin specific protease 6 424 rs9250 SENP6 26054 6 76482008 NM_015571 NP_056386 A/G Y1106C plus 1517681 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.4 0.3 0.06 522 5 0.02 0 44 1 123 "HapMap,doubleHit,submitter,freq,cluster" radical 605003 6q13-q14.3 SUMO1/sentrin specific protease 6 425 rs9250 SENP6 26054 6 76482008 NM_015571 NP_056386 A/G Y1106C plus 11824656 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.34 0.3 0.06 522 5 0.02 0 44 1 123 "HapMap,doubleHit,submitter,freq,cluster" radical 605003 6q13-q14.3 SUMO1/sentrin specific protease 6 426 rs9250 SENP6 26054 6 76482008 NM_015571 NP_056386 A/G Y1106C plus 11824656 1303 SEQUENOM CEPH CEPH (92) 92 0.25 0.3 0.06 522 5 0.02 0 44 1 123 "HapMap,doubleHit,submitter,freq,cluster" radical 605003 6q13-q14.3 SUMO1/sentrin specific protease 6 427 rs9250 SENP6 26054 6 76482008 NM_015571 NP_056386 A/G Y1106C plus 24408636 1371 PERLEGEN AFD_EUR_PANEL European American (24) 38 0.32 0.3 0.06 522 5 0.02 0 44 1 123 "HapMap,doubleHit,submitter,freq,cluster" radical 605003 6q13-q14.3 SUMO1/sentrin specific protease 6 428 rs9436 PELP1 27043 17 4521500 NM_014389 NP_055204 A/T T1126S minus 11526 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.27 0.26 0.03 400 3 120 "HapMap,submitter,freq" moderately conservative 17p13.3 "proline-, glutamic acid-, leucine-rich protein 1" 429 rs9436 PELP1 27043 17 4521500 NM_014389 NP_055204 A/T T1126S minus 11526 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.22 0.26 0.03 400 3 120 "HapMap,submitter,freq" moderately conservative 17p13.3 "proline-, glutamic acid-, leucine-rich protein 1" 430 rs9436 PELP1 27043 17 4521500 NM_014389 NP_055204 A/T T1126S minus 11526 1303 SEQUENOM CEPH CEPH (92) 92 0.27 0.26 0.03 400 3 120 "HapMap,submitter,freq" moderately conservative 17p13.3 "proline-, glutamic acid-, leucine-rich protein 1" 431 rs9438 DHX36 170506 3 155501589 NM_020865 NP_065916 C/G S416C plus 11529 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.41 0.39 0.03 400 3 120 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.437 6 moderately radical 3p13-q23 DEAH (Asp-Glu-Ala-His) box polypeptide 36 432 rs9438 DHX36 170506 3 155501589 NM_020865 NP_065916 C/G S416C plus 3110895 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.35 0.39 0.03 400 3 120 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.437 6 moderately radical 3p13-q23 DEAH (Asp-Glu-Ala-His) box polypeptide 36 433 rs9438 DHX36 170506 3 155501589 NM_020865 NP_065916 C/G S416C plus 3110895 1303 SEQUENOM CEPH CEPH (92) 92 0.41 0.39 0.03 400 3 120 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.437 6 moderately radical 3p13-q23 DEAH (Asp-Glu-Ala-His) box polypeptide 36 434 rs9508 ATPIF1 93974 1 28248421 NM_178190 NP_835497 C/T R63G minus 11605 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.23 0.22 0.02 328 3 0.24 0.23 94 2 123 "by doubleHit,submitter,freq" moderately radical 1p35.3 ATPase inhibitory factor 1 435 rs9508 ATPIF1 93974 1 28248421 NM_178190 NP_835497 C/T R63G minus 2287204 1303 SEQUENOM CEPH CEPH (92) 92 0.23 0.22 0.02 328 3 0.24 0.23 94 2 123 "by doubleHit,submitter,freq" moderately radical 1p35.3 ATPase inhibitory factor 1 436 rs9508 ATPIF1 93974 1 28248421 NM_178190 NP_835497 C/T R63G minus 23668319 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.22 0.02 328 3 0.24 0.23 94 2 123 "by doubleHit,submitter,freq" moderately radical 1p35.3 ATPase inhibitory factor 1 437 rs9600 NDUFS3 4722 11 47562560 NM_004551 NP_004542 A/C P249Q plus 11703 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.14 0.14 0 84 1 0.11 0 84 1 52 by freq Possibly damaging 1.872 14 Intolerant 0 3.17 19 moderately conservative 603846 11p11.11 "NADH dehydrogenase (ubiquinone) Fe-S protein 3, 30kDa (NADH-coenzyme Q reductase)" 438 rs9614 FBXO2 26232 1 11644827 NM_012168 NP_036300 A/C K118T minus 1343940 1303 SEQUENOM CEPH CEPH (92) 92 0.19 0.19 0 92 1 120 by freq Potentially damaging 1.363 11 Tolerant 0.23 2.81 33 moderately conservative 607112 1p36.21 F-box protein 2 439 rs10012 CYP1B1 1545 2 38214041 NM_000104 NP_000095 C/G R48G minus 6903740 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.23 0.3 0.13 326 3 0.34 0.04 346 4 123 "by doubleHit,freq,cluster" Benign 0.225 5 Tolerant 0.23 2.81 85 moderately radical 601771 2p21 "cytochrome P450, family 1, subfamily B, polypeptide 1" 440 rs10012 CYP1B1 1545 2 38214041 NM_000104 NP_000095 C/G R48G minus 12724380 693 EGP_SNPS PDR90 NIHPDR 172 0.4 0.3 0.13 326 3 0.34 0.04 346 4 123 "by doubleHit,freq,cluster" Benign 0.225 5 Tolerant 0.23 2.81 85 moderately radical 601771 2p21 "cytochrome P450, family 1, subfamily B, polypeptide 1" 441 rs10012 CYP1B1 1545 2 38214041 NM_000104 NP_000095 C/G R48G minus 12724380 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.3 0.13 326 3 0.34 0.04 346 4 123 "by doubleHit,freq,cluster" Benign 0.225 5 Tolerant 0.23 2.81 85 moderately radical 601771 2p21 "cytochrome P450, family 1, subfamily B, polypeptide 1" 442 rs10067 OVGP1 5016 1 111669353 NM_002557 NP_002548 C/G H604Q plus 12205 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.19 0.15 0.05 224 3 0.43 0.02 1542 5 123 "by submitter,freq,cluster" Probably damaging 2.063 6 conservative 603578 1p13 "oviductal glycoprotein 1, 120kDa (mucin 9, oviductin)" 443 rs10067 OVGP1 5016 1 111669353 NM_002557 NP_002548 C/G H604Q plus 2640019 1303 SEQUENOM CEPH CEPH (92) 92 0.1 0.15 0.05 224 3 0.43 0.02 1542 5 123 "by submitter,freq,cluster" Probably damaging 2.063 6 conservative 603578 1p13 "oviductal glycoprotein 1, 120kDa (mucin 9, oviductin)" 444 rs10067 OVGP1 5016 1 111669353 NM_002557 NP_002548 C/G H604Q plus 23860871 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.15 0.05 224 3 0.43 0.02 1542 5 123 "by submitter,freq,cluster" Probably damaging 2.063 6 conservative 603578 1p13 "oviductal glycoprotein 1, 120kDa (mucin 9, oviductin)" 445 rs10371 CACH-1 134526 5 80667398 NM_130767 NP_570123 C/T A403T plus 12523 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.2 0.2 0.01 520 4 120 "HapMap,submitter,freq,cluster" moderately conservative 5q14.1 cytosolic acetyl-CoA hydrolase 446 rs10371 CACH-1 134526 5 80667398 NM_130767 NP_570123 C/T A403T plus 1530425 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.21 0.2 0.01 520 4 120 "HapMap,submitter,freq,cluster" moderately conservative 5q14.1 cytosolic acetyl-CoA hydrolase 447 rs10371 CACH-1 134526 5 80667398 NM_130767 NP_570123 C/T A403T plus 17069119 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.21 0.2 0.01 520 4 120 "HapMap,submitter,freq,cluster" moderately conservative 5q14.1 cytosolic acetyl-CoA hydrolase 448 rs10371 CACH-1 134526 5 80667398 NM_130767 NP_570123 C/T A403T plus 17069119 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.2 0.01 520 4 120 "HapMap,submitter,freq,cluster" moderately conservative 5q14.1 cytosolic acetyl-CoA hydrolase 449 rs10502 UBE2J1 51465 6 90096389 NM_016021 NP_057105 C/G L229V minus 4963580 902 AFFY Caucasian 24 0.42 0.38 0.05 177 4 0.27 0.02 1636 6 123 by freq Benign 0.225 5 Tolerant 0.23 3.1 8 conservative 6q16.1 "ubiquitin-conjugating enzyme E2, J1 (UBC6 homolog, yeast)" 450 rs10502 UBE2J1 51465 6 90096389 NM_016021 NP_057105 C/G L229V minus 4963580 904 AFFY CEPH 12 0.33 0.38 0.05 177 4 0.27 0.02 1636 6 123 by freq Benign 0.225 5 Tolerant 0.23 3.1 8 conservative 6q16.1 "ubiquitin-conjugating enzyme E2, J1 (UBC6 homolog, yeast)" 451 rs10502 UBE2J1 51465 6 90096389 NM_016021 NP_057105 C/G L229V minus 12824947 1303 SEQUENOM CEPH CEPH (92) 93 0.41 0.38 0.05 177 4 0.27 0.02 1636 6 123 by freq Benign 0.225 5 Tolerant 0.23 3.1 8 conservative 6q16.1 "ubiquitin-conjugating enzyme E2, J1 (UBC6 homolog, yeast)" 452 rs10502 UBE2J1 51465 6 90096389 NM_016021 NP_057105 C/G L229V minus 24399052 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.38 0.05 177 4 0.27 0.02 1636 6 123 by freq Benign 0.225 5 Tolerant 0.23 3.1 8 conservative 6q16.1 "ubiquitin-conjugating enzyme E2, J1 (UBC6 homolog, yeast)" 453 rs10642 EIF5B 9669 2 99438715 NM_015904 NP_056988 A/G S337G plus 12805 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.03 0.03 0 84 1 0.09 0.05 168 2 52 by freq moderately conservative 606086 2p11.1-q11.1 eukaryotic translation initiation factor 5B 454 rs10963 RBP5 83758 12 7172584 NM_031491 NP_113679 C/T D19N plus 13141 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.23 0.23 0 84 1 0.4 0.03 1664 3 100 "by cluster,freq" Benign 0.338 26 Borderline 0.19 2.78 89 conservative 12p13.31 "retinol binding protein 5, cellular" 455 rs10988 LARS 51520 5 145480189 NM_020117 NP_064502 C/T R1088K plus 13168 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.17 0.25 0.06 532 5 0.21 0.05 1266 4 123 "HapMap,freq,cluster" Benign 0.984 13 conservative 151350 5q32 leucyl-tRNA synthetase 456 rs10988 LARS 51520 5 145480189 NM_020117 NP_064502 C/T R1088K plus 13168 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.24 0.25 0.06 532 5 0.21 0.05 1266 4 123 "HapMap,freq,cluster" Benign 0.984 13 conservative 151350 5q32 leucyl-tRNA synthetase 457 rs10988 LARS 51520 5 145480189 NM_020117 NP_064502 C/T R1088K plus 4949406 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.29 0.25 0.06 532 5 0.21 0.05 1266 4 123 "HapMap,freq,cluster" Benign 0.984 13 conservative 151350 5q32 leucyl-tRNA synthetase 458 rs10988 LARS 51520 5 145480189 NM_020117 NP_064502 C/T R1088K plus 4949406 1303 SEQUENOM CEPH CEPH (92) 92 0.24 0.25 0.06 532 5 0.21 0.05 1266 4 123 "HapMap,freq,cluster" Benign 0.984 13 conservative 151350 5q32 leucyl-tRNA synthetase 459 rs10988 LARS 51520 5 145480189 NM_020117 NP_064502 C/T R1088K plus 24351928 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.25 0.06 532 5 0.21 0.05 1266 4 123 "HapMap,freq,cluster" Benign 0.984 13 conservative 151350 5q32 leucyl-tRNA synthetase 460 rs11106 MKI67 4288 10 129789768 NM_002417 NP_002408 C/G T3150S minus 13291 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.43 0.43 0.01 364 3 0.47 0.03 126 2 121 "by doubleHit,freq,cluster" moderately conservative 176741 10q25-qter antigen identified by monoclonal antibody Ki-67 461 rs11106 MKI67 4288 10 129789768 NM_002417 NP_002408 C/G T3150S minus 1525715 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.45 0.43 0.01 364 3 0.47 0.03 126 2 121 "by doubleHit,freq,cluster" moderately conservative 176741 10q25-qter antigen identified by monoclonal antibody Ki-67 462 rs11106 MKI67 4288 10 129789768 NM_002417 NP_002408 C/G T3150S minus 10583404 1303 SEQUENOM CEPH CEPH (92) 92 0.42 0.43 0.01 364 3 0.47 0.03 126 2 121 "by doubleHit,freq,cluster" moderately conservative 176741 10q25-qter antigen identified by monoclonal antibody Ki-67 463 rs11159 RNASET2 8635 6 167313552 NM_003730 NP_003721 C/T R236W minus 13347 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.04 0.07 0.09 344 4 0.05 0.07 1754 5 123 "HapMap,freq,cluster" Benign 0.511 5 moderately radical 6q27 ribonuclease T2 464 rs11159 RNASET2 8635 6 167313552 NM_003730 NP_003721 C/T R236W minus 13347 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.07 0.09 344 4 0.05 0.07 1754 5 123 "HapMap,freq,cluster" Benign 0.511 5 moderately radical 6q27 ribonuclease T2 465 rs11159 RNASET2 8635 6 167313552 NM_003730 NP_003721 C/T R236W minus 1512972 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.21 0.07 0.09 344 4 0.05 0.07 1754 5 123 "HapMap,freq,cluster" Benign 0.511 5 moderately radical 6q27 ribonuclease T2 466 rs11159 RNASET2 8635 6 167313552 NM_003730 NP_003721 C/T R236W minus 24146236 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.07 0.09 344 4 0.05 0.07 1754 5 123 "HapMap,freq,cluster" Benign 0.511 5 moderately radical 6q27 ribonuclease T2 467 rs11250 CENPC1 1060 4 68208981 NM_001812 NP_001803 C/T L341F minus 5528842 1303 SEQUENOM CEPH CEPH (92) 92 0.35 0.35 0 92 1 121 "by doubleHit,freq,cluster" conservative 117141 4q12-q13.3 centromere protein C 1 468 rs11357 MTIF2 4528 2 55381766 NM_002453 NP_002444 A/G V556I minus 13561 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.15 0.2 0.13 240 2 121 "by doubleHit,freq,cluster" Benign 0.3 5 Tolerant 1 2.73 30 conservative 603766 2p14-p16 mitochondrial translational initiation factor 2 469 rs11357 MTIF2 4528 2 55381766 NM_002453 NP_002444 A/G V556I minus 3177497 619 WICVAR MITOGPOP6 CORIELL Mixed 52 0.37 0.2 0.13 240 2 121 "by doubleHit,freq,cluster" Benign 0.3 5 Tolerant 1 2.73 30 conservative 603766 2p14-p16 mitochondrial translational initiation factor 2 470 rs11479 ECGF1 1890 22 49254380 NM_001953 NP_001944 C/T S471L minus 13689 1303 SEQUENOM CEPH CEPH (92) 92 0.05 0.05 0 92 1 123 "by cluster,freq" Tolerant 0.46 2.92 57 moderately radical 131222 22q13.33 endothelial cell growth factor 1 (platelet-derived) 471 rs11551 FBLN1 2192 22 44279529 NM_001996 NP_001987 G/T R633L plus 13769 1303 SEQUENOM CEPH CEPH (92) 92 0.12 0.12 0 92 1 120 by freq Potentially damaging 1.278 14 Tolerant 1 2.77 19 moderately radical 135820 22q13.31 fibulin 1 472 rs11574 ID3 3399 1 23630804 NM_002167 NP_002158 A/G T105A minus 13793 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.2 0.23 0.06 308 2 121 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 600277 1p36.13-p36.12 "inhibitor of DNA binding 3, dominant negative helix-loop-helix protein" 473 rs11574 ID3 3399 1 23630804 NM_002167 NP_002158 A/G T105A minus 3069953 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.28 0.23 0.06 308 2 121 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 600277 1p36.13-p36.12 "inhibitor of DNA binding 3, dominant negative helix-loop-helix protein" 474 rs11607 MBTPS1 8720 16 82645548 NM_201268 NP_957720 A/G S627N minus 13830 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.39 0.36 0.06 306 2 0.42 0 1120 1 121 "HapMap,doubleHit,freq,cluster" conservative 603355 16q24 "membrane-bound transcription factor protease, site 1" 475 rs11607 MBTPS1 8720 16 82645548 NM_201268 NP_957720 A/G S627N minus 19343224 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.31 0.36 0.06 306 2 0.42 0 1120 1 121 "HapMap,doubleHit,freq,cluster" conservative 603355 16q24 "membrane-bound transcription factor protease, site 1" 476 rs11746 FREB 84824 1 158414794 NM_032738 NP_116127 A/G R349Q plus 13980 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.44 0.44 0.01 328 3 0.23 0.04 94 2 123 "by doubleHit,freq,cluster" conservative 606891 1q23.1 Fc receptor homolog expressed in B cells 477 rs11746 FREB 84824 1 158414794 NM_032738 NP_116127 A/G R349Q plus 1291097 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.44 0.01 328 3 0.23 0.04 94 2 123 "by doubleHit,freq,cluster" conservative 606891 1q23.1 Fc receptor homolog expressed in B cells 478 rs11746 FREB 84824 1 158414794 NM_032738 NP_116127 A/G R349Q plus 24244157 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.44 0.01 328 3 0.23 0.04 94 2 123 "by doubleHit,freq,cluster" conservative 606891 1q23.1 Fc receptor homolog expressed in B cells 479 rs12505 CKB 1152 14 103056022 NM_001823 NP_001814 C/T L360F minus 24796478 1303 SEQUENOM CEPH CEPH (92) 184 0.41 0.41 0 184 1 123 by freq Possibly damaging 1.696 116 Intolerant 0 2.79 153 conservative 123280 14q32 "creatine kinase, brain" 480 rs12529 AKR1C3 8644 10 5126651 NM_003739 NP_003730 C/G H5Q plus 14808 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.4 0.41 0.04 385 4 0.17 0.15 1996 7 121 "by doubleHit,freq,cluster" Benign 0.483 76 Tolerant 0.31 2.88 68 conservative 603966 10p15-p14 "aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II)" 481 rs12529 AKR1C3 8644 10 5126651 NM_003739 NP_003730 C/G H5Q plus 2827711 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 42 0.5 0.41 0.04 385 4 0.17 0.15 1996 7 121 "by doubleHit,freq,cluster" Benign 0.483 76 Tolerant 0.31 2.88 68 conservative 603966 10p15-p14 "aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II)" 482 rs12529 AKR1C3 8644 10 5126651 NM_003739 NP_003730 C/G H5Q plus 2827711 1303 SEQUENOM CEPH CEPH (92) 93 0.4 0.41 0.04 385 4 0.17 0.15 1996 7 121 "by doubleHit,freq,cluster" Benign 0.483 76 Tolerant 0.31 2.88 68 conservative 603966 10p15-p14 "aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II)" 483 rs12529 AKR1C3 8644 10 5126651 NM_003739 NP_003730 C/G H5Q plus 6903636 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.39 0.41 0.04 385 4 0.17 0.15 1996 7 121 "by doubleHit,freq,cluster" Benign 0.483 76 Tolerant 0.31 2.88 68 conservative 603966 10p15-p14 "aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II)" 484 rs12614 BF 629 6 32022158 NM_001710 NP_001701 C/T R32W plus 5606985 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 28 0.07 0.08 0.01 74 2 0.17 0 96 2 123 by freq moderately radical 138470 6p21.3 "B-factor, properdin" 485 rs12614 BF 629 6 32022158 NM_001710 NP_001701 C/T R32W plus 12674482 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.09 0.08 0.01 74 2 0.17 0 96 2 123 by freq moderately radical 138470 6p21.3 "B-factor, properdin" 486 rs12770 RANBP2 5903 2 108841187 NM_006267 NP_006258 C/G P1892A minus 15067 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.22 0.22 0 188 1 108 by freq conservative 601181 2q12.3 RAN binding protein 2 487 rs12917 MGMT 4255 10 131396273 NM_002412 NP_002403 C/T L84F plus 15222 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.25 0.18 0.04 1108 4 0.12 0.02 1902 7 123 "by cluster,freq" Benign 0.463 7 Tolerant 0.71 2.9 15 conservative 156569 10q26 O-6-methylguanine-DNA methyltransferase 488 rs12917 MGMT 4255 10 131396273 NM_002412 NP_002403 C/T L84F plus 2924003 506 NCBI NIHPDR NIHPDR 810 0.18 0.18 0.04 1108 4 0.12 0.02 1902 7 123 "by cluster,freq" Benign 0.463 7 Tolerant 0.71 2.9 15 conservative 156569 10q26 O-6-methylguanine-DNA methyltransferase 489 rs12917 MGMT 4255 10 131396273 NM_002412 NP_002403 C/T L84F plus 5586758 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.11 0.18 0.04 1108 4 0.12 0.02 1902 7 123 "by cluster,freq" Benign 0.463 7 Tolerant 0.71 2.9 15 conservative 156569 10q26 O-6-methylguanine-DNA methyltransferase 490 rs12917 MGMT 4255 10 131396273 NM_002412 NP_002403 C/T L84F plus 23564520 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.18 0.04 1108 4 0.12 0.02 1902 7 123 "by cluster,freq" Benign 0.463 7 Tolerant 0.71 2.9 15 conservative 156569 10q26 O-6-methylguanine-DNA methyltransferase 491 rs12960 SPG7 6687 16 88147829 NM_003119 NP_003110 A/G R688Q plus 75236 1303 SEQUENOM CEPH CEPH (92) 92 0.14 0.14 0.01 140 2 0.11 0.08 130 4 123 "by doubleHit,submitter,freq,cluster" Potentially damaging 1.357 9 Tolerant 0.41 2.75 61 conservative 602783 16q24.3 "spastic paraplegia 7, paraplegin (pure and complicated autosomal recessive)" 492 rs12960 SPG7 6687 16 88147829 NM_003119 NP_003110 A/G R688Q plus 24096097 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.14 0.01 140 2 0.11 0.08 130 4 123 "by doubleHit,submitter,freq,cluster" Potentially damaging 1.357 9 Tolerant 0.41 2.75 61 conservative 602783 16q24.3 "spastic paraplegia 7, paraplegin (pure and complicated autosomal recessive)" 493 rs13021 PNN 5411 14 38720675 NM_002687 NP_002678 A/G S671G plus 15334 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.12 0.1 0.03 448 4 0.2 0.13 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 603154 14q13.3 "pinin, desmosome associated protein" 494 rs13021 PNN 5411 14 38720675 NM_002687 NP_002678 A/G S671G plus 15334 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.08 0.1 0.03 448 4 0.2 0.13 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 603154 14q13.3 "pinin, desmosome associated protein" 495 rs13021 PNN 5411 14 38720675 NM_002687 NP_002678 A/G S671G plus 14373749 1303 SEQUENOM CEPH CEPH (92) 92 0.12 0.1 0.03 448 4 0.2 0.13 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 603154 14q13.3 "pinin, desmosome associated protein" 496 rs13021 PNN 5411 14 38720675 NM_002687 NP_002678 A/G S671G plus 24112453 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.1 0.03 448 4 0.2 0.13 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 603154 14q13.3 "pinin, desmosome associated protein" 497 rs13090 THRAP5 10025 19 819115 NM_005481 NP_005472 A/G E874K minus 15405 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.26 0.25 0.01 400 3 120 "HapMap,doubleHit,freq" moderately conservative 604062 19p13.3 thyroid hormone receptor associated protein 5 498 rs13090 THRAP5 10025 19 819115 NM_005481 NP_005472 A/G E874K minus 2513099 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.24 0.25 0.01 400 3 120 "HapMap,doubleHit,freq" moderately conservative 604062 19p13.3 thyroid hormone receptor associated protein 5 499 rs13090 THRAP5 10025 19 819115 NM_005481 NP_005472 A/G E874K minus 2513099 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.25 0.01 400 3 120 "HapMap,doubleHit,freq" moderately conservative 604062 19p13.3 thyroid hormone receptor associated protein 5 500 rs13181 ERCC2 2068 19 50546759 NM_000400 NP_000391 G/T K751Q plus 4385756 693 EGP_SNPS PDR90 NIHPDR 162 0.22 0.24 0.08 364 4 0.18 0.09 436 6 123 "by doubleHit,freq" Benign 0.472 5 Tolerant 0.7 3.14 28 moderately conservative 126340 19q13.3 "excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D)" 501 rs13181 ERCC2 2068 19 50546759 NM_000400 NP_000391 G/T K751Q plus 4385756 1303 SEQUENOM CEPH CEPH (92) 92 0.19 0.24 0.08 364 4 0.18 0.09 436 6 123 "by doubleHit,freq" Benign 0.472 5 Tolerant 0.7 3.14 28 moderately conservative 126340 19q13.3 "excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D)" 502 rs13181 ERCC2 2068 19 50546759 NM_000400 NP_000391 G/T K751Q plus 5586504 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.27 0.24 0.08 364 4 0.18 0.09 436 6 123 "by doubleHit,freq" Benign 0.472 5 Tolerant 0.7 3.14 28 moderately conservative 126340 19q13.3 "excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D)" 503 rs13181 ERCC2 2068 19 50546759 NM_000400 NP_000391 G/T K751Q plus 24431306 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.24 0.08 364 4 0.18 0.09 436 6 123 "by doubleHit,freq" Benign 0.472 5 Tolerant 0.7 3.14 28 moderately conservative 126340 19q13.3 "excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D)" 504 rs13321 TNC 3371 9 114872137 NM_002160 NP_002151 C/G E2008Q minus 15647 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.33 0.32 0.02 400 3 0.45 0 1502 1 121 "HapMap,doubleHit,submitter,freq,cluster" conservative 187380 9q33 tenascin C (hexabrachion) 505 rs13321 TNC 3371 9 114872137 NM_002160 NP_002151 C/G E2008Q minus 15647 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.29 0.32 0.02 400 3 0.45 0 1502 1 121 "HapMap,doubleHit,submitter,freq,cluster" conservative 187380 9q33 tenascin C (hexabrachion) 506 rs13321 TNC 3371 9 114872137 NM_002160 NP_002151 C/G E2008Q minus 17996538 1303 SEQUENOM CEPH CEPH (92) 92 0.33 0.32 0.02 400 3 0.45 0 1502 1 121 "HapMap,doubleHit,submitter,freq,cluster" conservative 187380 9q33 tenascin C (hexabrachion) 507 rs13428 ADPRTL1 143 13 23907441 NM_006437 NP_006428 C/G G1280R minus 15756 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.38 0.4 0.04 342 3 0.32 0.07 1832 5 123 "by doubleHit,freq,cluster" moderately radical 607519 13q11 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1 508 rs13428 ADPRTL1 143 13 23907441 NM_006437 NP_006428 C/G G1280R minus 5586208 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.47 0.4 0.04 342 3 0.32 0.07 1832 5 123 "by doubleHit,freq,cluster" moderately radical 607519 13q11 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1 509 rs13428 ADPRTL1 143 13 23907441 NM_006437 NP_006428 C/G G1280R minus 5586208 1303 SEQUENOM CEPH CEPH (92) 92 0.38 0.4 0.04 342 3 0.32 0.07 1832 5 123 "by doubleHit,freq,cluster" moderately radical 607519 13q11 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1 510 rs13706 CDC6 990 17 35710677 NM_001254 NP_001245 A/G V441I plus 3177778 619 WICVAR MITOGPOP6 CORIELL Mixed 42 0.29 0.15 0.08 474 5 0.44 0.01 1580 3 123 "HapMap,freq,cluster" Benign 0.62 11 Intolerant 0.05 2.86 15 conservative 602627 17q21.3 CDC6 cell division cycle 6 homolog (S. cerevisiae) 511 rs13706 CDC6 990 17 35710677 NM_001254 NP_001245 A/G V441I plus 5587265 693 EGP_SNPS PDR90 NIHPDR 176 0.2 0.15 0.08 474 5 0.44 0.01 1580 3 123 "HapMap,freq,cluster" Benign 0.62 11 Intolerant 0.05 2.86 15 conservative 602627 17q21.3 CDC6 cell division cycle 6 homolog (S. cerevisiae) 512 rs13706 CDC6 990 17 35710677 NM_001254 NP_001245 A/G V441I plus 5587265 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.15 0.15 0.08 474 5 0.44 0.01 1580 3 123 "HapMap,freq,cluster" Benign 0.62 11 Intolerant 0.05 2.86 15 conservative 602627 17q21.3 CDC6 cell division cycle 6 homolog (S. cerevisiae) 513 rs13706 CDC6 990 17 35710677 NM_001254 NP_001245 A/G V441I plus 5587265 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.15 0.08 474 5 0.44 0.01 1580 3 123 "HapMap,freq,cluster" Benign 0.62 11 Intolerant 0.05 2.86 15 conservative 602627 17q21.3 CDC6 cell division cycle 6 homolog (S. cerevisiae) 514 rs13706 CDC6 990 17 35710677 NM_001254 NP_001245 A/G V441I plus 23618880 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.15 0.08 474 5 0.44 0.01 1580 3 123 "HapMap,freq,cluster" Benign 0.62 11 Intolerant 0.05 2.86 15 conservative 602627 17q21.3 CDC6 cell division cycle 6 homolog (S. cerevisiae) 515 rs13807 FAU 2197 11 64645610 NM_001997 NP_001988 C/T T53I minus 870143 555 UUGC NIH90 NIHPDR 180 0.01 0.01 0 360 2 120 "by cluster,freq" Potentially damaging 1.387 22 Intolerant 0 3.11 399 moderately conservative 134690 11q13 Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed (fox derived); ribosomal protein S30 516 rs13807 FAU 2197 11 64645610 NM_001997 NP_001988 C/T T53I minus 12709616 693 EGP_SNPS PDR90 NIHPDR 180 0.01 0.01 0 360 2 120 "by cluster,freq" Potentially damaging 1.387 22 Intolerant 0 3.11 399 moderately conservative 134690 11q13 Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed (fox derived); ribosomal protein S30 517 rs13817 MUS81 80198 11 65384910 NM_025128 NP_079404 A/G R37H plus 16171 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.2 0.2 0 280 2 121 "by doubleHit,freq,cluster" conservative 606591 11q13 MUS81 endonuclease homolog (yeast) 518 rs13817 MUS81 80198 11 65384910 NM_025128 NP_079404 A/G R37H plus 1727380 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.2 0 280 2 121 "by doubleHit,freq,cluster" conservative 606591 11q13 MUS81 endonuclease homolog (yeast) 519 rs13894 SAT2 112483 17 7470627 NM_133491 NP_597998 C/T R126C minus 14295724 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.1 0.07 0.04 212 2 0.06 0 1476 1 120 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.987 5 Intolerant 0.02 2.76 32 radical 17p13.2 spermidine/spermine N1-acetyltransferase 2 520 rs13894 SAT2 112483 17 7470627 NM_133491 NP_597998 C/T R126C minus 14295724 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.07 0.04 212 2 0.06 0 1476 1 120 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.987 5 Intolerant 0.02 2.76 32 radical 17p13.2 spermidine/spermine N1-acetyltransferase 2 521 rs13898 AEBP1 165 7 43927065 NM_001129 NP_001120 A/G V1148I plus 4479021 693 EGP_SNPS PDR90 NIHPDR 170 0.01 0.03 0.04 382 3 121 "HapMap,freq,cluster" Benign 0.225 8 conservative 602981 7p13 AE binding protein 1 522 rs13898 AEBP1 165 7 43927065 NM_001129 NP_001120 A/G V1148I plus 4479021 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.08 0.03 0.04 382 3 121 "HapMap,freq,cluster" Benign 0.225 8 conservative 602981 7p13 AE binding protein 1 523 rs13898 AEBP1 165 7 43927065 NM_001129 NP_001120 A/G V1148I plus 4479021 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.03 0.04 382 3 121 "HapMap,freq,cluster" Benign 0.225 8 conservative 602981 7p13 AE binding protein 1 524 rs13926 TRAP1 10131 16 3664466 NM_016292 NP_057376 C/G R307G minus 89200 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.49 0.47 0.02 258 3 0.42 0.06 1484 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.189 11 moderately radical 606219 16p13.3 heat shock protein 75 525 rs13926 TRAP1 10131 16 3664466 NM_016292 NP_057376 C/G R307G minus 89200 1303 SEQUENOM CEPH CEPH (92) 92 0.46 0.47 0.02 258 3 0.42 0.06 1484 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.189 11 moderately radical 606219 16p13.3 heat shock protein 75 526 rs13926 TRAP1 10131 16 3664466 NM_016292 NP_057376 C/G R307G minus 24217057 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.47 0.02 258 3 0.42 0.06 1484 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.189 11 moderately radical 606219 16p13.3 heat shock protein 75 527 rs13928 AEBP1 165 7 43927020 NM_001129 NP_001120 A/G K1133E plus 3177826 619 WICVAR MITOGPOP6 CORIELL Mixed 44 0.45 0.44 0.01 136 2 121 "by doubleHit,freq,cluster" Benign 0.007 8 moderately conservative 602981 7p13 AE binding protein 1 528 rs13928 AEBP1 165 7 43927020 NM_001129 NP_001120 A/G K1133E plus 3177826 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.44 0.01 136 2 121 "by doubleHit,freq,cluster" Benign 0.007 8 moderately conservative 602981 7p13 AE binding protein 1 529 rs14008 TACSTD2 4070 1 58754202 NM_002353 NP_002344 A/C D216E minus 650638 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.04 0.03 276 2 0.11 0 1470 1 123 "by doubleHit,freq,cluster" conservative 137290 1p32-p31 tumor-associated calcium signal transducer 2 530 rs14008 TACSTD2 4070 1 58754202 NM_002353 NP_002344 A/C D216E minus 24796670 1303 SEQUENOM CEPH CEPH (92) 184 0.05 0.04 0.03 276 2 0.11 0 1470 1 123 "by doubleHit,freq,cluster" conservative 137290 1p32-p31 tumor-associated calcium signal transducer 2 531 rs14024 KRT1 3848 12 51355281 NM_006121 NP_006112 A/G K633R minus 16388 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.42 0.4 0.04 446 4 0.36 0.06 1592 3 123 "HapMap,doubleHit,freq,cluster" conservative 139350 12q12-q13 keratin 1 (epidermolytic hyperkeratosis) 532 rs14024 KRT1 3848 12 51355281 NM_006121 NP_006112 A/G K633R minus 3869018 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.34 0.4 0.04 446 4 0.36 0.06 1592 3 123 "HapMap,doubleHit,freq,cluster" conservative 139350 12q12-q13 keratin 1 (epidermolytic hyperkeratosis) 533 rs14024 KRT1 3848 12 51355281 NM_006121 NP_006112 A/G K633R minus 16565519 1303 SEQUENOM CEPH CEPH (92) 92 0.42 0.4 0.04 446 4 0.36 0.06 1592 3 123 "HapMap,doubleHit,freq,cluster" conservative 139350 12q12-q13 keratin 1 (epidermolytic hyperkeratosis) 534 rs14024 KRT1 3848 12 51355281 NM_006121 NP_006112 A/G K633R minus 23957083 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.4 0.04 446 4 0.36 0.06 1592 3 123 "HapMap,doubleHit,freq,cluster" conservative 139350 12q12-q13 keratin 1 (epidermolytic hyperkeratosis) 535 rs14115 HSPC051 29796 22 28488080 NM_013387 NP_037519 A/G I47V plus 3226471 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.03 0.03 0.01 168 2 0.06 0.06 1590 3 123 "HapMap,submitter,freq,cluster" Benign 0.959 9 Tolerant 0.75 2.98 19 conservative 22cen-q12.3 ubiquinol-cytochrome c reductase complex (7.2 kD) 536 rs14115 HSPC051 29796 22 28488080 NM_013387 NP_037519 A/G I47V plus 23592348 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.03 0.01 168 2 0.06 0.06 1590 3 123 "HapMap,submitter,freq,cluster" Benign 0.959 9 Tolerant 0.75 2.98 19 conservative 22cen-q12.3 ubiquinol-cytochrome c reductase complex (7.2 kD) 537 rs15895 OAS2 4939 12 111911008 NM_016817 NP_058197 C/T STOP720W minus 18316 665 CGAP-GAI POOLED_CEPH CEPH Caucasians (94) 188 0.33 0.37 0.05 526 5 0.12 0.05 70 2 123 "by doubleHit,submitter,freq,cluster" Probably damaging Intolerant radical 603350 12q24.2 "2'-5'-oligoadenylate synthetase 2, 69/71kDa" 538 rs15895 OAS2 4939 12 111911008 NM_016817 NP_058197 C/T STOP720W minus 2055335 1303 SEQUENOM CEPH CEPH (92) 92 0.33 0.37 0.05 526 5 0.12 0.05 70 2 123 "by doubleHit,submitter,freq,cluster" Probably damaging Intolerant radical 603350 12q24.2 "2'-5'-oligoadenylate synthetase 2, 69/71kDa" 539 rs15895 OAS2 4939 12 111911008 NM_016817 NP_058197 C/T STOP720W minus 2428576 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.43 0.37 0.05 526 5 0.12 0.05 70 2 123 "by doubleHit,submitter,freq,cluster" Probably damaging Intolerant radical 603350 12q24.2 "2'-5'-oligoadenylate synthetase 2, 69/71kDa" 540 rs15895 OAS2 4939 12 111911008 NM_016817 NP_058197 C/T STOP720W minus 2428576 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 184 0.41 0.37 0.05 526 5 0.12 0.05 70 2 123 "by doubleHit,submitter,freq,cluster" Probably damaging Intolerant radical 603350 12q24.2 "2'-5'-oligoadenylate synthetase 2, 69/71kDa" 541 rs15895 OAS2 4939 12 111911008 NM_016817 NP_058197 C/T STOP720W minus 24416187 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.37 0.05 526 5 0.12 0.05 70 2 123 "by doubleHit,submitter,freq,cluster" Probably damaging Intolerant radical 603350 12q24.2 "2'-5'-oligoadenylate synthetase 2, 69/71kDa" 542 rs15911 CTBS 1486 1 84741098 NM_004388 NP_004379 C/T V274I plus 4391078 1303 SEQUENOM CEPH CEPH (92) 92 0.48 0.45 0.07 140 2 0.07 0.05 94 2 123 by freq Benign 0.835 6 Tolerant 0.41 2.86 11 conservative 600873 1p22 "chitobiase, di-N-acetyl-" 543 rs15911 CTBS 1486 1 84741098 NM_004388 NP_004379 C/T V274I plus 24238464 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.45 0.07 140 2 0.07 0.05 94 2 123 by freq Benign 0.835 6 Tolerant 0.41 2.86 11 conservative 600873 1p22 "chitobiase, di-N-acetyl-" 544 rs15922 TAF11 6882 6 34958804 NM_005643 NP_005634 C/G T68R minus 6312498 693 EGP_SNPS PDR90 NIHPDR 180 0.02 0.03 0.02 320 3 123 "by cluster,freq" Benign 0.13 14 Tolerant 0.52 3 11 moderately conservative 600772 6p21.31 "TAF11 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 28kDa" 545 rs15922 TAF11 6882 6 34958804 NM_005643 NP_005634 C/G T68R minus 6312498 1303 SEQUENOM CEPH CEPH (92) 92 0.03 0.03 0.02 320 3 123 "by cluster,freq" Benign 0.13 14 Tolerant 0.52 3 11 moderately conservative 600772 6p21.31 "TAF11 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 28kDa" 546 rs15922 TAF11 6882 6 34958804 NM_005643 NP_005634 C/G T68R minus 24383722 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.03 0.02 320 3 123 "by cluster,freq" Benign 0.13 14 Tolerant 0.52 3 11 moderately conservative 600772 6p21.31 "TAF11 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 28kDa" 547 rs17456 FDPS 2224 1 152103384 NM_002004 NP_001995 C/T I391V minus 20086 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.04 0 92 1 60 by freq Benign 0.148 16 Borderline 0.16 2.77 75 conservative 134629 1q22 "farnesyl diphosphate synthase (farnesyl pyrophosphate synthetase, dimethylallyltranstransferase, geranyltranstransferase)" 548 rs17560 ANG 283 14 20231813 NM_001145 NP_001136 A/G K84E plus 20171 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 40 0.1 0.1 0 40 1 0.04 0 46 1 123 by freq Benign 0.019 31 Tolerant 0.78 2.89 173 moderately conservative 105850 14q11.1-q11.2 "angiogenin, ribonuclease, RNase A family, 5" 549 rs17561 IL1A 3552 2 113253454 NM_000575 NP_000566 G/T A114S minus 20172 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 40 0.33 0.37 0.08 360 5 0.22 0.03 394 5 113 "HapMap,submitter,freq,cluster" Potentially damaging 1.296 24 Intolerant 0.03 2.8 33 moderately conservative 147760 2q14 "interleukin 1, alpha" 550 rs17561 IL1A 3552 2 113253454 NM_000575 NP_000566 G/T A114S minus 4969895 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.33 0.37 0.08 360 5 0.22 0.03 394 5 113 "HapMap,submitter,freq,cluster" Potentially damaging 1.296 24 Intolerant 0.03 2.8 33 moderately conservative 147760 2q14 "interleukin 1, alpha" 551 rs17561 IL1A 3552 2 113253454 NM_000575 NP_000566 G/T A114S minus 4969895 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.31 0.37 0.08 360 5 0.22 0.03 394 5 113 "HapMap,submitter,freq,cluster" Potentially damaging 1.296 24 Intolerant 0.03 2.8 33 moderately conservative 147760 2q14 "interleukin 1, alpha" 552 rs17561 IL1A 3552 2 113253454 NM_000575 NP_000566 G/T A114S minus 4969895 1303 SEQUENOM CEPH CEPH (92) 92 0.48 0.37 0.08 360 5 0.22 0.03 394 5 113 "HapMap,submitter,freq,cluster" Potentially damaging 1.296 24 Intolerant 0.03 2.8 33 moderately conservative 147760 2q14 "interleukin 1, alpha" 553 rs17561 IL1A 3552 2 113253454 NM_000575 NP_000566 G/T A114S minus 5586646 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.36 0.37 0.08 360 5 0.22 0.03 394 5 113 "HapMap,submitter,freq,cluster" Potentially damaging 1.296 24 Intolerant 0.03 2.8 33 moderately conservative 147760 2q14 "interleukin 1, alpha" 554 rs17562 IL1A 3552 2 113253421 NM_000575 NP_000566 A/G N125D minus 20173 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 40 0.03 0.03 0 40 1 0.02 0.03 252 2 113 "by cluster,freq" Possibly damaging 1.691 25 Tolerant 0.27 2.91 31 conservative 147760 2q14 "interleukin 1, alpha" 555 rs17567 EPS15 2060 1 51538942 NM_001981 NP_001972 C/T I822M plus 20178 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 40 0.33 0.22 0.1 132 2 123 "by doubleHit,freq,cluster" Tolerant 0.22 3 12 conservative 600051 1p32 epidermal growth factor receptor pathway substrate 15 556 rs17567 EPS15 2060 1 51538942 NM_001981 NP_001972 C/T I822M plus 2755092 1303 SEQUENOM CEPH CEPH (92) 92 0.17 0.22 0.1 132 2 123 "by doubleHit,freq,cluster" Tolerant 0.22 3 12 conservative 600051 1p32 epidermal growth factor receptor pathway substrate 15 557 rs17571 CTSD 1509 11 1739170 NM_001909 NP_001900 C/T A58V minus 20182 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 40 0.1 0.08 0.01 252 3 63 "HapMap,freq" Benign 0.03 33 Tolerant 0.52 2.85 51 moderately conservative 116840 11p15.5 cathepsin D (lysosomal aspartyl protease) 558 rs17571 CTSD 1509 11 1739170 NM_001909 NP_001900 C/T A58V minus 20182 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.07 0.08 0.01 252 3 63 "HapMap,freq" Benign 0.03 33 Tolerant 0.52 2.85 51 moderately conservative 116840 11p15.5 cathepsin D (lysosomal aspartyl protease) 559 rs17571 CTSD 1509 11 1739170 NM_001909 NP_001900 C/T A58V minus 20182 1303 SEQUENOM CEPH CEPH (92) 92 0.08 0.08 0.01 252 3 63 "HapMap,freq" Benign 0.03 33 Tolerant 0.52 2.85 51 moderately conservative 116840 11p15.5 cathepsin D (lysosomal aspartyl protease) 560 rs17580 SERPINA1 5265 14 93917015 NM_000295 NP_000286 A/T E288V minus 20191 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 38 0.03 0.07 0.03 130 2 123 by freq Intolerant 0 2.75 79 moderately radical 107400 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1" 561 rs17580 SERPINA1 5265 14 93917015 NM_000295 NP_000286 A/T E288V minus 3881969 1303 SEQUENOM CEPH CEPH (92) 92 0.08 0.07 0.03 130 2 123 by freq Intolerant 0 2.75 79 moderately radical 107400 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1" 562 rs17607 CD68 968 17 7425506 NM_001251 NP_001242 A/G A340T plus 20219 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 38 0.03 0.06 0.01 250 3 63 "HapMap,freq" Benign 0.227 7 Tolerant 0.52 2.76 24 moderately conservative 153634 17p13 CD68 antigen 563 rs17607 CD68 968 17 7425506 NM_001251 NP_001242 A/G A340T plus 20219 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.06 0.06 0.01 250 3 63 "HapMap,freq" Benign 0.227 7 Tolerant 0.52 2.76 24 moderately conservative 153634 17p13 CD68 antigen 564 rs17607 CD68 968 17 7425506 NM_001251 NP_001242 A/G A340T plus 20219 1303 SEQUENOM CEPH CEPH (92) 92 0.06 0.06 0.01 250 3 63 "HapMap,freq" Benign 0.227 7 Tolerant 0.52 2.76 24 moderately conservative 153634 17p13 CD68 antigen 565 rs17608 CLC 1178 19 44917486 NM_001828 NP_001819 C/T A28V minus 20220 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 38 0.33 0.37 0.06 272 5 0.28 0.1 138 4 123 by freq Tolerant 0.53 2.77 24 moderately conservative 153310 19q13.1 Charcot-Leyden crystal protein 566 rs17608 CLC 1178 19 44917486 NM_001828 NP_001819 C/T A28V minus 477759 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.21 0.37 0.06 272 5 0.28 0.1 138 4 123 by freq Tolerant 0.53 2.77 24 moderately conservative 153310 19q13.1 Charcot-Leyden crystal protein 567 rs17608 CLC 1178 19 44917486 NM_001828 NP_001819 C/T A28V minus 477759 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 82 0.33 0.37 0.06 272 5 0.28 0.1 138 4 123 by freq Tolerant 0.53 2.77 24 moderately conservative 153310 19q13.1 Charcot-Leyden crystal protein 568 rs17608 CLC 1178 19 44917486 NM_001828 NP_001819 C/T A28V minus 477759 1303 SEQUENOM CEPH CEPH (92) 92 0.41 0.37 0.06 272 5 0.28 0.1 138 4 123 by freq Tolerant 0.53 2.77 24 moderately conservative 153310 19q13.1 Charcot-Leyden crystal protein 569 rs17608 CLC 1178 19 44917486 NM_001828 NP_001819 C/T A28V minus 24683968 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.43 0.37 0.06 272 5 0.28 0.1 138 4 123 by freq Tolerant 0.53 2.77 24 moderately conservative 153310 19q13.1 Charcot-Leyden crystal protein 570 rs17611 C5 727 9 120848754 NM_001735 NP_001726 A/G V802I minus 20223 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 40 0.33 0.36 0.02 160 2 0.5 0 1462 1 121 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.26 2.8 12 conservative 120900 9q33-q34 complement component 5 571 rs17611 C5 727 9 120848754 NM_001735 NP_001726 A/G V802I minus 4094354 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.37 0.36 0.02 160 2 0.5 0 1462 1 121 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.26 2.8 12 conservative 120900 9q33-q34 complement component 5 572 rs17655 ERCC5 2073 13 102326003 NM_000123 NP_000114 C/G D1104H minus 2924028 506 NCBI NIHPDR NIHPDR 80 0.46 0.31 0.1 612 7 0.34 0.07 413 6 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 133530 13q22 "excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))" 573 rs17655 ERCC5 2073 13 102326003 NM_000123 NP_000114 C/G D1104H minus 3172481 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 40 0.28 0.31 0.1 612 7 0.34 0.07 413 6 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 133530 13q22 "excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))" 574 rs17655 ERCC5 2073 13 102326003 NM_000123 NP_000114 C/G D1104H minus 5586520 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.15 0.31 0.1 612 7 0.34 0.07 413 6 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 133530 13q22 "excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))" 575 rs17655 ERCC5 2073 13 102326003 NM_000123 NP_000114 C/G D1104H minus 5605326 693 EGP_SNPS PDR90 NIHPDR 178 0.38 0.31 0.1 612 7 0.34 0.07 413 6 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 133530 13q22 "excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))" 576 rs17655 ERCC5 2073 13 102326003 NM_000123 NP_000114 C/G D1104H minus 5605326 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.27 0.31 0.1 612 7 0.34 0.07 413 6 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 133530 13q22 "excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))" 577 rs17655 ERCC5 2073 13 102326003 NM_000123 NP_000114 C/G D1104H minus 5605326 1303 SEQUENOM CEPH CEPH (92) 92 0.21 0.31 0.1 612 7 0.34 0.07 413 6 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 133530 13q22 "excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))" 578 rs17655 ERCC5 2073 13 102326003 NM_000123 NP_000114 C/G D1104H minus 23280293 1371 PERLEGEN AFD_EUR_PANEL European American (24) 40 0.25 0.31 0.1 612 7 0.34 0.07 413 6 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 133530 13q22 "excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))" 579 rs20541 IL13 3596 5 132023863 NM_002188 NP_002179 C/T Q144R minus 23200 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 36 0.33 0.23 0.07 230 5 0.2 0.06 482 7 123 "by doubleHit,freq,cluster" Potentially damaging 1.318 8 conservative 147683 5q31 interleukin 13 580 rs20541 IL13 3596 5 132023863 NM_002188 NP_002179 C/T Q144R minus 2981853 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 44 0.27 0.23 0.07 230 5 0.2 0.06 482 7 123 "by doubleHit,freq,cluster" Potentially damaging 1.318 8 conservative 147683 5q31 interleukin 13 581 rs20541 IL13 3596 5 132023863 NM_002188 NP_002179 C/T Q144R minus 4323324 649 FHCRC POPU1 USA (20) 40 0.23 0.23 0.07 230 5 0.2 0.06 482 7 123 "by doubleHit,freq,cluster" Potentially damaging 1.318 8 conservative 147683 5q31 interleukin 13 582 rs20541 IL13 3596 5 132023863 NM_002188 NP_002179 C/T Q144R minus 5586633 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.15 0.23 0.07 230 5 0.2 0.06 482 7 123 "by doubleHit,freq,cluster" Potentially damaging 1.318 8 conservative 147683 5q31 interleukin 13 583 rs20541 IL13 3596 5 132023863 NM_002188 NP_002179 C/T Q144R minus 24193850 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.23 0.07 230 5 0.2 0.06 482 7 123 "by doubleHit,freq,cluster" Potentially damaging 1.318 8 conservative 147683 5q31 interleukin 13 584 rs20551 EP300 2033 22 39872508 NM_001429 NP_001420 A/G I997V plus 23214 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 40 0.1 0.21 0.15 88 2 0.07 0.02 94 2 123 "by doubleHit,submitter,freq" Tolerant 0.36 3 95 conservative 602700 22q13.2 E1A binding protein p300 585 rs20551 EP300 2033 22 39872508 NM_001429 NP_001420 A/G I997V plus 24542191 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.21 0.15 88 2 0.07 0.02 94 2 123 "by doubleHit,submitter,freq" Tolerant 0.36 3 95 conservative 602700 22q13.2 E1A binding protein p300 586 rs20559 LAMC1 3915 1 179831217 NM_002293 NP_002284 A/G R1121Q plus 23222 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 40 0.1 0.1 0.04 180 3 0.02 0 46 1 123 by freq Benign 0.361 7 Tolerant 0.52 2.87 14 conservative 150290 1q31 "laminin, gamma 1 (formerly LAMB2)" 587 rs20559 LAMC1 3915 1 179831217 NM_002293 NP_002284 A/G R1121Q plus 23222 1303 SEQUENOM CEPH CEPH (92) 92 0.08 0.1 0.04 180 3 0.02 0 46 1 123 by freq Benign 0.361 7 Tolerant 0.52 2.87 14 conservative 150290 1q31 "laminin, gamma 1 (formerly LAMB2)" 588 rs20559 LAMC1 3915 1 179831217 NM_002293 NP_002284 A/G R1121Q plus 24257529 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.1 0.04 180 3 0.02 0 46 1 123 by freq Benign 0.361 7 Tolerant 0.52 2.87 14 conservative 150290 1q31 "laminin, gamma 1 (formerly LAMB2)" 589 rs20571 CA3 761 8 86539249 NM_005181 NP_005172 A/G V31I plus 23235 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 40 0.33 0.41 0.06 300 4 0.38 0.06 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.625 119 Tolerant 1 2.79 59 conservative 114750 8q13-q22 "carbonic anhydrase III, muscle specific" 590 rs20571 CA3 761 8 86539249 NM_005181 NP_005172 A/G V31I plus 10425508 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.39 0.41 0.06 300 4 0.38 0.06 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.625 119 Tolerant 1 2.79 59 conservative 114750 8q13-q22 "carbonic anhydrase III, muscle specific" 591 rs20571 CA3 761 8 86539249 NM_005181 NP_005172 A/G V31I plus 10425508 1303 SEQUENOM CEPH CEPH (92) 92 0.49 0.41 0.06 300 4 0.38 0.06 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.625 119 Tolerant 1 2.79 59 conservative 114750 8q13-q22 "carbonic anhydrase III, muscle specific" 592 rs20571 CA3 761 8 86539249 NM_005181 NP_005172 A/G V31I plus 24025169 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.41 0.06 300 4 0.38 0.06 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.625 119 Tolerant 1 2.79 59 conservative 114750 8q13-q22 "carbonic anhydrase III, muscle specific" 593 rs20577 TNFRSF10A 8797 8 23138422 NM_003844 NP_003835 C/T T33I minus 23242 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 38 0.33 0.33 0 38 1 67 by freq moderately conservative 603611 8p21 "tumor necrosis factor receptor superfamily, member 10a" 594 rs25487 XRCC1 7515 19 48747566 NM_006297 NP_006288 A/G Q399R minus 3254965 506 NCBI NIHPDR NIHPDR 844 0.27 0.29 0.07 1166 4 0.34 0.12 369 5 121 "by cluster,freq" Benign 0.059 8 conservative 194360 19q13.2 X-ray repair complementing defective repair in Chinese hamster cells 1 595 rs25487 XRCC1 7515 19 48747566 NM_006297 NP_006288 A/G Q399R minus 4473996 693 EGP_SNPS PDR90 NIHPDR 168 0.23 0.29 0.07 1166 4 0.34 0.12 369 5 121 "by cluster,freq" Benign 0.059 8 conservative 194360 19q13.2 X-ray repair complementing defective repair in Chinese hamster cells 1 596 rs25487 XRCC1 7515 19 48747566 NM_006297 NP_006288 A/G Q399R minus 4473996 1303 SEQUENOM CEPH CEPH (92) 92 0.42 0.29 0.07 1166 4 0.34 0.12 369 5 121 "by cluster,freq" Benign 0.059 8 conservative 194360 19q13.2 X-ray repair complementing defective repair in Chinese hamster cells 1 597 rs25487 XRCC1 7515 19 48747566 NM_006297 NP_006288 A/G Q399R minus 5586970 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.47 0.29 0.07 1166 4 0.34 0.12 369 5 121 "by cluster,freq" Benign 0.059 8 conservative 194360 19q13.2 X-ray repair complementing defective repair in Chinese hamster cells 1 598 rs25489 XRCC1 7515 19 48748252 NM_006297 NP_006288 A/G R280H minus 3176721 619 WICVAR MITOGPOP6 CORIELL Mixed 56 0.07 0.07 0.02 1110 4 0.06 0.07 349 5 116 "by cluster,freq" Possibly damaging 1.62 8 Tolerant 0.4 2.97 24 conservative 194360 19q13.2 X-ray repair complementing defective repair in Chinese hamster cells 1 599 rs25489 XRCC1 7515 19 48748252 NM_006297 NP_006288 A/G R280H minus 3254966 506 NCBI NIHPDR NIHPDR 818 0.07 0.07 0.02 1110 4 0.06 0.07 349 5 116 "by cluster,freq" Possibly damaging 1.62 8 Tolerant 0.4 2.97 24 conservative 194360 19q13.2 X-ray repair complementing defective repair in Chinese hamster cells 1 600 rs25489 XRCC1 7515 19 48748252 NM_006297 NP_006288 A/G R280H minus 4473987 693 EGP_SNPS PDR90 NIHPDR 174 0.1 0.07 0.02 1110 4 0.06 0.07 349 5 116 "by cluster,freq" Possibly damaging 1.62 8 Tolerant 0.4 2.97 24 conservative 194360 19q13.2 X-ray repair complementing defective repair in Chinese hamster cells 1 601 rs25489 XRCC1 7515 19 48748252 NM_006297 NP_006288 A/G R280H minus 5586971 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.03 0.07 0.02 1110 4 0.06 0.07 349 5 116 "by cluster,freq" Possibly damaging 1.62 8 Tolerant 0.4 2.97 24 conservative 194360 19q13.2 X-ray repair complementing defective repair in Chinese hamster cells 1 602 rs25490 XRCC1 7515 19 48748181 NM_006297 NP_006288 A/G T304A minus 4473989 693 EGP_SNPS PDR90 NIHPDR 172 0.01 0.01 0 172 1 0.02 0.06 299 4 113 "by cluster,freq" Borderline 1.038 8 Tolerant 0.73 2.98 22 moderately conservative 194360 19q13.2 X-ray repair complementing defective repair in Chinese hamster cells 1 603 rs25491 XRCC1 7515 19 48748166 NM_006297 NP_006288 C/T P309S minus 4473990 693 EGP_SNPS PDR90 NIHPDR 176 0.01 0.01 0 176 1 0.5 0 2 1 116 "by cluster,freq" Benign 0.244 8 Tolerant 0.7 3.01 22 moderately conservative 194360 19q13.2 X-ray repair complementing defective repair in Chinese hamster cells 1 604 rs25496 XRCC1 7515 19 48756942 NM_006297 NP_006288 C/T V72A minus 3254957 506 NCBI NIHPDR NIHPDR 866 0.02 0.02 0.01 1040 2 0.5 0 2 1 116 "HapMap,freq,cluster" Possibly damaging 1.51 7 moderately conservative 194360 19q13.2 X-ray repair complementing defective repair in Chinese hamster cells 1 605 rs25496 XRCC1 7515 19 48756942 NM_006297 NP_006288 C/T V72A minus 4473929 693 EGP_SNPS PDR90 NIHPDR 174 0.03 0.02 0.01 1040 2 0.5 0 2 1 116 "HapMap,freq,cluster" Possibly damaging 1.51 7 moderately conservative 194360 19q13.2 X-ray repair complementing defective repair in Chinese hamster cells 1 606 rs25640 HSD17B4 3295 5 118839432 NM_000414 NP_000405 A/G R106H plus 28362 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 36 0.33 0.43 0.07 250 4 0.4 0.04 1570 3 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.99 18 Intolerant 0.03 2.84 50 conservative 601860 5q21 hydroxysteroid (17-beta) dehydrogenase 4 607 rs25640 HSD17B4 3295 5 118839432 NM_000414 NP_000405 A/G R106H plus 28362 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 50 0.36 0.43 0.07 250 4 0.4 0.04 1570 3 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.99 18 Intolerant 0.03 2.84 50 conservative 601860 5q21 hydroxysteroid (17-beta) dehydrogenase 4 608 rs25640 HSD17B4 3295 5 118839432 NM_000414 NP_000405 A/G R106H plus 3447822 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.47 0.43 0.07 250 4 0.4 0.04 1570 3 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.99 18 Intolerant 0.03 2.84 50 conservative 601860 5q21 hydroxysteroid (17-beta) dehydrogenase 4 609 rs25640 HSD17B4 3295 5 118839432 NM_000414 NP_000405 A/G R106H plus 24346051 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.43 0.07 250 4 0.4 0.04 1570 3 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.99 18 Intolerant 0.03 2.84 50 conservative 601860 5q21 hydroxysteroid (17-beta) dehydrogenase 4 610 rs25644 P2RX4 5025 12 120129366 NM_002560 NP_002551 A/G S242G plus 28367 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 60 0.1 0.08 0.03 352 4 0.2 0.04 1596 3 123 "by cluster,freq" Borderline 1.224 30 Intolerant 0.05 2.81 63 moderately conservative 600846 12q24.32 "purinergic receptor P2X, ligand-gated ion channel, 4" 611 rs25644 P2RX4 5025 12 120129366 NM_002560 NP_002551 A/G S242G plus 3178007 619 WICVAR MITOGPOP6 CORIELL Mixed 60 0.12 0.08 0.03 352 4 0.2 0.04 1596 3 123 "by cluster,freq" Borderline 1.224 30 Intolerant 0.05 2.81 63 moderately conservative 600846 12q24.32 "purinergic receptor P2X, ligand-gated ion channel, 4" 612 rs25644 P2RX4 5025 12 120129366 NM_002560 NP_002551 A/G S242G plus 23933567 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.08 0.03 352 4 0.2 0.04 1596 3 123 "by cluster,freq" Borderline 1.224 30 Intolerant 0.05 2.81 63 moderately conservative 600846 12q24.32 "purinergic receptor P2X, ligand-gated ion channel, 4" 613 rs25644 P2RX4 5025 12 120129366 NM_002560 NP_002551 A/G S242G plus 24811130 1303 SEQUENOM CEPH CEPH (92) 184 0.08 0.08 0.03 352 4 0.2 0.04 1596 3 123 "by cluster,freq" Borderline 1.224 30 Intolerant 0.05 2.81 63 moderately conservative 600846 12q24.32 "purinergic receptor P2X, ligand-gated ion channel, 4" 614 rs25653 ANPEP 290 15 88150562 NM_001150 NP_001141 A/G R86Q minus 28376 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 38 0.33 0.42 0.04 326 5 0.42 0.06 1566 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.116 12 conservative 151530 15q25-q26 "alanyl (membrane) aminopeptidase (aminopeptidase N, aminopeptidase M, microsomal aminopeptidase, CD13, p150)" 615 rs25653 ANPEP 290 15 88150562 NM_001150 NP_001141 A/G R86Q minus 28376 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 32 0.47 0.42 0.04 326 5 0.42 0.06 1566 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.116 12 conservative 151530 15q25-q26 "alanyl (membrane) aminopeptidase (aminopeptidase N, aminopeptidase M, microsomal aminopeptidase, CD13, p150)" 616 rs25653 ANPEP 290 15 88150562 NM_001150 NP_001141 A/G R86Q minus 12586497 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.43 0.42 0.04 326 5 0.42 0.06 1566 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.116 12 conservative 151530 15q25-q26 "alanyl (membrane) aminopeptidase (aminopeptidase N, aminopeptidase M, microsomal aminopeptidase, CD13, p150)" 617 rs25653 ANPEP 290 15 88150562 NM_001150 NP_001141 A/G R86Q minus 12586497 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.42 0.04 326 5 0.42 0.06 1566 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.116 12 conservative 151530 15q25-q26 "alanyl (membrane) aminopeptidase (aminopeptidase N, aminopeptidase M, microsomal aminopeptidase, CD13, p150)" 618 rs25653 ANPEP 290 15 88150562 NM_001150 NP_001141 A/G R86Q minus 24057941 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.41 0.42 0.04 326 5 0.42 0.06 1566 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.116 12 conservative 151530 15q25-q26 "alanyl (membrane) aminopeptidase (aminopeptidase N, aminopeptidase M, microsomal aminopeptidase, CD13, p150)" 619 rs25655 CAPN2 824 1 220207143 NM_001748 NP_001739 C/G D22E plus 28378 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 40 0.1 0.06 0.05 100 2 123 by freq Benign 0.01 59 conservative 114230 1q41-q42 "calpain 2, (m/II) large subunit" 620 rs25655 CAPN2 824 1 220207143 NM_001748 NP_001739 C/G D22E plus 28378 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 60 0.03 0.06 0.05 100 2 123 by freq Benign 0.01 59 conservative 114230 1q41-q42 "calpain 2, (m/II) large subunit" 621 rs25680 TNFRSF7 939 12 6424889 NM_001242 NP_001233 A/G A59T plus 28404 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 38 0.33 0.22 0.11 646 9 0.12 0.02 236 5 123 "HapMap,freq" Tolerant 0.28 2.93 10 moderately conservative 186711 12p13 "tumor necrosis factor receptor superfamily, member 7" 622 rs25680 TNFRSF7 939 12 6424889 NM_001242 NP_001233 A/G A59T plus 28404 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 54 0.07 0.22 0.11 646 9 0.12 0.02 236 5 123 "HapMap,freq" Tolerant 0.28 2.93 10 moderately conservative 186711 12p13 "tumor necrosis factor receptor superfamily, member 7" 623 rs25680 TNFRSF7 939 12 6424889 NM_001242 NP_001233 A/G A59T plus 131069 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.29 0.22 0.11 646 9 0.12 0.02 236 5 123 "HapMap,freq" Tolerant 0.28 2.93 10 moderately conservative 186711 12p13 "tumor necrosis factor receptor superfamily, member 7" 624 rs25680 TNFRSF7 939 12 6424889 NM_001242 NP_001233 A/G A59T plus 131069 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.18 0.22 0.11 646 9 0.12 0.02 236 5 123 "HapMap,freq" Tolerant 0.28 2.93 10 moderately conservative 186711 12p13 "tumor necrosis factor receptor superfamily, member 7" 625 rs25680 TNFRSF7 939 12 6424889 NM_001242 NP_001233 A/G A59T plus 131069 902 AFFY Caucasian 18 0.22 0.22 0.11 646 9 0.12 0.02 236 5 123 "HapMap,freq" Tolerant 0.28 2.93 10 moderately conservative 186711 12p13 "tumor necrosis factor receptor superfamily, member 7" 626 rs25680 TNFRSF7 939 12 6424889 NM_001242 NP_001233 A/G A59T plus 131069 904 AFFY CEPH 12 0.08 0.22 0.11 646 9 0.12 0.02 236 5 123 "HapMap,freq" Tolerant 0.28 2.93 10 moderately conservative 186711 12p13 "tumor necrosis factor receptor superfamily, member 7" 627 rs25680 TNFRSF7 939 12 6424889 NM_001242 NP_001233 A/G A59T plus 131069 1303 SEQUENOM CEPH CEPH (92) 92 0.42 0.22 0.11 646 9 0.12 0.02 236 5 123 "HapMap,freq" Tolerant 0.28 2.93 10 moderately conservative 186711 12p13 "tumor necrosis factor receptor superfamily, member 7" 628 rs25680 TNFRSF7 939 12 6424889 NM_001242 NP_001233 A/G A59T plus 16340789 693 EGP_SNPS PDR90 NIHPDR 180 0.14 0.22 0.11 646 9 0.12 0.02 236 5 123 "HapMap,freq" Tolerant 0.28 2.93 10 moderately conservative 186711 12p13 "tumor necrosis factor receptor superfamily, member 7" 629 rs25680 TNFRSF7 939 12 6424889 NM_001242 NP_001233 A/G A59T plus 24697307 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.22 0.11 646 9 0.12 0.02 236 5 123 "HapMap,freq" Tolerant 0.28 2.93 10 moderately conservative 186711 12p13 "tumor necrosis factor receptor superfamily, member 7" 630 rs25683 ACAT2 39 6 160166754 NM_005891 NP_005882 A/G K211R plus 28408 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 40 0.33 0.25 0.1 88 2 0.18 0 1468 1 102 "by cluster,freq" Benign 0.715 106 Potentially intolerant 0.1 2.75 148 conservative 100678 6q25.3-q26 acetyl-Coenzyme A acetyltransferase 2 (acetoacetyl Coenzyme A thiolase) 631 rs25683 ACAT2 39 6 160166754 NM_005891 NP_005882 A/G K211R plus 28408 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 48 0.19 0.25 0.1 88 2 0.18 0 1468 1 102 "by cluster,freq" Benign 0.715 106 Potentially intolerant 0.1 2.75 148 conservative 100678 6q25.3-q26 acetyl-Coenzyme A acetyltransferase 2 (acetoacetyl Coenzyme A thiolase) 632 rs25882 CSF2 1437 5 131439359 NM_000758 NP_000749 C/T I117T plus 2981718 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.2 0.23 0.05 204 4 0.33 0.05 486 7 123 "by submitter,freq,cluster" Benign 0.092 25 moderately conservative 138960 5q31.1 colony stimulating factor 2 (granulocyte-macrophage) 633 rs25882 CSF2 1437 5 131439359 NM_000758 NP_000749 C/T I117T plus 3176020 619 WICVAR MITOGPOP6 CORIELL Mixed 48 0.29 0.23 0.05 204 4 0.33 0.05 486 7 123 "by submitter,freq,cluster" Benign 0.092 25 moderately conservative 138960 5q31.1 colony stimulating factor 2 (granulocyte-macrophage) 634 rs25882 CSF2 1437 5 131439359 NM_000758 NP_000749 C/T I117T plus 6903720 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.24 0.23 0.05 204 4 0.33 0.05 486 7 123 "by submitter,freq,cluster" Benign 0.092 25 moderately conservative 138960 5q31.1 colony stimulating factor 2 (granulocyte-macrophage) 635 rs25882 CSF2 1437 5 131439359 NM_000758 NP_000749 C/T I117T plus 23737224 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.23 0.05 204 4 0.33 0.05 486 7 123 "by submitter,freq,cluster" Benign 0.092 25 moderately conservative 138960 5q31.1 colony stimulating factor 2 (granulocyte-macrophage) 636 rs27230 ZNF434 54925 16 3374700 NM_017810 NP_060280 A/G Y120H plus 24479903 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.27 0 48 1 123 "by submitter,freq" Intolerant 0 3.02 13 moderately conservative 16p13.3 zinc finger protein 434 637 rs30461 IL29 282618 19 44480955 NM_172140 NP_742152 C/T N188D minus 689370 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.12 0.13 0.02 168 2 0.19 0.22 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.436 8 conservative 607403 19q13.13 "interleukin 29 (interferon, lambda 1)" 638 rs30461 IL29 282618 19 44480955 NM_172140 NP_742152 C/T N188D minus 23763490 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.13 0.02 168 2 0.19 0.22 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.436 8 conservative 607403 19q13.13 "interleukin 29 (interferon, lambda 1)" 639 rs30489 TCF7 6932 5 133509366 NM_201633 NP_963964 C/T G256R minus 3576863 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.05 0.04 0.03 260 3 0.17 0.21 94 2 123 "HapMap,submitter,freq,cluster" moderately radical 189908 5q31.1 "transcription factor 7 (T-cell specific, HMG-box)" 640 rs30489 TCF7 6932 5 133509366 NM_201633 NP_963964 C/T G256R minus 3576863 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.04 0.03 260 3 0.17 0.21 94 2 123 "HapMap,submitter,freq,cluster" moderately radical 189908 5q31.1 "transcription factor 7 (T-cell specific, HMG-box)" 641 rs30489 TCF7 6932 5 133509366 NM_201633 NP_963964 C/T G256R minus 23953339 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.04 0.03 260 3 0.17 0.21 94 2 123 "HapMap,submitter,freq,cluster" moderately radical 189908 5q31.1 "transcription factor 7 (T-cell specific, HMG-box)" 642 rs30842 GOT2 2806 16 57300955 NM_002080 NP_002071 G/T V346G minus 10819561 1303 SEQUENOM CEPH CEPH (92) 92 0.49 0.45 0.07 140 2 0.19 0.14 94 2 123 "by cluster,freq" Benign 0.67 67 moderately radical 138150 16q21 "glutamic-oxaloacetic transaminase 2, mitochondrial (aspartate aminotransferase 2)" 643 rs30842 GOT2 2806 16 57300955 NM_002080 NP_002071 G/T V346G minus 24614222 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.45 0.07 140 2 0.19 0.14 94 2 123 "by cluster,freq" Benign 0.67 67 moderately radical 138150 16q21 "glutamic-oxaloacetic transaminase 2, mitochondrial (aspartate aminotransferase 2)" 644 rs31849 PCDHB3 56132 5 140460539 NM_018937 NP_061760 C/T K41R minus 23350582 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.09 0.09 0 46 1 0.07 0.03 90 2 123 "by doubleHit,freq,cluster" Benign 0.483 97 Tolerant 0.45 2.78 123 conservative 606329 5q31 protocadherin beta 3 645 rs31853 PCDHB2 56133 5 140454940 NM_018936 NP_061759 A/G V128I plus 1335672 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 82 0.12 0.09 0.04 336 4 0.08 0.03 1522 5 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.625 98 Tolerant 1 2.77 126 conservative 606328 5q31 protocadherin beta 2 646 rs31853 PCDHB2 56133 5 140454940 NM_018936 NP_061759 A/G V128I plus 1335672 885 TSC-CSHL HapMap-CEPH-30-trios 114 0.05 0.09 0.04 336 4 0.08 0.03 1522 5 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.625 98 Tolerant 1 2.77 126 conservative 606328 5q31 protocadherin beta 2 647 rs31853 PCDHB2 56133 5 140454940 NM_018936 NP_061759 A/G V128I plus 1335672 1303 SEQUENOM CEPH CEPH (92) 92 0.12 0.09 0.04 336 4 0.08 0.03 1522 5 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.625 98 Tolerant 1 2.77 126 conservative 606328 5q31 protocadherin beta 2 648 rs31853 PCDHB2 56133 5 140454940 NM_018936 NP_061759 A/G V128I plus 23350563 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.09 0.04 336 4 0.08 0.03 1522 5 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.625 98 Tolerant 1 2.77 126 conservative 606328 5q31 protocadherin beta 2 649 rs34899 RHOBTB3 22836 5 95116957 NM_014899 NP_055714 A/G N262D plus 1788541 1303 SEQUENOM CEPH CEPH (92) 92 0.21 0.21 0 92 1 121 "by doubleHit,submitter,freq,cluster" conservative 607353 5q15 Rho-related BTB domain containing 3 650 rs36259 LASS4 79603 19 8232904 NM_024552 NP_078828 A/G A366T plus 496166 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.22 0.2 0.03 259 3 0.18 0.04 1590 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 19p13.3 LAG1 longevity assurance homolog 4 (S. cerevisiae) 651 rs36259 LASS4 79603 19 8232904 NM_024552 NP_078828 A/G A366T plus 496166 1303 SEQUENOM CEPH CEPH (92) 93 0.16 0.2 0.03 259 3 0.18 0.04 1590 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 19p13.3 LAG1 longevity assurance homolog 4 (S. cerevisiae) 652 rs36259 LASS4 79603 19 8232904 NM_024552 NP_078828 A/G A366T plus 23582637 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.2 0.03 259 3 0.18 0.04 1590 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 19p13.3 LAG1 longevity assurance homolog 4 (S. cerevisiae) 653 rs37369 AGXT2 64902 5 35072872 NM_031900 NP_114106 C/T V140I plus 14655015 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.11 0.11 0.02 260 3 0.36 0.03 1592 3 123 "HapMap,submitter,freq,cluster" Benign 0.3 8 Tolerant 1 2.77 36 conservative 5p13 alanine-glyoxylate aminotransferase 2 654 rs37369 AGXT2 64902 5 35072872 NM_031900 NP_114106 C/T V140I plus 14655015 1303 SEQUENOM CEPH CEPH (92) 92 0.13 0.11 0.02 260 3 0.36 0.03 1592 3 123 "HapMap,submitter,freq,cluster" Benign 0.3 8 Tolerant 1 2.77 36 conservative 5p13 alanine-glyoxylate aminotransferase 2 655 rs37369 AGXT2 64902 5 35072872 NM_031900 NP_114106 C/T V140I plus 23986321 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.11 0.02 260 3 0.36 0.03 1592 3 123 "HapMap,submitter,freq,cluster" Benign 0.3 8 Tolerant 1 2.77 36 conservative 5p13 alanine-glyoxylate aminotransferase 2 656 rs40401 IL3 3562 5 131424377 NM_000588 NP_000579 C/T P27S plus 830808 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.21 0.23 0.04 342 5 0.42 0.02 1620 4 123 "HapMap,doubleHit,freq,cluster" moderately conservative 147740 5q31.1 "interleukin 3 (colony-stimulating factor, multiple)" 657 rs40401 IL3 3562 5 131424377 NM_000588 NP_000579 C/T P27S plus 830808 1303 SEQUENOM CEPH CEPH (92) 92 0.19 0.23 0.04 342 5 0.42 0.02 1620 4 123 "HapMap,doubleHit,freq,cluster" moderately conservative 147740 5q31.1 "interleukin 3 (colony-stimulating factor, multiple)" 658 rs40401 IL3 3562 5 131424377 NM_000588 NP_000579 C/T P27S plus 2981902 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.26 0.23 0.04 342 5 0.42 0.02 1620 4 123 "HapMap,doubleHit,freq,cluster" moderately conservative 147740 5q31.1 "interleukin 3 (colony-stimulating factor, multiple)" 659 rs40401 IL3 3562 5 131424377 NM_000588 NP_000579 C/T P27S plus 4323372 649 FHCRC POPU1 USA (20) 40 0.3 0.23 0.04 342 5 0.42 0.02 1620 4 123 "HapMap,doubleHit,freq,cluster" moderately conservative 147740 5q31.1 "interleukin 3 (colony-stimulating factor, multiple)" 660 rs40401 IL3 3562 5 131424377 NM_000588 NP_000579 C/T P27S plus 23737132 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.24 0.23 0.04 342 5 0.42 0.02 1620 4 123 "HapMap,doubleHit,freq,cluster" moderately conservative 147740 5q31.1 "interleukin 3 (colony-stimulating factor, multiple)" 661 rs42524 COL1A2 1278 7 93687890 NM_000089 NP_000080 C/G P549A plus 3127654 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 83 0.31 0.37 0.08 175 2 0.19 0.07 166 2 121 "by cluster,freq" Tolerant 0.82 3.04 78 conservative 120160 7q22.1 "collagen, type I, alpha 2" 662 rs42524 COL1A2 1278 7 93687890 NM_000089 NP_000080 C/G P549A plus 3127654 1303 SEQUENOM CEPH CEPH (92) 92 0.42 0.37 0.08 175 2 0.19 0.07 166 2 121 "by cluster,freq" Tolerant 0.82 3.04 78 conservative 120160 7q22.1 "collagen, type I, alpha 2" 663 rs42942 PES1 23481 22 29301907 NM_014303 NP_055118 A/T T264S plus 13383550 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.04 0 92 1 120 by freq Benign 0.895 9 Tolerant 0.75 2.87 20 moderately conservative 605819 22q12.1 "pescadillo homolog 1, containing BRCT domain (zebrafish)" 664 rs103612 NUP214 8021 9 131049646 NM_005085 NP_005076 C/T P574S plus 110164 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.32 0.36 0.05 260 3 0.34 0.01 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.442 5 moderately conservative 114350 9q34.1 nucleoporin 214kDa 665 rs103612 NUP214 8021 9 131049646 NM_005085 NP_005076 C/T P574S plus 110164 1303 SEQUENOM CEPH CEPH (92) 92 0.4 0.36 0.05 260 3 0.34 0.01 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.442 5 moderately conservative 114350 9q34.1 nucleoporin 214kDa 666 rs103612 NUP214 8021 9 131049646 NM_005085 NP_005076 C/T P574S plus 24555978 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.36 0.05 260 3 0.34 0.01 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.442 5 moderately conservative 114350 9q34.1 nucleoporin 214kDa 667 rs132653 APOL3 80833 22 34881323 NM_145640 NP_663615 A/C S39R minus 1465169 760 TSC-CSHL CEL_CAUCASIAN CELERA Caucasians (30) 56 0.18 0.17 0.04 320 4 0.15 0.22 265 5 123 "HapMap,doubleHit,submitter,freq,cluster" moderately radical 607253 22q13.1 "apolipoprotein L, 3" 668 rs132653 APOL3 80833 22 34881323 NM_145640 NP_663615 A/C S39R minus 1465169 782 TSC-CSHL WICGR6_CAUCASIAN_POOLED WICGR Caucasian (48) 96 0.17 0.17 0.04 320 4 0.15 0.22 265 5 123 "HapMap,doubleHit,submitter,freq,cluster" moderately radical 607253 22q13.1 "apolipoprotein L, 3" 669 rs132653 APOL3 80833 22 34881323 NM_145640 NP_663615 A/C S39R minus 1465169 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.14 0.17 0.04 320 4 0.15 0.22 265 5 123 "HapMap,doubleHit,submitter,freq,cluster" moderately radical 607253 22q13.1 "apolipoprotein L, 3" 670 rs132653 APOL3 80833 22 34881323 NM_145640 NP_663615 A/C S39R minus 23644163 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.17 0.04 320 4 0.15 0.22 265 5 123 "HapMap,doubleHit,submitter,freq,cluster" moderately radical 607253 22q13.1 "apolipoprotein L, 3" 671 rs133885 MYO18B 84700 22 24483843 NM_032608 NP_115997 A/G G44E plus 24581329 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.07 0.07 0 44 1 0.02 0 46 1 123 "by doubleHit,freq" moderately conservative 607295 22q11.2-q12.1 myosin XVIIIB 672 rs136467 RFPL2 10739 22 30911408 NM_006605 NP_006596 C/T V258I plus 8288357 1303 SEQUENOM CEPH CEPH (92) 92 0.18 0.18 0 92 1 123 "by doubleHit,freq,cluster" Benign 0.906 11 conservative 605969 22q12.3 ret finger protein-like 2 673 rs136470 RFPL2 10739 22 30911480 NM_006605 NP_006596 C/T S234G plus 8293332 1303 SEQUENOM CEPH CEPH (92) 92 0.23 0.23 0 92 1 121 "by doubleHit,freq,cluster" Benign 0.006 11 moderately conservative 605969 22q12.3 ret finger protein-like 2 674 rs136478 RFPL2 10739 22 30913577 NM_006605 NP_006596 C/T C51Y plus 144631 1303 SEQUENOM CEPH CEPH (92) 92 0.45 0.45 0 92 1 119 "by doubleHit,freq,cluster" Possibly damaging 1.744 11 radical 605969 22q12.3 ret finger protein-like 2 675 rs140054 GTSE1 51512 22 45042919 NM_016426 NP_057510 A/G W506R minus 8021617 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.08 0.14 0.09 212 2 121 "HapMap,submitter,freq,cluster" moderately radical 607477 22q13.2-q13.3 G-2 and S-phase expressed 1 676 rs140054 GTSE1 51512 22 45042919 NM_016426 NP_057510 A/G W506R minus 8021617 1303 SEQUENOM CEPH CEPH (92) 92 0.21 0.14 0.09 212 2 121 "HapMap,submitter,freq,cluster" moderately radical 607477 22q13.2-q13.3 G-2 and S-phase expressed 1 677 rs140693 MBD4 8930 3 130638149 NM_003925 NP_003916 A/G E346K minus 149192 524 LDN AUTISM USA (autistic probands) 24 0.09 0.08 0.01 1074 3 0.23 0.3 94 2 123 "by submitter,freq,cluster" moderately conservative 603574 3q21-q22 methyl-CpG binding domain protein 4 678 rs140693 MBD4 8930 3 130638149 NM_003925 NP_003916 A/G E346K minus 3255099 506 NCBI NIHPDR NIHPDR 872 0.08 0.08 0.01 1074 3 0.23 0.3 94 2 123 "by submitter,freq,cluster" moderately conservative 603574 3q21-q22 methyl-CpG binding domain protein 4 679 rs140693 MBD4 8930 3 130638149 NM_003925 NP_003916 A/G E346K minus 4385591 693 EGP_SNPS PDR90 NIHPDR 178 0.07 0.08 0.01 1074 3 0.23 0.3 94 2 123 "by submitter,freq,cluster" moderately conservative 603574 3q21-q22 methyl-CpG binding domain protein 4 680 rs144848 BRCA2 675 13 31804729 NM_000059 NP_000050 G/T N372H minus 153384 902 AFFY Caucasian 14 0.29 0.32 0.06 656 9 0.27 0.09 506 9 123 "by doubleHit,submitter,freq,cluster" Benign 0.229 9 moderately conservative 600185 13q12.3 "breast cancer 2, early onset" 681 rs144848 BRCA2 675 13 31804729 NM_000059 NP_000050 G/T N372H minus 153384 904 AFFY CEPH 12 0.42 0.32 0.06 656 9 0.27 0.09 506 9 123 "by doubleHit,submitter,freq,cluster" Benign 0.229 9 moderately conservative 600185 13q12.3 "breast cancer 2, early onset" 682 rs144848 BRCA2 675 13 31804729 NM_000059 NP_000050 G/T N372H minus 153384 1303 SEQUENOM CEPH CEPH (92) 92 0.37 0.32 0.06 656 9 0.27 0.09 506 9 123 "by doubleHit,submitter,freq,cluster" Benign 0.229 9 moderately conservative 600185 13q12.3 "breast cancer 2, early onset" 683 rs144848 BRCA2 675 13 31804729 NM_000059 NP_000050 G/T N372H minus 887467 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.36 0.32 0.06 656 9 0.27 0.09 506 9 123 "by doubleHit,submitter,freq,cluster" Benign 0.229 9 moderately conservative 600185 13q12.3 "breast cancer 2, early onset" 684 rs144848 BRCA2 675 13 31804729 NM_000059 NP_000050 G/T N372H minus 887467 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 176 0.38 0.32 0.06 656 9 0.27 0.09 506 9 123 "by doubleHit,submitter,freq,cluster" Benign 0.229 9 moderately conservative 600185 13q12.3 "breast cancer 2, early onset" 685 rs144848 BRCA2 675 13 31804729 NM_000059 NP_000050 G/T N372H minus 3172559 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 60 0.23 0.32 0.06 656 9 0.27 0.09 506 9 123 "by doubleHit,submitter,freq,cluster" Benign 0.229 9 moderately conservative 600185 13q12.3 "breast cancer 2, early onset" 686 rs144848 BRCA2 675 13 31804729 NM_000059 NP_000050 G/T N372H minus 5586305 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.28 0.32 0.06 656 9 0.27 0.09 506 9 123 "by doubleHit,submitter,freq,cluster" Benign 0.229 9 moderately conservative 600185 13q12.3 "breast cancer 2, early onset" 687 rs144848 BRCA2 675 13 31804729 NM_000059 NP_000050 G/T N372H minus 16355781 693 EGP_SNPS PDR90 NIHPDR 180 0.26 0.32 0.06 656 9 0.27 0.09 506 9 123 "by doubleHit,submitter,freq,cluster" Benign 0.229 9 moderately conservative 600185 13q12.3 "breast cancer 2, early onset" 688 rs144848 BRCA2 675 13 31804729 NM_000059 NP_000050 G/T N372H minus 24664348 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.32 0.06 656 9 0.27 0.09 506 9 123 "by doubleHit,submitter,freq,cluster" Benign 0.229 9 moderately conservative 600185 13q12.3 "breast cancer 2, early onset" 689 rs150857 CARKL 23729 17 3473386 NM_013276 NP_037408 C/T E215K plus 4063916 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.09 0.14 0.06 258 3 0.23 0.05 1590 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 605060 17p13 carbohydrate kinase-like 690 rs150857 CARKL 23729 17 3473386 NM_013276 NP_037408 C/T E215K plus 4063916 1303 SEQUENOM CEPH CEPH (92) 92 0.19 0.14 0.06 258 3 0.23 0.05 1590 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 605060 17p13 carbohydrate kinase-like 691 rs150857 CARKL 23729 17 3473386 NM_013276 NP_037408 C/T E215K plus 23624334 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.14 0.06 258 3 0.23 0.05 1590 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 605060 17p13 carbohydrate kinase-like 692 rs156697 GSTO2 119391 10 106029175 NM_183239 NP_899062 C/T N142D minus 773736 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.4 0.38 0.05 278 4 0.25 0.04 892 6 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.401 14 Tolerant 0.87 2.82 26 conservative 10q25.1 glutathione S-transferase omega 2 693 rs156697 GSTO2 119391 10 106029175 NM_183239 NP_899062 C/T N142D minus 773736 1303 SEQUENOM CEPH CEPH (92) 92 0.32 0.38 0.05 278 4 0.25 0.04 892 6 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.401 14 Tolerant 0.87 2.82 26 conservative 10q25.1 glutathione S-transferase omega 2 694 rs156697 GSTO2 119391 10 106029175 NM_183239 NP_899062 C/T N142D minus 16334038 902 AFFY Caucasian 18 0.44 0.38 0.05 278 4 0.25 0.04 892 6 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.401 14 Tolerant 0.87 2.82 26 conservative 10q25.1 glutathione S-transferase omega 2 695 rs156697 GSTO2 119391 10 106029175 NM_183239 NP_899062 C/T N142D minus 24503173 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.38 0.05 278 4 0.25 0.04 892 6 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.401 14 Tolerant 0.87 2.82 26 conservative 10q25.1 glutathione S-transferase omega 2 696 rs157496 PDZK3 23037 5 32123131 NM_178140 NP_835260 A/G T1274A plus 698075 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.24 0.25 0.1 260 3 0.41 0.07 92 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 5p13.3 PDZ domain containing 3 697 rs157496 PDZK3 23037 5 32123131 NM_178140 NP_835260 A/G T1274A plus 698075 1303 SEQUENOM CEPH CEPH (92) 92 0.33 0.25 0.1 260 3 0.41 0.07 92 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 5p13.3 PDZ domain containing 3 698 rs157496 PDZK3 23037 5 32123131 NM_178140 NP_835260 A/G T1274A plus 24009438 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.25 0.1 260 3 0.41 0.07 92 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 5p13.3 PDZ domain containing 3 699 rs158551 BCAS1 8537 20 52078573 NM_003657 NP_003648 C/T V163A minus 614289 1303 SEQUENOM CEPH CEPH (92) 92 0.1 0.09 0.03 140 2 0.24 0.31 94 2 123 "by cluster,freq" Tolerant 0.73 2.88 10 moderately conservative 602968 20q13.2-q13.3 breast carcinoma amplified sequence 1 700 rs158551 BCAS1 8537 20 52078573 NM_003657 NP_003648 C/T V163A minus 24095060 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.09 0.03 140 2 0.24 0.31 94 2 123 "by cluster,freq" Tolerant 0.73 2.88 10 moderately conservative 602968 20q13.2-q13.3 breast carcinoma amplified sequence 1 701 rs160277 CSPG2 1462 5 82873387 NM_004385 NP_004376 A/C D2937Y minus 666549 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.43 0.37 0.04 272 4 0.45 0.04 1599 5 123 "HapMap,doubleHit,freq,cluster" Benign 0.23 5 Intolerant 0.04 2.79 15 radical 118661 5q14.3 chondroitin sulfate proteoglycan 2 (versican) 702 rs160277 CSPG2 1462 5 82873387 NM_004385 NP_004376 A/C D2937Y minus 666549 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 92 0.34 0.37 0.04 272 4 0.45 0.04 1599 5 123 "HapMap,doubleHit,freq,cluster" Benign 0.23 5 Intolerant 0.04 2.79 15 radical 118661 5q14.3 chondroitin sulfate proteoglycan 2 (versican) 703 rs160277 CSPG2 1462 5 82873387 NM_004385 NP_004376 A/C D2937Y minus 666549 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.35 0.37 0.04 272 4 0.45 0.04 1599 5 123 "HapMap,doubleHit,freq,cluster" Benign 0.23 5 Intolerant 0.04 2.79 15 radical 118661 5q14.3 chondroitin sulfate proteoglycan 2 (versican) 704 rs160277 CSPG2 1462 5 82873387 NM_004385 NP_004376 A/C D2937Y minus 23674326 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.37 0.04 272 4 0.45 0.04 1599 5 123 "HapMap,doubleHit,freq,cluster" Benign 0.23 5 Intolerant 0.04 2.79 15 radical 118661 5q14.3 chondroitin sulfate proteoglycan 2 (versican) 705 rs160278 CSPG2 1462 5 82871480 NM_004385 NP_004376 A/T F2301Y minus 739666 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.43 0.47 0.03 240 4 0.47 0.05 1598 4 123 "by doubleHit,freq,cluster" Benign 0.172 5 Tolerant 1 3.04 10 conservative 118661 5q14.3 chondroitin sulfate proteoglycan 2 (versican) 706 rs160278 CSPG2 1462 5 82871480 NM_004385 NP_004376 A/T F2301Y minus 739666 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 88 0.47 0.47 0.03 240 4 0.47 0.05 1598 4 123 "by doubleHit,freq,cluster" Benign 0.172 5 Tolerant 1 3.04 10 conservative 118661 5q14.3 chondroitin sulfate proteoglycan 2 (versican) 707 rs160278 CSPG2 1462 5 82871480 NM_004385 NP_004376 A/T F2301Y minus 1295190 1303 SEQUENOM CEPH CEPH (92) 92 0.49 0.47 0.03 240 4 0.47 0.05 1598 4 123 "by doubleHit,freq,cluster" Benign 0.172 5 Tolerant 1 3.04 10 conservative 118661 5q14.3 chondroitin sulfate proteoglycan 2 (versican) 708 rs160278 CSPG2 1462 5 82871480 NM_004385 NP_004376 A/T F2301Y minus 23674325 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.43 0.47 0.03 240 4 0.47 0.05 1598 4 123 "by doubleHit,freq,cluster" Benign 0.172 5 Tolerant 1 3.04 10 conservative 118661 5q14.3 chondroitin sulfate proteoglycan 2 (versican) 709 rs160838 RGL3 57139 19 11387759 XM_290867 XP_290867 C/T A164V minus 1873156 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.47 0 92 1 121 "by doubleHit,freq,cluster" Tolerant 0.63 2.9 21 moderately conservative 19p13.2 ral guanine nucleotide dissociation stimulator-like 3 710 rs161704 IL31RA 133396 5 55242201 NM_139017 NP_620586 C/T S497N minus 1991445 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.22 0.28 0.05 252 3 0.35 0.13 258 4 123 "HapMap,doubleHit,freq,cluster" Borderline 1.098 6 Tolerant 0.24 2.8 21 conservative 5q11.2 interleukin 31 receptor A 711 rs161704 IL31RA 133396 5 55242201 NM_139017 NP_620586 C/T S497N minus 1991445 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.3 0.28 0.05 252 3 0.35 0.13 258 4 123 "HapMap,doubleHit,freq,cluster" Borderline 1.098 6 Tolerant 0.24 2.8 21 conservative 5q11.2 interleukin 31 receptor A 712 rs161704 IL31RA 133396 5 55242201 NM_139017 NP_620586 C/T S497N minus 23352578 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.28 0.05 252 3 0.35 0.13 258 4 123 "HapMap,doubleHit,freq,cluster" Borderline 1.098 6 Tolerant 0.24 2.8 21 conservative 5q11.2 interleukin 31 receptor A 713 rs164075 PCDH12 51294 5 141316448 NM_016580 NP_057664 A/C H385N minus 849396 1303 SEQUENOM CEPH CEPH (92) 92 0.36 0.37 0.03 140 2 0.14 0.03 1574 3 123 "by submitter,freq,cluster" Benign 0.246 5 Tolerant 0.54 2.75 339 moderately conservative 605622 5q31 protocadherin 12 714 rs164075 PCDH12 51294 5 141316448 NM_016580 NP_057664 A/C H385N minus 24667595 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.37 0.03 140 2 0.14 0.03 1574 3 123 "by submitter,freq,cluster" Benign 0.246 5 Tolerant 0.54 2.75 339 moderately conservative 605622 5q31 protocadherin 12 715 rs164515 PCDH12 51294 5 141315682 NM_016580 NP_057664 A/G S640N minus 24621926 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.25 0 48 1 0.12 0.03 1586 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.272 5 Tolerant 0.21 2.75 331 conservative 605622 5q31 protocadherin 12 716 rs165815 ARVCF 421 22 18334027 NM_001670 NP_001661 C/T R906Q plus 481084 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 24 0.08 0.12 0.05 374 5 0.44 0.02 138 4 123 "HapMap,doubleHit,freq,cluster" Benign 0.098 15 Borderline 0.16 2.99 34 conservative 602269 22q11.21 armadillo repeat gene deletes in velocardiofacial syndrome 717 rs165815 ARVCF 421 22 18334027 NM_001670 NP_001661 C/T R906Q plus 481084 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 90 0.12 0.12 0.05 374 5 0.44 0.02 138 4 123 "HapMap,doubleHit,freq,cluster" Benign 0.098 15 Borderline 0.16 2.99 34 conservative 602269 22q11.21 armadillo repeat gene deletes in velocardiofacial syndrome 718 rs165815 ARVCF 421 22 18334027 NM_001670 NP_001661 C/T R906Q plus 8287556 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.12 0.12 0.05 374 5 0.44 0.02 138 4 123 "HapMap,doubleHit,freq,cluster" Benign 0.098 15 Borderline 0.16 2.99 34 conservative 602269 22q11.21 armadillo repeat gene deletes in velocardiofacial syndrome 719 rs165815 ARVCF 421 22 18334027 NM_001670 NP_001661 C/T R906Q plus 8287556 1303 SEQUENOM CEPH CEPH (92) 92 0.07 0.12 0.05 374 5 0.44 0.02 138 4 123 "HapMap,doubleHit,freq,cluster" Benign 0.098 15 Borderline 0.16 2.99 34 conservative 602269 22q11.21 armadillo repeat gene deletes in velocardiofacial syndrome 720 rs165815 ARVCF 421 22 18334027 NM_001670 NP_001661 C/T R906Q plus 23789050 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.12 0.05 374 5 0.44 0.02 138 4 123 "HapMap,doubleHit,freq,cluster" Benign 0.098 15 Borderline 0.16 2.99 34 conservative 602269 22q11.21 armadillo repeat gene deletes in velocardiofacial syndrome 721 rs167479 RGL3 57139 19 11387765 XM_290867 XP_290867 A/C P162H minus 1937759 1303 SEQUENOM CEPH CEPH (92) 92 0.14 0.16 0.12 98 2 0.28 0.06 44 2 121 "by doubleHit,freq,cluster" Intolerant 0.02 2.9 21 moderately conservative 19p13.2 ral guanine nucleotide dissociation stimulator-like 3 722 rs167479 RGL3 57139 19 11387765 XM_290867 XP_290867 A/C P162H minus 1937780 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 6 0.5 0.16 0.12 98 2 0.28 0.06 44 2 121 "by doubleHit,freq,cluster" Intolerant 0.02 2.9 21 moderately conservative 19p13.2 ral guanine nucleotide dissociation stimulator-like 3 723 rs169068 SSTR5 6755 16 1069873 NM_001053 NP_001044 C/T P335L plus 3173187 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 36 0.39 0.39 0 36 1 0.16 0 1488 1 113 "by doubleHit,freq,cluster" Possibly damaging 1.87 20 Borderline 0.14 2.92 27 moderately conservative 182455 16p13.3 somatostatin receptor 5 724 rs169547 BRCA2 675 13 31827387 NM_000059 NP_000050 A/G V2466A minus 16355878 693 EGP_SNPS PDR90 NIHPDR 148 0.03 0.03 0.01 266 2 0.01 0.01 248 2 121 "HapMap,freq,cluster" moderately conservative 600185 13q12.3 "breast cancer 2, early onset" 725 rs169547 BRCA2 675 13 31827387 NM_000059 NP_000050 A/G V2466A minus 16355878 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.02 0.03 0.01 266 2 0.01 0.01 248 2 121 "HapMap,freq,cluster" moderately conservative 600185 13q12.3 "breast cancer 2, early onset" 726 rs172562 TBX18 9096 6 85530477 XM_496819 XP_496819 C/T G48R plus 1746987 1303 SEQUENOM CEPH CEPH (92) 92 0.38 0.38 0 92 1 120 "by doubleHit,freq,cluster" moderately radical 604613 6q14-q15 T-box 18 727 rs180749 AGXT2 64902 5 35069362 NM_031900 NP_114106 A/G T212I plus 626437 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.01 0 92 1 0.2 0.01 1572 3 123 "by doubleHit,freq,cluster" Benign 0.247 8 Tolerant 0.53 2.77 36 moderately conservative 5p13 alanine-glyoxylate aminotransferase 2 728 rs181206 IL27 246778 16 28420904 NM_145659 NP_663634 C/T L119P minus 617395 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.29 0.36 0.08 198 3 0.09 0.06 48 2 87 by freq moderately conservative 608273 16p11 interleukin 27 729 rs181206 IL27 246778 16 28420904 NM_145659 NP_663634 C/T L119P minus 617395 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 92 0.3 0.36 0.08 198 3 0.09 0.06 48 2 87 by freq moderately conservative 608273 16p11 interleukin 27 730 rs181206 IL27 246778 16 28420904 NM_145659 NP_663634 C/T L119P minus 1971619 1303 SEQUENOM CEPH CEPH (92) 92 0.43 0.36 0.08 198 3 0.09 0.06 48 2 87 by freq moderately conservative 608273 16p11 interleukin 27 731 rs185819 TNXB 7148 6 32158045 NM_019105 NP_061978 C/T H1248R plus 80760 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 83 0.13 0.3 0.16 223 3 0.38 0.06 260 4 123 "by doubleHit,freq,cluster" Tolerant 1 2.85 16 conservative 600985 6p21.3 tenascin XB 732 rs185819 TNXB 7148 6 32158045 NM_019105 NP_061978 C/T H1248R plus 7852581 1303 SEQUENOM CEPH CEPH (92) 92 0.38 0.3 0.16 223 3 0.38 0.06 260 4 123 "by doubleHit,freq,cluster" Tolerant 1 2.85 16 conservative 600985 6p21.3 tenascin XB 733 rs185819 TNXB 7148 6 32158045 NM_019105 NP_061978 C/T H1248R plus 24308158 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.3 0.16 223 3 0.38 0.06 260 4 123 "by doubleHit,freq,cluster" Tolerant 1 2.85 16 conservative 600985 6p21.3 tenascin XB 734 rs188703 CSPG2 1462 5 82870055 NM_004385 NP_004376 C/T R1826H minus 648869 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.44 0 92 1 121 "by doubleHit,submitter,freq,cluster" Benign 0.626 5 Borderline 0.13 2.95 9 conservative 118661 5q14.3 chondroitin sulfate proteoglycan 2 (versican) 735 rs194520 STEAP2 261729 7 89499097 NM_152999 NP_694544 G/T F17C plus 256300 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 83 0.4 0.44 0.07 143 2 0.2 0.14 166 2 79 "HapMap,freq" radical 605094 7q21 six transmembrane epithelial antigen of prostate 2 736 rs194520 STEAP2 261729 7 89499097 NM_152999 NP_694544 G/T F17C plus 256300 885 TSC-CSHL HapMap-CEPH-30-trios 60 0.5 0.44 0.07 143 2 0.2 0.14 166 2 79 "HapMap,freq" radical 605094 7q21 six transmembrane epithelial antigen of prostate 2 737 rs194524 STEAP2 261729 7 89506483 NM_152999 NP_694544 A/G R456Q plus 256305 885 TSC-CSHL HapMap-CEPH-30-trios 60 0.5 0.5 0 84 2 0.28 0.08 92 2 123 "HapMap,freq" Potentially damaging 1.415 6 conservative 605094 7q21 six transmembrane epithelial antigen of prostate 2 738 rs194524 STEAP2 261729 7 89506483 NM_152999 NP_694544 A/G R456Q plus 24680669 1371 PERLEGEN AFD_EUR_PANEL European American (24) 24 0.5 0.5 0 84 2 0.28 0.08 92 2 123 "HapMap,freq" Potentially damaging 1.415 6 conservative 605094 7q21 six transmembrane epithelial antigen of prostate 2 739 rs194525 STEAP2 261729 7 89506541 NM_152999 NP_694544 G/T M475I plus 14567838 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.13 0.13 0 120 1 121 "HapMap,doubleHit,freq,cluster" conservative 605094 7q21 six transmembrane epithelial antigen of prostate 2 740 rs198977 KLK2 3817 19 56073589 NM_005551 NP_005542 C/T R250W plus 2041639 1303 SEQUENOM CEPH CEPH (92) 92 0.24 0.24 0 92 1 0.25 0 1498 1 106 "by cluster,freq" Possibly damaging 1.823 77 Borderline 0.18 2.78 71 moderately radical 147960 19q13.41 "kallikrein 2, prostatic" 741 rs202676 FOLH1 2346 11 49184196 NM_004476 NP_004467 C/T Y75H minus 605502 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.14 0.19 0.04 62 2 0.4 0.07 140 4 123 "by doubleHit,freq,cluster" Possibly damaging 1.528 9 Tolerant 0.36 2.83 16 moderately conservative 600934 11p11.2 folate hydrolase (prostate-specific membrane antigen) 1 742 rs202676 FOLH1 2346 11 49184196 NM_004476 NP_004467 C/T Y75H minus 23739871 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.19 0.04 62 2 0.4 0.07 140 4 123 "by doubleHit,freq,cluster" Possibly damaging 1.528 9 Tolerant 0.36 2.83 16 moderately conservative 600934 11p11.2 folate hydrolase (prostate-specific membrane antigen) 1 743 rs203462 AKAP10 11216 17 19753133 NM_007202 NP_009133 A/G I646V minus 266958 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.07 0.42 0.12 202 4 0.27 0.14 142 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.62 9 conservative 604694 17p11.1 A kinase (PRKA) anchor protein 10 744 rs203462 AKAP10 11216 17 19753133 NM_007202 NP_009133 A/G I646V minus 1647656 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.41 0.42 0.12 202 4 0.27 0.14 142 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.62 9 conservative 604694 17p11.1 A kinase (PRKA) anchor protein 10 745 rs203462 AKAP10 11216 17 19753133 NM_007202 NP_009133 A/G I646V minus 1647656 1303 SEQUENOM CEPH CEPH (92) 46 0.5 0.42 0.12 202 4 0.27 0.14 142 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.62 9 conservative 604694 17p11.1 A kinase (PRKA) anchor protein 10 746 rs203462 AKAP10 11216 17 19753133 NM_007202 NP_009133 A/G I646V minus 24590791 1371 PERLEGEN AFD_EUR_PANEL European American (24) 24 0.5 0.42 0.12 202 4 0.27 0.14 142 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.62 9 conservative 604694 17p11.1 A kinase (PRKA) anchor protein 10 747 rs203710 PVR 5817 19 49853878 NM_006505 NP_006496 A/G I340M plus 484460 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.07 0.02 0.01 226 3 121 "HapMap,freq,cluster" Benign 0.946 9 conservative 173850 19q13.2 poliovirus receptor 748 rs203710 PVR 5817 19 49853878 NM_006505 NP_006496 A/G I340M plus 484460 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 94 0.02 0.02 0.01 226 3 121 "HapMap,freq,cluster" Benign 0.946 9 conservative 173850 19q13.2 poliovirus receptor 749 rs203710 PVR 5817 19 49853878 NM_006505 NP_006496 A/G I340M plus 1821115 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.02 0.02 0.01 226 3 121 "HapMap,freq,cluster" Benign 0.946 9 conservative 173850 19q13.2 poliovirus receptor 750 rs204896 TNXB 7148 6 32172076 NM_019105 NP_061978 C/T R511H plus 661712 1303 SEQUENOM CEPH CEPH (92) 92 0.07 0.07 0.01 140 2 0.11 0.02 1582 3 123 "by cluster,freq" Potentially intolerant 0.09 2.92 14 conservative 600985 6p21.3 tenascin XB 751 rs204896 TNXB 7148 6 32172076 NM_019105 NP_061978 C/T R511H plus 23714822 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.07 0.01 140 2 0.11 0.02 1582 3 123 "by cluster,freq" Potentially intolerant 0.09 2.92 14 conservative 600985 6p21.3 tenascin XB 752 rs204900 TNXB 7148 6 32164558 NM_019105 NP_061978 G/T S873A minus 268677 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 83 0.06 0.11 0.07 175 2 0.18 0 83 1 121 "by doubleHit,freq,cluster" Intolerant 0.05 2.8 17 moderately conservative 600985 6p21.3 tenascin XB 753 rs204900 TNXB 7148 6 32164558 NM_019105 NP_061978 G/T S873A minus 466452 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.11 0.07 175 2 0.18 0 83 1 121 "by doubleHit,freq,cluster" Intolerant 0.05 2.8 17 moderately conservative 600985 6p21.3 tenascin XB 754 rs205498 TRIM25 7706 17 52333793 NM_005082 NP_005073 C/T P358L minus 1830958 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.28 0.28 0 120 1 0.2 0 1490 1 121 "HapMap,doubleHit,freq,cluster" moderately conservative 600453 17q23.1 tripartite motif-containing 25 755 rs208696 SASH1 23328 6 148906950 NM_015278 NP_056093 A/G Q884R plus 5221682 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.16 0.29 140 2 0.39 0.06 1586 3 123 "by doubleHit,freq,cluster" Benign 0.084 5 conservative 607955 6q24.3 SAM and SH3 domain containing 1 756 rs208696 SASH1 23328 6 148906950 NM_015278 NP_056093 A/G Q884R plus 24484549 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.16 0.29 140 2 0.39 0.06 1586 3 123 "by doubleHit,freq,cluster" Benign 0.084 5 conservative 607955 6q24.3 SAM and SH3 domain containing 1 757 rs208753 PCM1 5108 8 17859195 NM_006197 NP_006188 A/G M597V plus 1846412 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.26 0.26 0 260 3 0.29 0.04 1558 3 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.882 5 conservative 600299 8p22-p21.3 pericentriolar material 1 758 rs208753 PCM1 5108 8 17859195 NM_006197 NP_006188 A/G M597V plus 1846412 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.26 0 260 3 0.29 0.04 1558 3 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.882 5 conservative 600299 8p22-p21.3 pericentriolar material 1 759 rs208753 PCM1 5108 8 17859195 NM_006197 NP_006188 A/G M597V plus 24664200 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.26 0 260 3 0.29 0.04 1558 3 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.882 5 conservative 600299 8p22-p21.3 pericentriolar material 1 760 rs210280 ZNF11B 7558 10 42409971 NM_006955 NP_008886 A/G R145C plus 2677121 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.26 0 92 1 122 "by doubleHit,freq,cluster" Probably damaging 2.631 7 Borderline 0.19 2.76 27 radical 194522 10q11.2 zinc finger protein 11b (KOX 2) 761 rs213950 CFTR 1080 7 116793484 NM_000492 NP_000483 A/G V470M plus 24012792 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.44 0 48 1 0.3 0.26 94 2 123 "by doubleHit,submitter,freq,cluster" Potentially damaging 1.258 29 conservative 602421 7q31.2 "cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)" 762 rs216321 VWF 7450 12 6014245 NM_000552 NP_000543 C/T Q852R plus 667776 1303 SEQUENOM CEPH CEPH (92) 92 0.05 0.07 0.03 140 2 0.19 0.01 1590 3 123 "by submitter,freq,cluster" Potentially damaging 1.357 10 conservative 193400 12p13.3 von Willebrand factor 763 rs216321 VWF 7450 12 6014245 NM_000552 NP_000543 C/T Q852R plus 24166811 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.07 0.03 140 2 0.19 0.01 1590 3 123 "by submitter,freq,cluster" Potentially damaging 1.357 10 conservative 193400 12p13.3 von Willebrand factor 764 rs217086 CTSC 1075 11 87685231 NM_001814 NP_001805 A/G I153T plus 745848 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 10 0.4 0.18 0.15 56 2 0.25 0.1 66 2 123 "by doubleHit,freq,cluster" Borderline 1.041 14 moderately conservative 602365 11q14.1-q14.3 cathepsin C 765 rs217086 CTSC 1075 11 87685231 NM_001814 NP_001805 A/G I153T plus 23377436 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.13 0.18 0.15 56 2 0.25 0.1 66 2 123 "by doubleHit,freq,cluster" Borderline 1.041 14 moderately conservative 602365 11q14.1-q14.3 cathepsin C 766 rs217180 PMFBP1 83449 16 70742130 NM_031293 NP_112583 A/G A172T minus 3288372 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.08 0.15 0.09 260 3 0.12 0.04 94 2 123 "HapMap,submitter,freq" moderately conservative 16q22.2 polyamine modulated factor 1 binding protein 1 767 rs217180 PMFBP1 83449 16 70742130 NM_031293 NP_112583 A/G A172T minus 3288372 1303 SEQUENOM CEPH CEPH (92) 92 0.25 0.15 0.09 260 3 0.12 0.04 94 2 123 "HapMap,submitter,freq" moderately conservative 16q22.2 polyamine modulated factor 1 binding protein 1 768 rs217180 PMFBP1 83449 16 70742130 NM_031293 NP_112583 A/G A172T minus 24576958 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0.09 260 3 0.12 0.04 94 2 123 "HapMap,submitter,freq" moderately conservative 16q22.2 polyamine modulated factor 1 binding protein 1 769 rs220379 ZNF263 10127 16 3279436 NM_005741 NP_005732 C/G C310S plus 595513 1303 SEQUENOM CEPH CEPH (92) 92 0.42 0.42 0 92 1 116 "by doubleHit,freq,cluster" Tolerant 0.8 2.8 19 moderately radical 604191 16p13.3 zinc finger protein 263 770 rs220461 GSG2 83903 17 3574961 NM_031965 NP_114171 A/G I328T minus 1629759 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.27 0.25 0.06 260 3 0.37 0.06 1592 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 17p13 haspin 771 rs220461 GSG2 83903 17 3574961 NM_031965 NP_114171 A/G I328T minus 1629759 1303 SEQUENOM CEPH CEPH (92) 92 0.19 0.25 0.06 260 3 0.37 0.06 1592 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 17p13 haspin 772 rs220461 GSG2 83903 17 3574961 NM_031965 NP_114171 A/G I328T minus 24443575 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.25 0.06 260 3 0.37 0.06 1592 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 17p13 haspin 773 rs220462 GSG2 83903 17 3574589 NM_031965 NP_114171 C/T G204D minus 1629760 1303 SEQUENOM CEPH CEPH (92) 92 0.46 0.46 0 92 1 121 "by doubleHit,freq" moderately conservative 17p13 haspin 774 rs220479 ITGAE 3682 17 3603924 NM_002208 NP_002199 A/G I477V minus 21431179 1303 SEQUENOM CEPH CEPH (92) 92 0.29 0.29 0 92 1 121 "by cluster,freq" Benign 0.62 6 conservative 604682 17p13 "integrin, alpha E (antigen CD103, human mucosal lymphocyte antigen 1; alpha polypeptide)" 775 rs224331 GDF5 8200 20 33485801 NM_000557 NP_000548 A/C S276A plus 8375421 1303 SEQUENOM CEPH CEPH (92) 92 0.37 0.37 0 138 2 0.36 0.17 92 2 123 "by doubleHit,freq,cluster" Tolerant 0.4 2.79 81 moderately conservative 601146 20q11.2 growth differentiation factor 5 (cartilage-derived morphogenetic protein-1) 776 rs224331 GDF5 8200 20 33485801 NM_000557 NP_000548 A/C S276A plus 23566430 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.37 0.37 0 138 2 0.36 0.17 92 2 123 "by doubleHit,freq,cluster" Tolerant 0.4 2.79 81 moderately conservative 601146 20q11.2 growth differentiation factor 5 (cartilage-derived morphogenetic protein-1) 777 rs226794 ADAMTS5 11096 21 27224226 NM_007038 NP_008969 A/G L692P plus 2775282 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.14 0.09 159 3 0.28 0.29 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.899 7 moderately conservative 605007 21q21.3 "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)" 778 rs226794 ADAMTS5 11096 21 27224226 NM_007038 NP_008969 A/G L692P plus 4008063 634 PERLEGEN NCBI|NIHPDR NIHPDR 19 0.11 0.14 0.09 159 3 0.28 0.29 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.899 7 moderately conservative 605007 21q21.3 "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)" 779 rs226794 ADAMTS5 11096 21 27224226 NM_007038 NP_008969 A/G L692P plus 24025516 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.14 0.09 159 3 0.28 0.29 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.899 7 moderately conservative 605007 21q21.3 "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)" 780 rs228942 IL2RB 3560 22 35849119 NM_000878 NP_000869 A/C D391E minus 4479476 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 42 0.17 0.19 0.03 254 3 0.24 0.04 1548 2 120 "HapMap,doubleHit,freq,cluster" Benign 0.114 5 conservative 146710 22q13.1 "interleukin 2 receptor, beta" 781 rs228942 IL2RB 3560 22 35849119 NM_000878 NP_000869 A/C D391E minus 4479476 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.17 0.19 0.03 254 3 0.24 0.04 1548 2 120 "HapMap,doubleHit,freq,cluster" Benign 0.114 5 conservative 146710 22q13.1 "interleukin 2 receptor, beta" 782 rs228942 IL2RB 3560 22 35849119 NM_000878 NP_000869 A/C D391E minus 4479476 1303 SEQUENOM CEPH CEPH (92) 92 0.22 0.19 0.03 254 3 0.24 0.04 1548 2 120 "HapMap,doubleHit,freq,cluster" Benign 0.114 5 conservative 146710 22q13.1 "interleukin 2 receptor, beta" 783 rs229150 SCFD1 23256 14 30169489 NM_016106 NP_057190 C/T K63R minus 24542261 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.35 0 48 1 0.27 0.04 94 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.325 11 Tolerant 0.31 2.82 15 conservative 14q12 sec1 family domain containing 1 784 rs231775 CTLA4 1493 2 204558220 NM_005214 NP_005205 A/G T17A plus 545243 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.07 0.3 0.09 254 4 0.27 0.06 1676 7 123 "by doubleHit,submitter,freq,cluster" Borderline 1.016 18 moderately conservative 123890 2q33 cytotoxic T-lymphocyte-associated protein 4 785 rs231775 CTLA4 1493 2 204558220 NM_005214 NP_005205 A/G T17A plus 545243 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 90 0.37 0.3 0.09 254 4 0.27 0.06 1676 7 123 "by doubleHit,submitter,freq,cluster" Borderline 1.016 18 moderately conservative 123890 2q33 cytotoxic T-lymphocyte-associated protein 4 786 rs231775 CTLA4 1493 2 204558220 NM_005214 NP_005205 A/G T17A plus 6903722 775 SNP500CANCER CAUC1 Caucasian (31) 58 0.21 0.3 0.09 254 4 0.27 0.06 1676 7 123 "by doubleHit,submitter,freq,cluster" Borderline 1.016 18 moderately conservative 123890 2q33 cytotoxic T-lymphocyte-associated protein 4 787 rs231775 CTLA4 1493 2 204558220 NM_005214 NP_005205 A/G T17A plus 6903722 1303 SEQUENOM CEPH CEPH (92) 92 0.31 0.3 0.09 254 4 0.27 0.06 1676 7 123 "by doubleHit,submitter,freq,cluster" Borderline 1.016 18 moderately conservative 123890 2q33 cytotoxic T-lymphocyte-associated protein 4 788 rs232518 NCAM2 4685 21 21668058 NM_004540 NP_004531 C/T L350P plus 2257786 782 TSC-CSHL WICGR6_CAUCASIAN_POOLED WICGR Caucasian (48) 96 0.32 0.27 0.05 254 4 0.45 0.01 1662 4 123 "by doubleHit,submitter,freq,cluster" Probably damaging 2.383 7 Tolerant 0.3 2.82 32 moderately conservative 602040 21q21.1 neural cell adhesion molecule 2 789 rs232518 NCAM2 4685 21 21668058 NM_004540 NP_004531 C/T L350P plus 2257786 1303 SEQUENOM CEPH CEPH (92) 92 0.25 0.27 0.05 254 4 0.45 0.01 1662 4 123 "by doubleHit,submitter,freq,cluster" Probably damaging 2.383 7 Tolerant 0.3 2.82 32 moderately conservative 602040 21q21.1 neural cell adhesion molecule 2 790 rs232518 NCAM2 4685 21 21668058 NM_004540 NP_004531 C/T L350P plus 4002906 634 PERLEGEN NCBI|NIHPDR NIHPDR 18 0.22 0.27 0.05 254 4 0.45 0.01 1662 4 123 "by doubleHit,submitter,freq,cluster" Probably damaging 2.383 7 Tolerant 0.3 2.82 32 moderately conservative 602040 21q21.1 neural cell adhesion molecule 2 791 rs232518 NCAM2 4685 21 21668058 NM_004540 NP_004531 C/T L350P plus 24209420 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.27 0.05 254 4 0.45 0.01 1662 4 123 "by doubleHit,submitter,freq,cluster" Probably damaging 2.383 7 Tolerant 0.3 2.82 32 moderately conservative 602040 21q21.1 neural cell adhesion molecule 2 792 rs233223 MEP1B 4225 18 28049099 NM_005925 NP_005916 A/G S546P minus 557201 1303 SEQUENOM CEPH CEPH (92) 92 0.12 0.12 0 92 1 120 "by doubleHit,cluster" Possibly damaging 1.74 7 moderately conservative 600389 18q12.2-q12.3 "meprin A, beta" 793 rs235768 BMP2 650 20 6707115 NM_001200 NP_001191 A/T R190S plus 304296 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 7 0.5 0.32 0.08 239 4 0.21 0.06 48 2 121 "by doubleHit,freq,cluster" Probably damaging 2.152 60 Intolerant 0.01 2.83 81 moderately radical 112261 20p12 bone morphogenetic protein 2 794 rs235768 BMP2 650 20 6707115 NM_001200 NP_001191 A/T R190S plus 304296 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 90 0.39 0.32 0.08 239 4 0.21 0.06 48 2 121 "by doubleHit,freq,cluster" Probably damaging 2.152 60 Intolerant 0.01 2.83 81 moderately radical 112261 20p12 bone morphogenetic protein 2 795 rs235768 BMP2 650 20 6707115 NM_001200 NP_001191 A/T R190S plus 3176830 619 WICVAR MITOGPOP6 CORIELL Mixed 50 0.22 0.32 0.08 239 4 0.21 0.06 48 2 121 "by doubleHit,freq,cluster" Probably damaging 2.152 60 Intolerant 0.01 2.83 81 moderately radical 112261 20p12 bone morphogenetic protein 2 796 rs235768 BMP2 650 20 6707115 NM_001200 NP_001191 A/T R190S plus 8367997 1303 SEQUENOM CEPH CEPH (92) 92 0.29 0.32 0.08 239 4 0.21 0.06 48 2 121 "by doubleHit,freq,cluster" Probably damaging 2.152 60 Intolerant 0.01 2.83 81 moderately radical 112261 20p12 bone morphogenetic protein 2 797 rs237831 DDX28 55794 16 66614597 NM_018380 NP_060850 A/G T4A minus 129227 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 78 0.14 0.11 0.04 304 4 121 "HapMap,freq" moderately conservative 607618 16q22.1 DEAD (Asp-Glu-Ala-Asp) box polypeptide 28 798 rs237831 DDX28 55794 16 66614597 NM_018380 NP_060850 A/G T4A minus 129227 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.07 0.11 0.04 304 4 121 "HapMap,freq" moderately conservative 607618 16q22.1 DEAD (Asp-Glu-Ala-Asp) box polypeptide 28 799 rs237831 DDX28 55794 16 66614597 NM_018380 NP_060850 A/G T4A minus 129227 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.07 0.11 0.04 304 4 121 "HapMap,freq" moderately conservative 607618 16q22.1 DEAD (Asp-Glu-Ala-Asp) box polypeptide 28 800 rs237831 DDX28 55794 16 66614597 NM_018380 NP_060850 A/G T4A minus 129227 1303 SEQUENOM CEPH CEPH (92) 92 0.14 0.11 0.04 304 4 121 "HapMap,freq" moderately conservative 607618 16q22.1 DEAD (Asp-Glu-Ala-Asp) box polypeptide 28 801 rs238234 CAMTA2 23125 17 4824542 NM_015099 NP_055914 C/G A267P plus 129424 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.26 0 92 1 121 "by doubleHit,freq,cluster" conservative 17p13.3 calmodulin binding transcription activator 2 802 rs240768 HELIC1 10973 6 101064065 NM_006828 NP_006819 C/T Y2176C plus 1631964 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.04 0.05 164 3 0.12 0.03 1658 6 123 "by doubleHit,submitter,freq,cluster" Potentially intolerant 0.07 2.89 16 radical 6q16 "helicase, ATP binding 1" 803 rs240768 HELIC1 10973 6 101064065 NM_006828 NP_006819 C/T Y2176C plus 16335969 902 AFFY Caucasian 24 0.13 0.04 0.05 164 3 0.12 0.03 1658 6 123 "by doubleHit,submitter,freq,cluster" Potentially intolerant 0.07 2.89 16 radical 6q16 "helicase, ATP binding 1" 804 rs240768 HELIC1 10973 6 101064065 NM_006828 NP_006819 C/T Y2176C plus 23407849 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.04 0.05 164 3 0.12 0.03 1658 6 123 "by doubleHit,submitter,freq,cluster" Potentially intolerant 0.07 2.89 16 radical 6q16 "helicase, ATP binding 1" 805 rs240780 HELIC1 10973 6 101070868 NM_006828 NP_006819 C/G S1995C plus 1631950 1303 SEQUENOM CEPH CEPH (92) 92 0.34 0.38 0.08 140 2 0.21 0.09 92 2 123 "by doubleHit,submitter,freq,cluster" Probably damaging 2.068 6 Intolerant 0.03 2.77 20 moderately radical 6q16 "helicase, ATP binding 1" 806 rs240780 HELIC1 10973 6 101070868 NM_006828 NP_006819 C/G S1995C plus 24425049 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.38 0.08 140 2 0.21 0.09 92 2 123 "by doubleHit,submitter,freq,cluster" Probably damaging 2.068 6 Intolerant 0.03 2.77 20 moderately radical 6q16 "helicase, ATP binding 1" 807 rs241447 TAP2 6891 6 32904729 NM_000544 NP_000535 A/G T665A minus 1954321 1303 SEQUENOM CEPH CEPH (92) 92 0.13 0.22 0.07 326 3 0.35 0 1474 1 123 "by doubleHit,freq,cluster" Benign 0.502 20 moderately conservative 170261 6p21.3 "transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)" 808 rs241447 TAP2 6891 6 32904729 NM_000544 NP_000535 A/G T665A minus 3173073 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 50 0.22 0.22 0.07 326 3 0.35 0 1474 1 123 "by doubleHit,freq,cluster" Benign 0.502 20 moderately conservative 170261 6p21.3 "transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)" 809 rs241447 TAP2 6891 6 32904729 NM_000544 NP_000535 A/G T665A minus 24796293 1303 SEQUENOM CEPH CEPH (92) 184 0.27 0.22 0.07 326 3 0.35 0 1474 1 123 "by doubleHit,freq,cluster" Benign 0.502 20 moderately conservative 170261 6p21.3 "transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)" 810 rs241448 TAP2 6891 6 32904663 NM_000544 NP_000535 C/T STOP687Q minus 1954322 1303 SEQUENOM CEPH CEPH (92) 92 0.3 0.26 0.07 140 2 120 "by doubleHit,freq,cluster" Probably damaging Intolerant radical 170261 6p21.3 "transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)" 811 rs241448 TAP2 6891 6 32904663 NM_000544 NP_000535 C/T STOP687Q minus 3173074 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 48 0.19 0.26 0.07 140 2 120 "by doubleHit,freq,cluster" Probably damaging Intolerant radical 170261 6p21.3 "transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)" 812 rs244903 RARS 5917 5 167846088 NM_002887 NP_002878 A/G V3I plus 818727 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.29 0.44 0.05 364 5 0.1 0.01 1616 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.004 8 conservative 107820 5q35.1 arginyl-tRNA synthetase 813 rs244903 RARS 5917 5 167846088 NM_002887 NP_002878 A/G V3I plus 818727 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 90 0.44 0.44 0.05 364 5 0.1 0.01 1616 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.004 8 conservative 107820 5q35.1 arginyl-tRNA synthetase 814 rs244903 RARS 5917 5 167846088 NM_002887 NP_002878 A/G V3I plus 2274905 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.49 0.44 0.05 364 5 0.1 0.01 1616 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.004 8 conservative 107820 5q35.1 arginyl-tRNA synthetase 815 rs244903 RARS 5917 5 167846088 NM_002887 NP_002878 A/G V3I plus 2274905 1303 SEQUENOM CEPH CEPH (92) 92 0.42 0.44 0.05 364 5 0.1 0.01 1616 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.004 8 conservative 107820 5q35.1 arginyl-tRNA synthetase 816 rs244903 RARS 5917 5 167846088 NM_002887 NP_002878 A/G V3I plus 24671348 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.44 0.05 364 5 0.1 0.01 1616 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.004 8 conservative 107820 5q35.1 arginyl-tRNA synthetase 817 rs246669 PCDHB4 56131 5 140483421 NM_018938 NP_061761 C/T T553A minus 24811105 1303 SEQUENOM CEPH CEPH (92) 184 0.18 0.18 0 184 1 123 by freq Borderline 1.218 103 Tolerant 0.48 2.77 130 moderately conservative 606330 5q31 protocadherin beta 4 818 rs246679 PCDHB1 29930 5 140413573 NM_013340 NP_037472 C/G F778L minus 521335 1303 SEQUENOM CEPH CEPH (92) 92 0.03 0.03 0 92 1 98 by freq Tolerant 1 2.77 95 conservative 606327 5q31 protocadherin beta 1 819 rs246703 PCDHB6 56130 5 140511930 NM_018939 NP_061762 C/G H636Q minus 1652768 1303 SEQUENOM CEPH CEPH (92) 92 0.46 0.46 0 92 1 121 by freq Borderline 1.205 104 Tolerant 1 2.77 130 conservative 606332 5q31 protocadherin beta 6 820 rs259028 ZFYVE16 9765 5 79770053 NM_014733 NP_055548 C/T I598T plus 2228689 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 76 0.05 0.03 0.01 334 4 0.21 0.1 222 4 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.711 5 moderately conservative 608880 5p15.2-q14.3 "zinc finger, FYVE domain containing 16" 821 rs259028 ZFYVE16 9765 5 79770053 NM_014733 NP_055548 C/T I598T plus 2228689 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.03 0.03 0.01 334 4 0.21 0.1 222 4 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.711 5 moderately conservative 608880 5p15.2-q14.3 "zinc finger, FYVE domain containing 16" 822 rs259028 ZFYVE16 9765 5 79770053 NM_014733 NP_055548 C/T I598T plus 2228689 1303 SEQUENOM CEPH CEPH (92) 92 0.03 0.03 0.01 334 4 0.21 0.1 222 4 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.711 5 moderately conservative 608880 5p15.2-q14.3 "zinc finger, FYVE domain containing 16" 823 rs259028 ZFYVE16 9765 5 79770053 NM_014733 NP_055548 C/T I598T plus 23399732 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.03 0.01 334 4 0.21 0.1 222 4 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.711 5 moderately conservative 608880 5p15.2-q14.3 "zinc finger, FYVE domain containing 16" 824 rs260462 ZNF544 27300 19 63465883 NM_014480 NP_055295 A/G Q700R plus 540180 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 8 0.38 0.46 0.03 308 5 0.41 0.01 1638 5 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 19q13.43 zinc finger protein 544 825 rs260462 ZNF544 27300 19 63465883 NM_014480 NP_055295 A/G Q700R plus 540180 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 46 0.5 0.46 0.03 308 5 0.41 0.01 1638 5 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 19q13.43 zinc finger protein 544 826 rs260462 ZNF544 27300 19 63465883 NM_014480 NP_055295 A/G Q700R plus 540180 885 TSC-CSHL HapMap-CEPH-30-trios 114 0.45 0.46 0.03 308 5 0.41 0.01 1638 5 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 19q13.43 zinc finger protein 544 827 rs260462 ZNF544 27300 19 63465883 NM_014480 NP_055295 A/G Q700R plus 540180 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.46 0.03 308 5 0.41 0.01 1638 5 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 19q13.43 zinc finger protein 544 828 rs260462 ZNF544 27300 19 63465883 NM_014480 NP_055295 A/G Q700R plus 24536462 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.46 0.03 308 5 0.41 0.01 1638 5 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 19q13.43 zinc finger protein 544 829 rs266880 KLK3 354 19 56050283 NM_145864 NP_665863 C/G P87R plus 2041378 1303 SEQUENOM CEPH CEPH (92) 92 0.45 0.45 0 92 1 0.2 0 1494 1 120 "by doubleHit,freq,cluster" moderately radical 176820 19q13.41 "kallikrein 3, (prostate specific antigen)" 830 rs267561 ITGA9 3680 3 37549955 NM_002207 NP_002198 C/T G507E minus 1490039 1303 SEQUENOM CEPH CEPH (92) 92 0.49 0.47 0.03 140 2 0.29 0.21 71 2 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.35 2.82 16 moderately conservative 603963 3p21.3 "integrin, alpha 9" 831 rs267561 ITGA9 3680 3 37549955 NM_002207 NP_002198 C/T G507E minus 23257496 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.47 0.03 140 2 0.29 0.21 71 2 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.35 2.82 16 moderately conservative 603963 3p21.3 "integrin, alpha 9" 832 rs268671 PRX 57716 19 45593454 NM_181882 NP_870998 C/T V882A minus 599856 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.29 0.32 0.15 194 3 0.24 0.08 46 2 121 "by doubleHit,freq,cluster" Tolerant 0.75 2.82 11 moderately conservative 605725 19q13.13-q13.2 periaxin 833 rs268671 PRX 57716 19 45593454 NM_181882 NP_870998 C/T V882A minus 599856 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 88 0.19 0.32 0.15 194 3 0.24 0.08 46 2 121 "by doubleHit,freq,cluster" Tolerant 0.75 2.82 11 moderately conservative 605725 19q13.13-q13.2 periaxin 834 rs268671 PRX 57716 19 45593454 NM_181882 NP_870998 C/T V882A minus 599856 1303 SEQUENOM CEPH CEPH (92) 92 0.45 0.32 0.15 194 3 0.24 0.08 46 2 121 "by doubleHit,freq,cluster" Tolerant 0.75 2.82 11 moderately conservative 605725 19q13.13-q13.2 periaxin 835 rs268673 PRX 57716 19 45593336 NM_181882 NP_870998 A/G I921M minus 508093 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.4 0.32 0.13 212 2 121 "HapMap,submitter,freq,cluster" Borderline 0.16 2.87 10 conservative 605725 19q13.13-q13.2 periaxin 836 rs268673 PRX 57716 19 45593336 NM_181882 NP_870998 A/G I921M minus 508093 1303 SEQUENOM CEPH CEPH (92) 92 0.22 0.32 0.13 212 2 121 "HapMap,submitter,freq,cluster" Borderline 0.16 2.87 10 conservative 605725 19q13.13-q13.2 periaxin 837 rs268674 PRX 57716 19 45592705 NM_181882 NP_870998 A/G G1132R minus 528679 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.05 0.07 0.05 168 2 0.02 0.01 1550 2 123 "HapMap,freq,cluster" moderately radical 605725 19q13.13-q13.2 periaxin 838 rs268674 PRX 57716 19 45592705 NM_181882 NP_870998 A/G G1132R minus 24595982 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.07 0.05 168 2 0.02 0.01 1550 2 123 "HapMap,freq,cluster" moderately radical 605725 19q13.13-q13.2 periaxin 839 rs269868 DUOX2 50506 15 43179367 NM_014080 NP_054799 C/T S1067L minus 2032138 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.02 0.03 0.03 168 2 0.2 0.23 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.464 14 Potentially intolerant 0.1 2.86 42 moderately radical 606759 15q15.3 dual oxidase 2 840 rs269868 DUOX2 50506 15 43179367 NM_014080 NP_054799 C/T S1067L minus 23462795 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.03 0.03 168 2 0.2 0.23 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.464 14 Potentially intolerant 0.1 2.86 42 moderately radical 606759 15q15.3 dual oxidase 2 841 rs283526 ATF5 22809 19 55127674 NM_012068 NP_036200 C/T P121L plus 2039819 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.02 0 92 1 120 "by doubleHit,freq,cluster" Tolerant 0.88 2.81 23 moderately conservative 606398 19q13.3 activating transcription factor 5 842 rs285584 PDZRN4 29951 12 40232806 NM_013377 NP_037509 A/G G171S plus 627828 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.13 0.14 0.01 166 2 0.2 0.21 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.722 13 Potentially intolerant 0.1 3.06 372 moderately conservative 12q12 PDZ domain containing RING finger 4 843 rs285584 PDZRN4 29951 12 40232806 NM_013377 NP_037509 A/G G171S plus 23342080 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.14 0.01 166 2 0.2 0.21 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.722 13 Potentially intolerant 0.1 3.06 372 moderately conservative 12q12 PDZ domain containing RING finger 4 844 rs288334 DNAJC10 54431 2 183448053 NM_018981 NP_061854 A/C H646Q minus 24151124 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.26 0.26 0 46 1 0.34 0.2 94 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.187 11 Tolerant 0.67 2.9 27 conservative 607987 2q32.1 "DnaJ (Hsp40) homolog, subfamily C, member 10" 845 rs291102 PIGR 5284 1 203494873 NM_002644 NP_002635 C/T A580V minus 1342427 1303 SEQUENOM CEPH CEPH (92) 92 0.07 0.07 0 92 1 0.16 0 1494 1 100 "by doubleHit,submitter,freq,cluster" Benign 0.095 9 moderately conservative 173880 1q31-q41 polymeric immunoglobulin receptor 846 rs305974 CYP2F1 1572 19 46319708 NM_000774 NP_000765 A/G D218N plus 1609735 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.33 0.39 0.1 210 2 113 "HapMap,freq" Borderline 1.027 90 Tolerant 1 2.78 165 conservative 124070 19q13.2 "cytochrome P450, family 2, subfamily F, polypeptide 1" 847 rs305974 CYP2F1 1572 19 46319708 NM_000774 NP_000765 A/G D218N plus 1609735 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.39 0.1 210 2 113 "HapMap,freq" Borderline 1.027 90 Tolerant 1 2.78 165 conservative 124070 19q13.2 "cytochrome P450, family 2, subfamily F, polypeptide 1" 848 rs306547 DDX31 64794 9 132499968 NM_022779 NP_073616 C/T I799V plus 504735 1303 SEQUENOM CEPH CEPH (92) 92 0.41 0.41 0 92 1 121 "by cluster,freq" conservative 9q34.3 DEAD (Asp-Glu-Ala-Asp) box polypeptide 31 849 rs307821 FLT4 2324 5 179962919 NM_182925 NP_891555 G/T R1324L minus 1765465 1303 SEQUENOM CEPH CEPH (92) 92 0.12 0.12 0 92 1 100 by freq Tolerant 0.4 3.02 20 moderately radical 136352 5q34-q35 fms-related tyrosine kinase 4 850 rs309559 CSPG2 1462 5 82869125 NM_004385 NP_004376 C/T K1516R minus 731523 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.43 0.47 0.02 242 4 0.45 0.05 872 5 123 "by doubleHit,submitter,freq,cluster" Benign 0.118 5 Borderline 0.11 3.14 7 conservative 118661 5q14.3 chondroitin sulfate proteoglycan 2 (versican) 851 rs309559 CSPG2 1462 5 82869125 NM_004385 NP_004376 C/T K1516R minus 731523 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 92 0.48 0.47 0.02 242 4 0.45 0.05 872 5 123 "by doubleHit,submitter,freq,cluster" Benign 0.118 5 Borderline 0.11 3.14 7 conservative 118661 5q14.3 chondroitin sulfate proteoglycan 2 (versican) 852 rs309559 CSPG2 1462 5 82869125 NM_004385 NP_004376 C/T K1516R minus 2225096 1303 SEQUENOM CEPH CEPH (92) 92 0.48 0.47 0.02 242 4 0.45 0.05 872 5 123 "by doubleHit,submitter,freq,cluster" Benign 0.118 5 Borderline 0.11 3.14 7 conservative 118661 5q14.3 chondroitin sulfate proteoglycan 2 (versican) 853 rs309559 CSPG2 1462 5 82869125 NM_004385 NP_004376 C/T K1516R minus 24621156 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.45 0.47 0.02 242 4 0.45 0.05 872 5 123 "by doubleHit,submitter,freq,cluster" Benign 0.118 5 Borderline 0.11 3.14 7 conservative 118661 5q14.3 chondroitin sulfate proteoglycan 2 (versican) 854 rs310632 PRIC285 85441 20 61667251 NM_033405 NP_208384 A/G H554R minus 8378779 1303 SEQUENOM CEPH CEPH (92) 92 0.18 0.18 0 92 1 121 "by cluster,freq" conservative 20q13.33 peroxisomal proliferator-activated receptor A interacting complex 285 855 rs310791 E2F7 144455 12 75952258 NM_203394 NP_976328 A/G F72L plus 492242 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.07 0.08 0.02 168 2 0.18 0.23 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 12q21.1 E2F transcription factor 7 856 rs310791 E2F7 144455 12 75952258 NM_203394 NP_976328 A/G F72L plus 23379876 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.08 0.02 168 2 0.18 0.23 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 12q21.1 E2F transcription factor 7 857 rs310831 E2F7 144455 12 75921809 NM_203394 NP_976328 A/T H854Q plus 502756 902 AFFY Caucasian 20 0.15 0.14 0.03 80 3 0.02 0 46 1 123 "by doubleHit,submitter,freq" conservative 12q21.1 E2F transcription factor 7 858 rs310831 E2F7 144455 12 75921809 NM_203394 NP_976328 A/T H854Q plus 502756 904 AFFY CEPH 12 0.08 0.14 0.03 80 3 0.02 0 46 1 123 "by doubleHit,submitter,freq" conservative 12q21.1 E2F transcription factor 7 859 rs310831 E2F7 144455 12 75921809 NM_203394 NP_976328 A/T H854Q plus 24403096 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.14 0.03 80 3 0.02 0 46 1 123 "by doubleHit,submitter,freq" conservative 12q21.1 E2F transcription factor 7 860 rs311685 DDX43 55510 6 74182609 NM_018665 NP_061135 C/T Q629R minus 5253350 1303 SEQUENOM CEPH CEPH (92) 92 0.3 0.36 0.08 167 4 0.34 0.03 166 5 123 "by doubleHit,freq,cluster" conservative 606286 6q12-q13 DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 861 rs311685 DDX43 55510 6 74182609 NM_018665 NP_061135 C/T Q629R minus 16335927 902 AFFY Caucasian 22 0.41 0.36 0.08 167 4 0.34 0.03 166 5 123 "by doubleHit,freq,cluster" conservative 606286 6q12-q13 DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 862 rs311685 DDX43 55510 6 74182609 NM_018665 NP_061135 C/T Q629R minus 16335927 904 AFFY CEPH 5 0.5 0.36 0.08 167 4 0.34 0.03 166 5 123 "by doubleHit,freq,cluster" conservative 606286 6q12-q13 DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 863 rs311685 DDX43 55510 6 74182609 NM_018665 NP_061135 C/T Q629R minus 24402124 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.36 0.08 167 4 0.34 0.03 166 5 123 "by doubleHit,freq,cluster" conservative 606286 6q12-q13 DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 864 rs311686 DDX43 55510 6 74182596 NM_018665 NP_061135 C/T K625E minus 5384030 1303 SEQUENOM CEPH CEPH (92) 92 0.46 0.45 0.01 140 2 0.36 0.04 94 2 123 "by doubleHit,freq,cluster" moderately conservative 606286 6q12-q13 DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 865 rs311686 DDX43 55510 6 74182596 NM_018665 NP_061135 C/T K625E minus 24402117 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.45 0.01 140 2 0.36 0.04 94 2 123 "by doubleHit,freq,cluster" moderately conservative 606286 6q12-q13 DEAD (Asp-Glu-Ala-Asp) box polypeptide 43 866 rs315675 ZCCHC4 29063 4 25040170 XM_376310 XP_376310 A/T L395H minus 899412 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.21 0.14 0.04 318 4 0.15 0.03 742 2 121 "HapMap,submitter,freq,cluster" Possibly damaging 1.695 8 moderately conservative 4p15.31 "zinc finger, CCHC domain containing 4" 867 rs315675 ZCCHC4 29063 4 25040170 XM_376310 XP_376310 A/T L395H minus 899412 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 92 0.09 0.14 0.04 318 4 0.15 0.03 742 2 121 "HapMap,submitter,freq,cluster" Possibly damaging 1.695 8 moderately conservative 4p15.31 "zinc finger, CCHC domain containing 4" 868 rs315675 ZCCHC4 29063 4 25040170 XM_376310 XP_376310 A/T L395H minus 2754883 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.15 0.14 0.04 318 4 0.15 0.03 742 2 121 "HapMap,submitter,freq,cluster" Possibly damaging 1.695 8 moderately conservative 4p15.31 "zinc finger, CCHC domain containing 4" 869 rs315675 ZCCHC4 29063 4 25040170 XM_376310 XP_376310 A/T L395H minus 2754883 1303 SEQUENOM CEPH CEPH (92) 92 0.18 0.14 0.04 318 4 0.15 0.03 742 2 121 "HapMap,submitter,freq,cluster" Possibly damaging 1.695 8 moderately conservative 4p15.31 "zinc finger, CCHC domain containing 4" 870 rs321937 ZNF610 162963 19 57561090 NM_173530 NP_775801 C/G R216P minus 4058648 902 AFFY Caucasian 20 0.1 0.13 0.05 32 2 0.27 0.05 66 3 121 "by doubleHit,submitter,freq,cluster" Possibly damaging 1.692 7 moderately radical 19q13.41 zinc finger protein 610 871 rs321937 ZNF610 162963 19 57561090 NM_173530 NP_775801 C/G R216P minus 4058648 904 AFFY CEPH 12 0.17 0.13 0.05 32 2 0.27 0.05 66 3 121 "by doubleHit,submitter,freq,cluster" Possibly damaging 1.692 7 moderately radical 19q13.41 zinc finger protein 610 872 rs324420 FAAH 2166 1 46582781 NM_001441 NP_001432 A/C P129T plus 587534 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 12 0.42 0.24 0.05 224 3 0.19 0.18 32 2 121 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.945 9 Borderline 0.13 2.79 18 conservative 602935 1p35-p34 fatty acid amide hydrolase 873 rs324420 FAAH 2166 1 46582781 NM_001441 NP_001432 A/C P129T plus 587534 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.23 0.24 0.05 224 3 0.19 0.18 32 2 121 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.945 9 Borderline 0.13 2.79 18 conservative 602935 1p35-p34 fatty acid amide hydrolase 874 rs324420 FAAH 2166 1 46582781 NM_001441 NP_001432 A/C P129T plus 587534 1303 SEQUENOM CEPH CEPH (92) 92 0.23 0.24 0.05 224 3 0.19 0.18 32 2 121 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.945 9 Borderline 0.13 2.79 18 conservative 602935 1p35-p34 fatty acid amide hydrolase 875 rs344140 ShrmL 57619 4 78017341 NM_020859 NP_065910 C/G G278A plus 569841 1303 SEQUENOM CEPH CEPH (92) 92 0.17 0.17 0 92 1 120 "by doubleHit,freq,cluster" moderately conservative 604570 4q21.22 Shroom-related protein 876 rs344141 ShrmL 57619 4 78017910 NM_020859 NP_065910 C/G P468A plus 1335241 1303 SEQUENOM CEPH CEPH (92) 92 0.39 0.39 0 92 1 120 "by doubleHit,freq,cluster" conservative 604570 4q21.22 Shroom-related protein 877 rs346821 FLJ10060 55065 17 4877696 NM_017986 NP_060456 A/G A271V plus 609695 1303 SEQUENOM CEPH CEPH (92) 92 0.28 0.28 0 92 1 0.22 0 1498 1 121 "by doubleHit,freq,cluster" Benign 0.228 11 moderately conservative 607883 17p13.3 putative G-protein coupled receptor GPCR42 878 rs346822 FLJ10060 55065 17 4878299 NM_017986 NP_060456 A/G Q70R minus 1322665 1303 SEQUENOM CEPH CEPH (92) 92 0.09 0.07 0.03 140 2 0.1 0.08 94 2 123 "by doubleHit,freq,cluster" Benign 0.394 11 conservative 607883 17p13.3 putative G-protein coupled receptor GPCR42 879 rs346822 FLJ10060 55065 17 4878299 NM_017986 NP_060456 A/G Q70R minus 24213524 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.07 0.03 140 2 0.1 0.08 94 2 123 "by doubleHit,freq,cluster" Benign 0.394 11 conservative 607883 17p13.3 putative G-protein coupled receptor GPCR42 880 rs351111 PRTN3 5657 19 795020 NM_002777 NP_002768 A/G V119I plus 1745256 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.43 0.43 0.01 212 2 102 "HapMap,submitter,freq" Benign 0.469 20 conservative 177020 19p13.3 "proteinase 3 (serine proteinase, neutrophil, Wegener granulomatosis autoantigen)" 881 rs351111 PRTN3 5657 19 795020 NM_002777 NP_002768 A/G V119I plus 1745256 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.43 0.01 212 2 102 "HapMap,submitter,freq" Benign 0.469 20 conservative 177020 19p13.3 "proteinase 3 (serine proteinase, neutrophil, Wegener granulomatosis autoantigen)" 882 rs352493 SIRT6 51548 19 4131836 NM_016539 NP_057623 C/T S46N plus 566893 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 94 0.05 0.04 0.03 232 3 0.19 0.13 134 4 123 "by cluster,freq" Benign 0.23 9 Tolerant 0.22 2.75 25 conservative 606211 19p13.3 sirtuin (silent mating type information regulation 2 homolog) 6 (S. cerevisiae) 883 rs352493 SIRT6 51548 19 4131836 NM_016539 NP_057623 C/T S46N plus 566893 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.04 0.03 232 3 0.19 0.13 134 4 123 "by cluster,freq" Benign 0.23 9 Tolerant 0.22 2.75 25 conservative 606211 19p13.3 sirtuin (silent mating type information regulation 2 homolog) 6 (S. cerevisiae) 884 rs352493 SIRT6 51548 19 4131836 NM_016539 NP_057623 C/T S46N plus 24081883 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.07 0.04 0.03 232 3 0.19 0.13 134 4 123 "by cluster,freq" Benign 0.23 9 Tolerant 0.22 2.75 25 conservative 606211 19p13.3 sirtuin (silent mating type information regulation 2 homolog) 6 (S. cerevisiae) 885 rs357564 PTCH 5727 9 95289149 NM_000264 NP_000255 A/G P1315L plus 3176045 619 WICVAR MITOGPOP6 CORIELL Mixed 28 0.32 0.4 0.04 212 2 123 by freq moderately conservative 601309 9q22.3 patched homolog (Drosophila) 886 rs357564 PTCH 5727 9 95289149 NM_000264 NP_000255 A/G P1315L plus 24796376 1303 SEQUENOM CEPH CEPH (92) 184 0.41 0.4 0.04 212 2 123 by freq moderately conservative 601309 9q22.3 patched homolog (Drosophila) 887 rs359974 IHH 3549 2 219755696 XM_050846 XP_050846 C/T M1I plus 548265 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.2 0.23 0.04 212 2 121 "HapMap,doubleHit,submitter,freq,cluster" conservative 600726 2q33-q35 Indian hedgehog homolog (Drosophila) 888 rs359974 IHH 3549 2 219755696 XM_050846 XP_050846 C/T M1I plus 17685878 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.23 0.04 212 2 121 "HapMap,doubleHit,submitter,freq,cluster" conservative 600726 2q33-q35 Indian hedgehog homolog (Drosophila) 889 rs360057 LEFTB 10637 1 222381298 NM_020997 NP_066277 G/T D322A plus 3063905 1303 SEQUENOM CEPH CEPH (92) 92 0.25 0.25 0 92 1 119 "by doubleHit,freq" Potentially damaging 1.268 7 Tolerant 0.77 2.85 17 moderately radical 603037 1q42.1 "left-right determination, factor B" 890 rs363294 PDZK8 118987 10 119033544 NM_173791 NP_776152 C/T R897Q plus 1467278 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.14 0.04 140 2 0.02 0 46 1 123 "by submitter,freq,cluster" conservative 10q26.12 PDZ domain containing 8 891 rs363294 PDZK8 118987 10 119033544 NM_173791 NP_776152 C/T R897Q plus 24568899 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.14 0.04 140 2 0.02 0 46 1 123 "by submitter,freq,cluster" conservative 10q26.12 PDZ domain containing 8 892 rs363504 GRIK1 2897 21 29847799 NM_000830 NP_000821 C/T L902S minus 4010646 634 PERLEGEN NCBI|NIHPDR NIHPDR 11 0.18 0.18 0 11 1 102 "by submitter,freq,cluster" moderately radical 138245 21q22.11 "glutamate receptor, ionotropic, kainate 1" 893 rs366439 EBAF 7044 1 222434413 NM_003240 NP_003231 A/G S92L plus 464983 1303 SEQUENOM CEPH CEPH (92) 46 0.5 0.5 0 46 1 0.25 0 1464 1 98 "by cluster,freq" moderately radical 601877 1q42.1 "endometrial bleeding associated factor (left-right determination, factor A; transforming growth factor beta superfamily)" 894 rs370429 PCM1 5108 8 17893427 NM_006197 NP_006188 A/G T1543I minus 4092407 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.03 0.03 0.01 260 3 0.24 0.05 92 2 123 "HapMap,submitter,freq,cluster" moderately conservative 600299 8p22-p21.3 pericentriolar material 1 895 rs370429 PCM1 5108 8 17893427 NM_006197 NP_006188 A/G T1543I minus 4092407 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.03 0.01 260 3 0.24 0.05 92 2 123 "HapMap,submitter,freq,cluster" moderately conservative 600299 8p22-p21.3 pericentriolar material 1 896 rs370429 PCM1 5108 8 17893427 NM_006197 NP_006188 A/G T1543I minus 23980890 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.03 0.01 260 3 0.24 0.05 92 2 123 "HapMap,submitter,freq,cluster" moderately conservative 600299 8p22-p21.3 pericentriolar material 1 897 rs373496 TNFRSF17 608 16 11967664 NM_001192 NP_001183 C/T N81S minus 16341954 693 EGP_SNPS PDR90 NIHPDR 174 0.03 0.03 0.01 266 2 121 "by cluster,freq" conservative 109545 16p13.1 "tumor necrosis factor receptor superfamily, member 17" 898 rs373496 TNFRSF17 608 16 11967664 NM_001192 NP_001183 C/T N81S minus 16728545 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.03 0.01 266 2 121 "by cluster,freq" conservative 109545 16p13.1 "tumor necrosis factor receptor superfamily, member 17" 899 rs373572 RAD18 56852 3 8930389 NM_020165 NP_064550 A/G R302Q minus 2293973 885 TSC-CSHL HapMap-CEPH-30-trios 100 0.18 0.18 0 240 3 0.33 0.01 92 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.9 5 conservative 605256 3p25-p24 RAD18 homolog (S. cerevisiae) 900 rs373572 RAD18 56852 3 8930389 NM_020165 NP_064550 A/G R302Q minus 2293973 1303 SEQUENOM CEPH CEPH (92) 92 0.18 0.18 0 240 3 0.33 0.01 92 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.9 5 conservative 605256 3p25-p24 RAD18 homolog (S. cerevisiae) 901 rs373572 RAD18 56852 3 8930389 NM_020165 NP_064550 A/G R302Q minus 23886577 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.18 0 240 3 0.33 0.01 92 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.9 5 conservative 605256 3p25-p24 RAD18 homolog (S. cerevisiae) 902 rs382627 FCGR2A 2212 1 158300860 NM_021642 NP_067674 C/T L272P plus 16450684 1303 SEQUENOM CEPH CEPH (92) 92 0.46 0.46 0 92 1 0.02 0 46 1 123 "by doubleHit,cluster" moderately conservative 146790 1q23 "Fc fragment of IgG, low affinity IIa, receptor for (CD32)" 903 rs383369 LILRB2 10288 19 59475942 NM_005874 NP_005865 C/T H20R plus 5464668 1303 SEQUENOM CEPH CEPH (92) 92 0.24 0.24 0 92 1 108 "by doubleHit,freq" Benign 0.659 61 Tolerant 0.47 2.97 51 conservative 604815 19q13.4 "leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2" 904 rs386056 LILRB2 10288 19 59474731 NM_005874 NP_005865 A/G V235M minus 497545 1303 SEQUENOM CEPH CEPH (92) 92 0.21 0.21 0 92 1 120 "by cluster,freq" Benign 0.277 63 Intolerant 0.02 2.78 214 conservative 604815 19q13.4 "leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2" 905 rs388685 ZNF45 7596 19 49110520 NM_003425 NP_003416 C/G P303R plus 24685147 1371 PERLEGEN AFD_EUR_PANEL European American (24) 24 0.5 0.48 0.01 208 2 0.26 0.05 1493 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.927 13 Intolerant 0.03 2.73 29 moderately radical 601781 19q13.2 zinc finger protein 45 (a Kruppel-associated box (KRAB) domain polypeptide) 906 rs388685 ZNF45 7596 19 49110520 NM_003425 NP_003416 C/G P303R plus 24811382 1303 SEQUENOM CEPH CEPH (92) 184 0.48 0.48 0.01 208 2 0.26 0.05 1493 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.927 13 Intolerant 0.03 2.73 29 moderately radical 601781 19q13.2 zinc finger protein 45 (a Kruppel-associated box (KRAB) domain polypeptide) 907 rs388706 ZNF45 7596 19 49110533 NM_003425 NP_003416 C/T T299A plus 2995829 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 78 0.47 0.43 0.06 218 3 0.19 0.09 242 4 123 "by doubleHit,freq,cluster" Benign 0.891 13 Potentially intolerant 0.1 2.73 29 moderately conservative 601781 19q13.2 zinc finger protein 45 (a Kruppel-associated box (KRAB) domain polypeptide) 908 rs388706 ZNF45 7596 19 49110533 NM_003425 NP_003416 C/T T299A plus 2995829 1303 SEQUENOM CEPH CEPH (92) 92 0.38 0.43 0.06 218 3 0.19 0.09 242 4 123 "by doubleHit,freq,cluster" Benign 0.891 13 Potentially intolerant 0.1 2.73 29 moderately conservative 601781 19q13.2 zinc finger protein 45 (a Kruppel-associated box (KRAB) domain polypeptide) 909 rs388706 ZNF45 7596 19 49110533 NM_003425 NP_003416 C/T T299A plus 24685149 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.43 0.06 218 3 0.19 0.09 242 4 123 "by doubleHit,freq,cluster" Benign 0.891 13 Potentially intolerant 0.1 2.73 29 moderately conservative 601781 19q13.2 zinc finger protein 45 (a Kruppel-associated box (KRAB) domain polypeptide) 910 rs390659 RDS 5961 6 42774142 NM_000322 NP_000313 C/G Q304E plus 505147 1303 SEQUENOM CEPH CEPH (92) 92 0.06 0.06 0 92 1 121 "by cluster,freq" Possibly damaging 1.528 27 conservative 179605 6p21.2-p12.3 "retinal degeneration, slow" 911 rs394558 TATDN2 9797 3 10277172 XM_376203 XP_376203 A/G V256I plus 4078742 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.42 0.36 0.09 260 3 0.16 0.18 88 2 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 3p25.3 TatD DNase domain containing 1 912 rs394558 TATDN2 9797 3 10277172 XM_376203 XP_376203 A/G V256I plus 4078742 1303 SEQUENOM CEPH CEPH (92) 92 0.34 0.36 0.09 260 3 0.16 0.18 88 2 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 3p25.3 TatD DNase domain containing 1 913 rs394558 TATDN2 9797 3 10277172 XM_376203 XP_376203 A/G V256I plus 23241729 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.36 0.09 260 3 0.16 0.18 88 2 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 3p25.3 TatD DNase domain containing 1 914 rs394732 BCAS1 8537 20 52108595 NM_003657 NP_003648 G/T Q24K plus 2993255 760 TSC-CSHL CEL_CAUCASIAN CELERA Caucasians (30) 60 0.4 0.43 0.01 546 4 0.29 0.02 208 4 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 602968 20q13.2-q13.3 breast carcinoma amplified sequence 1 915 rs394732 BCAS1 8537 20 52108595 NM_003657 NP_003648 G/T Q24K plus 2993255 761 TSC-CSHL CEL_CAUCASIAN_CEPH CELERA CEPH Caucasians (661) 320 0.43 0.43 0.01 546 4 0.29 0.02 208 4 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 602968 20q13.2-q13.3 breast carcinoma amplified sequence 1 916 rs394732 BCAS1 8537 20 52108595 NM_003657 NP_003648 G/T Q24K plus 2993255 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.42 0.43 0.01 546 4 0.29 0.02 208 4 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 602968 20q13.2-q13.3 breast carcinoma amplified sequence 1 917 rs394732 BCAS1 8537 20 52108595 NM_003657 NP_003648 G/T Q24K plus 24558206 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.43 0.01 546 4 0.29 0.02 208 4 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 602968 20q13.2-q13.3 breast carcinoma amplified sequence 1 918 rs396716 FCGR3A 2214 1 158327651 NM_000569 NP_000560 C/T Y194H minus 515045 885 TSC-CSHL HapMap-CEPH-30-trios 114 0.01 0.17 0.25 206 2 120 "HapMap,doubleHit,cluster" Benign 0.383 23 Tolerant 0.55 2.82 48 moderately conservative 146740 1q23 "Fc fragment of IgG, low affinity IIIa, receptor for (CD16)" 919 rs396716 FCGR3A 2214 1 158327651 NM_000569 NP_000560 C/T Y194H minus 515045 1303 SEQUENOM CEPH CEPH (92) 92 0.36 0.17 0.25 206 2 120 "HapMap,doubleHit,cluster" Benign 0.383 23 Tolerant 0.55 2.82 48 moderately conservative 146740 1q23 "Fc fragment of IgG, low affinity IIIa, receptor for (CD16)" 920 rs396991 FCGR3A 2214 1 158327597 NM_000569 NP_000560 G/T F212V minus 515482 1303 SEQUENOM CEPH CEPH (92) 92 0.45 0.45 0 92 1 121 "by doubleHit,cluster" Benign 0.202 23 Tolerant 0.33 2.84 40 conservative 146740 1q23 "Fc fragment of IgG, low affinity IIIa, receptor for (CD16)" 921 rs398829 ADAMTS2 9509 5 178567278 NM_014244 NP_055059 A/G V245I minus 17097424 1303 SEQUENOM CEPH CEPH (92) 92 0.25 0.25 0 92 1 0.36 0 1490 1 121 "by doubleHit,freq,cluster" Benign 0.883 12 Tolerant 0.85 2.78 21 conservative 604539 5qter "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2" 922 rs399098 ZNF45 7596 19 49110664 NM_003425 NP_003416 A/G R255K minus 2995828 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.39 0.41 0.04 256 3 0.39 0.09 774 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.067 13 Tolerant 1 2.73 29 conservative 601781 19q13.2 zinc finger protein 45 (a Kruppel-associated box (KRAB) domain polypeptide) 923 rs399098 ZNF45 7596 19 49110664 NM_003425 NP_003416 A/G R255K minus 2995828 1303 SEQUENOM CEPH CEPH (92) 92 0.4 0.41 0.04 256 3 0.39 0.09 774 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.067 13 Tolerant 1 2.73 29 conservative 601781 19q13.2 zinc finger protein 45 (a Kruppel-associated box (KRAB) domain polypeptide) 924 rs399098 ZNF45 7596 19 49110664 NM_003425 NP_003416 A/G R255K minus 24197170 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.48 0.41 0.04 256 3 0.39 0.09 774 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.067 13 Tolerant 1 2.73 29 conservative 601781 19q13.2 zinc finger protein 45 (a Kruppel-associated box (KRAB) domain polypeptide) 925 rs402680 AOC3 8639 17 38257119 NM_003734 NP_003725 C/T R78Q minus 24811429 1303 SEQUENOM CEPH CEPH (92) 184 0.3 0.3 0 184 1 123 "by cluster,freq" Benign 0.071 15 Tolerant 0.24 2.85 24 conservative 603735 17q21 "amine oxidase, copper containing 3 (vascular adhesion protein 1)" 926 rs403016 FCGR3A 2214 1 158331477 NM_000569 NP_000560 C/G R72S plus 24788817 1303 SEQUENOM CEPH CEPH (92) 184 0.45 0.4 0.07 368 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.785 23 Tolerant 0.45 2.82 48 moderately radical 146740 1q23 "Fc fragment of IgG, low affinity IIIa, receptor for (CD16)" 927 rs403016 FCGR3A 2214 1 158331477 NM_000569 NP_000560 C/G R72S plus 24796109 1303 SEQUENOM CEPH CEPH (92) 184 0.35 0.4 0.07 368 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.785 23 Tolerant 0.45 2.82 48 moderately radical 146740 1q23 "Fc fragment of IgG, low affinity IIIa, receptor for (CD16)" 928 rs407731 ZNF45 7596 19 49109917 NM_003425 NP_003416 A/G R504K minus 1315616 1303 SEQUENOM CEPH CEPH (92) 92 0.27 0.34 0.14 140 2 0.21 0.01 94 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.225 11 Tolerant 0.33 2.74 28 conservative 601781 19q13.2 zinc finger protein 45 (a Kruppel-associated box (KRAB) domain polypeptide) 929 rs407731 ZNF45 7596 19 49109917 NM_003425 NP_003416 A/G R504K minus 24685139 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.34 0.14 140 2 0.21 0.01 94 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.225 11 Tolerant 0.33 2.74 28 conservative 601781 19q13.2 zinc finger protein 45 (a Kruppel-associated box (KRAB) domain polypeptide) 930 rs408038 AOC3 8639 17 38257397 NM_003734 NP_003725 C/T V171M minus 24796534 1303 SEQUENOM CEPH CEPH (92) 184 0.27 0.18 0.13 368 2 123 by freq Benign 0.246 15 Borderline 0.16 2.85 24 conservative 603735 17q21 "amine oxidase, copper containing 3 (vascular adhesion protein 1)" 931 rs408038 AOC3 8639 17 38257397 NM_003734 NP_003725 C/T V171M minus 24811443 1303 SEQUENOM CEPH CEPH (92) 184 0.08 0.18 0.13 368 2 123 by freq Benign 0.246 15 Borderline 0.16 2.85 24 conservative 603735 17q21 "amine oxidase, copper containing 3 (vascular adhesion protein 1)" 932 rs412750 PCM1 5108 8 17840662 NM_006197 NP_006188 A/G N159S plus 541750 1303 SEQUENOM CEPH CEPH (92) 92 0.03 0.03 0 92 1 121 "by doubleHit,freq,cluster" conservative 600299 8p22-p21.3 pericentriolar material 1 933 rs414352 RP1 6101 8 55704066 NM_006269 NP_006260 C/T S1691P plus 544417 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.23 0.23 0.04 260 3 0.32 0.23 90 2 123 "HapMap,doubleHit,submitter,freq" Benign 0.284 6 moderately conservative 603937 8q11-q13 retinitis pigmentosa 1 (autosomal dominant) 934 rs414352 RP1 6101 8 55704066 NM_006269 NP_006260 C/T S1691P plus 544417 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.23 0.04 260 3 0.32 0.23 90 2 123 "HapMap,doubleHit,submitter,freq" Benign 0.284 6 moderately conservative 603937 8q11-q13 retinitis pigmentosa 1 (autosomal dominant) 935 rs414352 RP1 6101 8 55704066 NM_006269 NP_006260 C/T S1691P plus 24077580 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.23 0.04 260 3 0.32 0.23 90 2 123 "HapMap,doubleHit,submitter,freq" Benign 0.284 6 moderately conservative 603937 8q11-q13 retinitis pigmentosa 1 (autosomal dominant) 936 rs414408 COL1A2 1278 7 93686590 NM_000089 NP_000080 C/T A483V plus 544512 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 83 0.16 0.16 0 83 1 80 by freq Tolerant 0.29 3.03 75 moderately conservative 120160 7q22.1 "collagen, type I, alpha 2" 937 rs417012 PAPPA 5069 9 115996019 NM_002581 NP_002572 G/T S5I plus 548739 1303 SEQUENOM CEPH CEPH (92) 92 0.06 0.06 0 92 1 80 by freq moderately radical 176385 9q33.2 pregnancy-associated plasma protein A 938 rs428073 JIK 51347 12 117145471 NM_016281 NP_057365 C/T S47N plus 1994738 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.29 0.29 0 120 1 121 "HapMap,freq,cluster" Benign 0.503 21 conservative 12q STE20-like kinase 939 rs428785 ADAMTS1 9510 21 27138466 NM_006988 NP_008919 C/G A210P plus 568349 1303 SEQUENOM CEPH CEPH (92) 92 0.42 0.33 0.18 140 2 0.3 0.26 94 2 123 "by doubleHit,freq,cluster" conservative 605174 21q21.2 "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 1" 940 rs428785 ADAMTS1 9510 21 27138466 NM_006988 NP_008919 C/G A210P plus 24024745 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.33 0.18 140 2 0.3 0.26 94 2 123 "by doubleHit,freq,cluster" conservative 605174 21q21.2 "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 1" 941 rs428888 FCGR3A 2214 1 158331341 NM_000569 NP_000560 C/T D118N plus 5518768 1303 SEQUENOM CEPH CEPH (92) 92 0.38 0.38 0 92 1 116 "by doubleHit,freq,cluster" Benign 0.084 23 Tolerant 1 2.82 48 conservative 146740 1q23 "Fc fragment of IgG, low affinity IIIa, receptor for (CD16)" 942 rs429358 APOE 348 19 50103781 NM_000041 NP_000032 C/T C130R plus 870163 563 DEBNICK MDECODE-1 European-Americans 48 0.12 0.15 0.02 1953 3 0.1 0 96 2 123 "by doubleHit,freq,cluster" Benign 0.62 29 Tolerant 1 2.79 33 radical 107741 19q13.2 apolipoprotein E 943 rs429358 APOE 348 19 50103781 NM_000041 NP_000032 C/T C130R plus 870163 564 DEBNICK MDECODE-2 Finnish 48 0.23 0.15 0.02 1953 3 0.1 0 96 2 123 "by doubleHit,freq,cluster" Benign 0.62 29 Tolerant 1 2.79 33 radical 107741 19q13.2 apolipoprotein E 944 rs429358 APOE 348 19 50103781 NM_000041 NP_000032 C/T C130R plus 12568607 887 CUORCGL AMERICAN CAUCASIANS American Caucasians 1857 0.15 0.15 0.02 1953 3 0.1 0 96 2 123 "by doubleHit,freq,cluster" Benign 0.62 29 Tolerant 1 2.79 33 radical 107741 19q13.2 apolipoprotein E 945 rs430554 SNF1LK 150094 21 43661983 NM_173354 NP_775490 A/G A615V plus 571239 1303 SEQUENOM CEPH CEPH (92) 92 0.34 0.34 0 92 1 121 "by doubleHit,freq,cluster" moderately conservative 605705 21q22.3 SNF1-like kinase 946 rs430665 U2AF1L1 7310 5 112256566 NM_005083 NP_005074 C/T S444N minus 571422 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 24 0.21 0.35 0.11 244 4 0.34 0.1 132 4 123 "by cluster,freq" conservative 601079 5q22 U2(RNU2) small nuclear RNA auxillary factor 1-like 1 947 rs430665 U2AF1L1 7310 5 112256566 NM_005083 NP_005074 C/T S444N minus 571422 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 80 0.29 0.35 0.11 244 4 0.34 0.1 132 4 123 "by cluster,freq" conservative 601079 5q22 U2(RNU2) small nuclear RNA auxillary factor 1-like 1 948 rs430665 U2AF1L1 7310 5 112256566 NM_005083 NP_005074 C/T S444N minus 1998866 1303 SEQUENOM CEPH CEPH (92) 92 0.46 0.35 0.11 244 4 0.34 0.1 132 4 123 "by cluster,freq" conservative 601079 5q22 U2(RNU2) small nuclear RNA auxillary factor 1-like 1 949 rs430665 U2AF1L1 7310 5 112256566 NM_005083 NP_005074 C/T S444N minus 23418331 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.35 0.11 244 4 0.34 0.1 132 4 123 "by cluster,freq" conservative 601079 5q22 U2(RNU2) small nuclear RNA auxillary factor 1-like 1 950 rs434473 ALOX12 239 17 6845658 NM_000697 NP_000688 A/G N322S plus 577623 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.36 0.39 0.1 446 6 0.28 0.02 1172 4 120 "HapMap,freq,cluster" Benign 0.274 24 Tolerant 0.25 2.77 32 conservative 152391 17p13.1 arachidonate 12-lipoxygenase 951 rs434473 ALOX12 239 17 6845658 NM_000697 NP_000688 A/G N322S plus 577623 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 90 0.44 0.39 0.1 446 6 0.28 0.02 1172 4 120 "HapMap,freq,cluster" Benign 0.274 24 Tolerant 0.25 2.77 32 conservative 152391 17p13.1 arachidonate 12-lipoxygenase 952 rs434473 ALOX12 239 17 6845658 NM_000697 NP_000688 A/G N322S plus 3255020 506 NCBI NIHPDR NIHPDR 86 0.4 0.39 0.1 446 6 0.28 0.02 1172 4 120 "HapMap,freq,cluster" Benign 0.274 24 Tolerant 0.25 2.77 32 conservative 152391 17p13.1 arachidonate 12-lipoxygenase 953 rs434473 ALOX12 239 17 6845658 NM_000697 NP_000688 A/G N322S plus 16343724 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.37 0.39 0.1 446 6 0.28 0.02 1172 4 120 "HapMap,freq,cluster" Benign 0.274 24 Tolerant 0.25 2.77 32 conservative 152391 17p13.1 arachidonate 12-lipoxygenase 954 rs434473 ALOX12 239 17 6845658 NM_000697 NP_000688 A/G N322S plus 16343724 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.47 0.39 0.1 446 6 0.28 0.02 1172 4 120 "HapMap,freq,cluster" Benign 0.274 24 Tolerant 0.25 2.77 32 conservative 152391 17p13.1 arachidonate 12-lipoxygenase 955 rs434473 ALOX12 239 17 6845658 NM_000697 NP_000688 A/G N322S plus 16343724 1303 SEQUENOM CEPH CEPH (92) 92 0.23 0.39 0.1 446 6 0.28 0.02 1172 4 120 "HapMap,freq,cluster" Benign 0.274 24 Tolerant 0.25 2.77 32 conservative 152391 17p13.1 arachidonate 12-lipoxygenase 956 rs438287 AOC3 8639 17 38257835 NM_003734 NP_003725 A/G Y317H minus 5494071 1303 SEQUENOM CEPH CEPH (92) 92 0.28 0.28 0 92 1 123 by freq Probably damaging 2.092 15 Tolerant 0.8 2.82 27 moderately conservative 603735 17q21 "amine oxidase, copper containing 3 (vascular adhesion protein 1)" 957 rs438766 SIM1 6492 6 101003980 NM_005068 NP_005059 A/G L175F plus 3060752 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.44 0 92 1 96 by freq Potentially damaging 1.435 7 Borderline 0.18 2.76 123 conservative 603128 6q16.3-q21 single-minded homolog 1 (Drosophila) 958 rs443082 FCGR3A 2214 1 158327683 NM_000569 NP_000560 A/G G183D minus 591980 1303 SEQUENOM CEPH CEPH (92) 92 0.11 0.13 0.02 276 2 123 "by doubleHit,freq,cluster" Benign 0.409 23 Potentially intolerant 0.08 2.85 46 moderately conservative 146740 1q23 "Fc fragment of IgG, low affinity IIIa, receptor for (CD16)" 959 rs443082 FCGR3A 2214 1 158327683 NM_000569 NP_000560 A/G G183D minus 24820795 1303 SEQUENOM CEPH CEPH (92) 184 0.14 0.13 0.02 276 2 123 "by doubleHit,freq,cluster" Benign 0.409 23 Potentially intolerant 0.08 2.85 46 moderately conservative 146740 1q23 "Fc fragment of IgG, low affinity IIIa, receptor for (CD16)" 960 rs444772 RP1 6101 8 55701610 NM_006269 NP_006260 A/G R872H plus 594770 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.23 0.18 0.08 212 2 0.37 0 1486 1 123 "HapMap,submitter,freq,cluster" Benign 0.225 6 conservative 603937 8q11-q13 retinitis pigmentosa 1 (autosomal dominant) 961 rs444772 RP1 6101 8 55701610 NM_006269 NP_006260 A/G R872H plus 594770 1303 SEQUENOM CEPH CEPH (92) 92 0.12 0.18 0.08 212 2 0.37 0 1486 1 123 "HapMap,submitter,freq,cluster" Benign 0.225 6 conservative 603937 8q11-q13 retinitis pigmentosa 1 (autosomal dominant) 962 rs446227 RP1 6101 8 55704003 NM_006269 NP_006260 A/G A1670T plus 597189 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.23 0.2 0.08 260 3 0.27 0.3 92 2 123 "HapMap,submitter,freq" Benign 0.211 6 moderately conservative 603937 8q11-q13 retinitis pigmentosa 1 (autosomal dominant) 963 rs446227 RP1 6101 8 55704003 NM_006269 NP_006260 A/G A1670T plus 597189 1303 SEQUENOM CEPH CEPH (92) 92 0.12 0.2 0.08 260 3 0.27 0.3 92 2 123 "HapMap,submitter,freq" Benign 0.211 6 moderately conservative 603937 8q11-q13 retinitis pigmentosa 1 (autosomal dominant) 964 rs446227 RP1 6101 8 55704003 NM_006269 NP_006260 A/G A1670T plus 24077575 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.2 0.08 260 3 0.27 0.3 92 2 123 "HapMap,submitter,freq" Benign 0.211 6 moderately conservative 603937 8q11-q13 retinitis pigmentosa 1 (autosomal dominant) 965 rs448740 FCGR3A 2214 1 158331391 NM_000569 NP_000560 C/T S101N plus 5523031 1303 SEQUENOM CEPH CEPH (92) 92 0.31 0.31 0 92 1 108 "by doubleHit,freq,cluster" Benign 0.221 23 Tolerant 0.22 2.82 48 conservative 146740 1q23 "Fc fragment of IgG, low affinity IIIa, receptor for (CD16)" 966 rs450046 PRODH 5625 22 17275558 NM_016335 NP_057419 C/T R521Q plus 7993762 1303 SEQUENOM CEPH CEPH (92) 92 0.12 0.09 0.05 140 2 0.15 0.13 94 2 123 "by cluster,freq" Borderline 1.052 7 Tolerant 0.61 2.8 28 conservative 606810 22q11.21 proline dehydrogenase (oxidase) 1 967 rs450046 PRODH 5625 22 17275558 NM_016335 NP_057419 C/T R521Q plus 23788056 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.09 0.05 140 2 0.15 0.13 94 2 123 "by cluster,freq" Borderline 1.052 7 Tolerant 0.61 2.8 28 conservative 606810 22q11.21 proline dehydrogenase (oxidase) 1 968 rs451195 PPIC 5480 5 122387539 NM_000943 NP_000934 C/T N190S plus 605510 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 24 0.25 0.32 0.09 374 5 0.06 0.03 116 3 123 "HapMap,doubleHit,submitter,freq" Benign 0.044 71 Tolerant 0.45 2.75 291 conservative 123842 5q23.2 peptidylprolyl isomerase C (cyclophilin C) 969 rs451195 PPIC 5480 5 122387539 NM_000943 NP_000934 C/T N190S plus 605510 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 94 0.35 0.32 0.09 374 5 0.06 0.03 116 3 123 "HapMap,doubleHit,submitter,freq" Benign 0.044 71 Tolerant 0.45 2.75 291 conservative 123842 5q23.2 peptidylprolyl isomerase C (cyclophilin C) 970 rs451195 PPIC 5480 5 122387539 NM_000943 NP_000934 C/T N190S plus 605510 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.4 0.32 0.09 374 5 0.06 0.03 116 3 123 "HapMap,doubleHit,submitter,freq" Benign 0.044 71 Tolerant 0.45 2.75 291 conservative 123842 5q23.2 peptidylprolyl isomerase C (cyclophilin C) 971 rs451195 PPIC 5480 5 122387539 NM_000943 NP_000934 C/T N190S plus 605510 1303 SEQUENOM CEPH CEPH (92) 92 0.19 0.32 0.09 374 5 0.06 0.03 116 3 123 "HapMap,doubleHit,submitter,freq" Benign 0.044 71 Tolerant 0.45 2.75 291 conservative 123842 5q23.2 peptidylprolyl isomerase C (cyclophilin C) 972 rs451195 PPIC 5480 5 122387539 NM_000943 NP_000934 C/T N190S plus 24346271 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.32 0.09 374 5 0.06 0.03 116 3 123 "HapMap,doubleHit,submitter,freq" Benign 0.044 71 Tolerant 0.45 2.75 291 conservative 123842 5q23.2 peptidylprolyl isomerase C (cyclophilin C) 973 rs457947 ADAMTS5 11096 21 27260169 NM_007038 NP_008969 C/G G138A plus 2857357 1303 SEQUENOM CEPH CEPH (92) 92 0.11 0.11 0 92 1 100 by freq moderately conservative 605007 21q21.3 "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)" 974 rs458017 REV3L 5980 6 111802784 NM_002912 NP_002903 C/T Y1078C plus 617419 1303 SEQUENOM CEPH CEPH (92) 92 0.07 0.08 0.01 278 3 0.11 0 46 1 123 "by cluster,freq" radical 602776 6q21 "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)" 975 rs458017 REV3L 5980 6 111802784 NM_002912 NP_002903 C/T Y1078C plus 4479764 506 NCBI NIHPDR NIHPDR 138 0.08 0.08 0.01 278 3 0.11 0 46 1 123 "by cluster,freq" radical 602776 6q21 "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)" 976 rs458017 REV3L 5980 6 111802784 NM_002912 NP_002903 C/T Y1078C plus 23497123 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0.01 278 3 0.11 0 46 1 123 "by cluster,freq" radical 602776 6q21 "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)" 977 rs459102 U2AF1L1 7310 5 112256664 NM_005083 NP_005074 G/T Q477K minus 1998865 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.26 0 92 1 106 "by doubleHit,submitter,freq" moderately conservative 601079 5q22 U2(RNU2) small nuclear RNA auxillary factor 1-like 1 978 rs459552 APC 324 5 112204655 NM_000038 NP_000029 A/T V1822D minus 620343 1303 SEQUENOM CEPH CEPH (92) 92 0.14 0.13 0.05 188 3 0.12 0.07 94 2 123 "by doubleHit,submitter,freq,cluster" radical 175100 5q21-q22 adenomatosis polyposis coli 979 rs459552 APC 324 5 112204655 NM_000038 NP_000029 A/T V1822D minus 3177080 619 WICVAR MITOGPOP6 CORIELL Mixed 48 0.17 0.13 0.05 188 3 0.12 0.07 94 2 123 "by doubleHit,submitter,freq,cluster" radical 175100 5q21-q22 adenomatosis polyposis coli 980 rs459552 APC 324 5 112204655 NM_000038 NP_000029 A/T V1822D minus 23991403 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.13 0.05 188 3 0.12 0.07 94 2 123 "by doubleHit,submitter,freq,cluster" radical 175100 5q21-q22 adenomatosis polyposis coli 981 rs462779 REV3L 5980 6 111802580 NM_002912 NP_002903 C/T T1146I minus 626446 1303 SEQUENOM CEPH CEPH (92) 92 0.23 0.31 0.13 284 3 0.45 0.05 70 2 123 "by doubleHit,freq,cluster" moderately conservative 602776 6q21 "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)" 982 rs462779 REV3L 5980 6 111802580 NM_002912 NP_002903 C/T T1146I minus 4479749 506 NCBI NIHPDR NIHPDR 144 0.41 0.31 0.13 284 3 0.45 0.05 70 2 123 "by doubleHit,freq,cluster" moderately conservative 602776 6q21 "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)" 983 rs462779 REV3L 5980 6 111802580 NM_002912 NP_002903 C/T T1146I minus 24038973 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.31 0.13 284 3 0.45 0.05 70 2 123 "by doubleHit,freq,cluster" moderately conservative 602776 6q21 "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)" 984 rs470428 HP 3240 16 70652183 NM_005143 NP_005134 C/T T372A minus 757475 1303 SEQUENOM CEPH CEPH (92) 92 0.1 0.1 0 92 1 83 by freq Benign 0.039 34 Tolerant 1 2.81 50 moderately conservative 140100 16q22.1 haptoglobin 985 rs473267 PGM3 5238 6 83936886 NM_015599 NP_056414 C/T D466N plus 1383970 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.25 0.24 0.05 224 3 0.36 0.1 262 4 123 "by doubleHit,submitter,freq,cluster" Possibly damaging 1.614 9 Tolerant 0.48 2.78 20 conservative 172100 6q14.1-q15 phosphoglucomutase 3 986 rs473267 PGM3 5238 6 83936886 NM_015599 NP_056414 C/T D466N plus 1383970 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.24 0.05 224 3 0.36 0.1 262 4 123 "by doubleHit,submitter,freq,cluster" Possibly damaging 1.614 9 Tolerant 0.48 2.78 20 conservative 172100 6q14.1-q15 phosphoglucomutase 3 987 rs473267 PGM3 5238 6 83936886 NM_015599 NP_056414 C/T D466N plus 23404224 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.24 0.05 224 3 0.36 0.1 262 4 123 "by doubleHit,submitter,freq,cluster" Possibly damaging 1.614 9 Tolerant 0.48 2.78 20 conservative 172100 6q14.1-q15 phosphoglucomutase 3 988 rs475002 SNAPC2 6618 19 7892638 NM_003083 NP_003074 C/G L118V minus 644418 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.44 0.45 0.09 267 4 0.31 0.01 42 2 121 "HapMap,doubleHit,freq" conservative 605076 19p13.3-p13.2 "small nuclear RNA activating complex, polypeptide 2, 45kDa" 989 rs475002 SNAPC2 6618 19 7892638 NM_003083 NP_003074 C/G L118V minus 644418 1303 SEQUENOM CEPH CEPH (92) 92 0.48 0.45 0.09 267 4 0.31 0.01 42 2 121 "HapMap,doubleHit,freq" conservative 605076 19p13.3-p13.2 "small nuclear RNA activating complex, polypeptide 2, 45kDa" 990 rs475002 SNAPC2 6618 19 7892638 NM_003083 NP_003074 C/G L118V minus 980252 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.14 0.45 0.09 267 4 0.31 0.01 42 2 121 "HapMap,doubleHit,freq" conservative 605076 19p13.3-p13.2 "small nuclear RNA activating complex, polypeptide 2, 45kDa" 991 rs475002 SNAPC2 6618 19 7892638 NM_003083 NP_003074 C/G L118V minus 980252 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 45 0.5 0.45 0.09 267 4 0.31 0.01 42 2 121 "HapMap,doubleHit,freq" conservative 605076 19p13.3-p13.2 "small nuclear RNA activating complex, polypeptide 2, 45kDa" 992 rs477207 AOC3 8639 17 38261899 NM_003734 NP_003725 C/T G700S minus 646683 687 TSC-SANGER SC_12_CA CEPH Caucasians (12) 11 0.5 0.5 0 17 2 0.31 0.14 121 5 119 "by cluster,freq" Benign 0.318 14 Tolerant 0.47 2.82 27 moderately conservative 603735 17q21 "amine oxidase, copper containing 3 (vascular adhesion protein 1)" 993 rs477207 AOC3 8639 17 38261899 NM_003734 NP_003725 C/T G700S minus 646683 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 6 0.5 0.5 0 17 2 0.31 0.14 121 5 119 "by cluster,freq" Benign 0.318 14 Tolerant 0.47 2.82 27 moderately conservative 603735 17q21 "amine oxidase, copper containing 3 (vascular adhesion protein 1)" 994 rs479632 PITX1 5307 5 134392417 NM_002653 NP_002644 C/G G299A minus 649161 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.47 0 92 1 100 "by doubleHit,freq,cluster" Benign 0.333 40 moderately conservative 602149 5q31 paired-like homeodomain transcription factor 1 995 rs482912 LAMP3 27074 3 184336372 NM_014398 NP_055213 A/G I318V minus 652506 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 16 0.31 0.31 0.06 184 3 0.39 0.03 1616 5 123 "HapMap,doubleHit,freq,cluster" Tolerant 1 2.75 25 conservative 605883 3q26.3-q27 lysosomal-associated membrane protein 3 996 rs482912 LAMP3 27074 3 184336372 NM_014398 NP_055213 A/G I318V minus 652506 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.34 0.31 0.06 184 3 0.39 0.03 1616 5 123 "HapMap,doubleHit,freq,cluster" Tolerant 1 2.75 25 conservative 605883 3q26.3-q27 lysosomal-associated membrane protein 3 997 rs482912 LAMP3 27074 3 184336372 NM_014398 NP_055213 A/G I318V minus 23973747 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.31 0.06 184 3 0.39 0.03 1616 5 123 "HapMap,doubleHit,freq,cluster" Tolerant 1 2.75 25 conservative 605883 3q26.3-q27 lysosomal-associated membrane protein 3 998 rs486055 MMP10 4319 11 102155634 NM_002425 NP_002416 C/T R53K plus 655712 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 10 0.2 0.14 0.06 150 3 0.02 0 46 1 123 by freq Benign 0.463 26 Tolerant 1 2.83 57 conservative 185260 11q22.3 matrix metalloproteinase 10 (stromelysin 2) 999 rs486055 MMP10 4319 11 102155634 NM_002425 NP_002416 C/T R53K plus 655712 1303 SEQUENOM CEPH CEPH (92) 92 0.1 0.14 0.06 150 3 0.02 0 46 1 123 by freq Benign 0.463 26 Tolerant 1 2.83 57 conservative 185260 11q22.3 matrix metalloproteinase 10 (stromelysin 2) 1000 rs486055 MMP10 4319 11 102155634 NM_002425 NP_002416 C/T R53K plus 24531742 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.14 0.06 150 3 0.02 0 46 1 123 by freq Benign 0.463 26 Tolerant 1 2.83 57 conservative 185260 11q22.3 matrix metalloproteinase 10 (stromelysin 2) 1001 rs486907 RNASEL 6041 1 179286214 NM_021133 NP_066956 A/G R462Q minus 12675607 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.44 0.46 0.02 154 2 0.27 0.05 346 4 118 "by doubleHit,submitter,freq,cluster" Borderline 1.218 5 Tolerant 0.6 3.15 28 conservative 180435 1q25 "ribonuclease L (2',5'-oligoisoadenylate synthetase-dependent)" 1002 rs486907 RNASEL 6041 1 179286214 NM_021133 NP_066956 A/G R462Q minus 12675607 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.46 0.02 154 2 0.27 0.05 346 4 118 "by doubleHit,submitter,freq,cluster" Borderline 1.218 5 Tolerant 0.6 3.15 28 conservative 180435 1q25 "ribonuclease L (2',5'-oligoisoadenylate synthetase-dependent)" 1003 rs487989 POLA2 23649 11 64821266 NM_002689 NP_002680 A/G G583R plus 657678 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 24 0.13 0.09 0.02 236 3 0.13 0.08 40 2 111 "HapMap,doubleHit,freq" Borderline 1.186 8 Borderline 0.2 2.98 12 moderately radical 11q13.1 "polymerase (DNA-directed), alpha (70kD)" 1004 rs487989 POLA2 23649 11 64821266 NM_002689 NP_002680 A/G G583R plus 657678 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 94 0.07 0.09 0.02 236 3 0.13 0.08 40 2 111 "HapMap,doubleHit,freq" Borderline 1.186 8 Borderline 0.2 2.98 12 moderately radical 11q13.1 "polymerase (DNA-directed), alpha (70kD)" 1005 rs487989 POLA2 23649 11 64821266 NM_002689 NP_002680 A/G G583R plus 5350029 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.1 0.09 0.02 236 3 0.13 0.08 40 2 111 "HapMap,doubleHit,freq" Borderline 1.186 8 Borderline 0.2 2.98 12 moderately radical 11q13.1 "polymerase (DNA-directed), alpha (70kD)" 1006 rs500079 PPP1R15A 23645 19 54070806 NM_014330 NP_055145 C/T T597A minus 2132902 1303 SEQUENOM CEPH CEPH (92) 92 0.17 0.2 0.05 140 2 0.32 0.16 94 2 123 "by doubleHit,freq,cluster" moderately conservative 19q13.2 "protein phosphatase 1, regulatory (inhibitor) subunit 15A" 1007 rs500079 PPP1R15A 23645 19 54070806 NM_014330 NP_055145 C/T T597A minus 23812937 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.2 0.05 140 2 0.32 0.16 94 2 123 "by doubleHit,freq,cluster" moderately conservative 19q13.2 "protein phosphatase 1, regulatory (inhibitor) subunit 15A" 1008 rs504122 SPRY2 10253 13 79809526 NM_005842 NP_005833 C/T P106S minus 674139 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 5 0.5 0.22 0.15 469 6 0.23 0.23 114 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.913 9 Borderline 0.15 2.94 24 moderately conservative 602466 13q22.2 sprouty homolog 2 (Drosophila) 1009 rs504122 SPRY2 10253 13 79809526 NM_005842 NP_005833 C/T P106S minus 674139 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 94 0.35 0.22 0.15 469 6 0.23 0.23 114 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.913 9 Borderline 0.15 2.94 24 moderately conservative 602466 13q22.2 sprouty homolog 2 (Drosophila) 1010 rs504122 SPRY2 10253 13 79809526 NM_005842 NP_005833 C/T P106S minus 674139 1303 SEQUENOM CEPH CEPH (92) 92 0.36 0.22 0.15 469 6 0.23 0.23 114 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.913 9 Borderline 0.15 2.94 24 moderately conservative 602466 13q22.2 sprouty homolog 2 (Drosophila) 1011 rs504122 SPRY2 10253 13 79809526 NM_005842 NP_005833 C/T P106S minus 3177960 619 WICVAR MITOGPOP6 CORIELL Mixed 46 0.28 0.22 0.15 469 6 0.23 0.23 114 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.913 9 Borderline 0.15 2.94 24 moderately conservative 602466 13q22.2 sprouty homolog 2 (Drosophila) 1012 rs504122 SPRY2 10253 13 79809526 NM_005842 NP_005833 C/T P106S minus 23975354 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.22 0.15 469 6 0.23 0.23 114 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.913 9 Borderline 0.15 2.94 24 moderately conservative 602466 13q22.2 sprouty homolog 2 (Drosophila) 1013 rs504122 SPRY2 10253 13 79809526 NM_005842 NP_005833 C/T P106S minus 24811651 1303 SEQUENOM CEPH CEPH (92) 184 0.06 0.22 0.15 469 6 0.23 0.23 114 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.913 9 Borderline 0.15 2.94 24 moderately conservative 602466 13q22.2 sprouty homolog 2 (Drosophila) 1014 rs506504 CHEK1 1111 11 125030405 NM_001274 NP_001265 C/T I471V minus 12675356 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.06 0.07 0.01 110 2 0.03 0.02 346 4 123 "by doubleHit,freq,cluster" Benign 0.088 10 conservative 603078 11q24-q24 CHK1 checkpoint homolog (S. pombe) 1015 rs506504 CHEK1 1111 11 125030405 NM_001274 NP_001265 C/T I471V minus 24363886 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.07 0.01 110 2 0.03 0.02 346 4 123 "by doubleHit,freq,cluster" Benign 0.088 10 conservative 603078 11q24-q24 CHK1 checkpoint homolog (S. pombe) 1016 rs507879 CASP5 838 11 104383137 NM_004347 NP_004338 A/G T90A minus 677961 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.43 0.45 0.04 192 4 0.25 0.03 1132 3 123 "by doubleHit,freq,cluster" moderately conservative 602665 11q22.2-q22.3 "caspase 5, apoptosis-related cysteine protease" 1017 rs507879 CASP5 838 11 104383137 NM_004347 NP_004338 A/G T90A minus 677961 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 92 0.45 0.45 0.04 192 4 0.25 0.03 1132 3 123 "by doubleHit,freq,cluster" moderately conservative 602665 11q22.2-q22.3 "caspase 5, apoptosis-related cysteine protease" 1018 rs507879 CASP5 838 11 104383137 NM_004347 NP_004338 A/G T90A minus 2832698 1303 SEQUENOM CEPH CEPH (92) 46 0.5 0.45 0.04 192 4 0.25 0.03 1132 3 123 "by doubleHit,freq,cluster" moderately conservative 602665 11q22.2-q22.3 "caspase 5, apoptosis-related cysteine protease" 1019 rs507879 CASP5 838 11 104383137 NM_004347 NP_004338 A/G T90A minus 4403105 649 FHCRC POPU1 USA (20) 40 0.4 0.45 0.04 192 4 0.25 0.03 1132 3 123 "by doubleHit,freq,cluster" moderately conservative 602665 11q22.2-q22.3 "caspase 5, apoptosis-related cysteine protease" 1020 rs508405 CAPN13 92291 2 30892591 NM_144575 NP_653176 A/G A280T minus 24636906 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.33 0 48 1 0.12 0.07 94 2 123 "by submitter,freq,cluster" Potentially intolerant 0.06 3.03 62 moderately conservative 2p22-p21 calpain 13 1021 rs523104 CASP5 838 11 104374918 NM_004347 NP_004338 C/G L318V plus 16124289 1303 SEQUENOM CEPH CEPH (92) 92 0.36 0.39 0.07 140 2 0.31 0.04 92 2 123 "by doubleHit,freq,cluster" Benign 0.088 10 conservative 602665 11q22.2-q22.3 "caspase 5, apoptosis-related cysteine protease" 1022 rs523104 CASP5 838 11 104374918 NM_004347 NP_004338 C/G L318V plus 24610835 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.39 0.07 140 2 0.31 0.04 92 2 123 "by doubleHit,freq,cluster" Benign 0.088 10 conservative 602665 11q22.2-q22.3 "caspase 5, apoptosis-related cysteine protease" 1023 rs527221 DMPK 1760 19 50967816 NM_004409 NP_004400 C/G L423V plus 24109680 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.15 0.15 0 46 1 0.11 0.1 88 2 123 "by cluster,freq" Benign 0.058 17 Tolerant 0.51 2.8 48 conservative 605377 19q13.3 dystrophia myotonica-protein kinase 1024 rs532648 FOXN1 8456 17 23888429 NM_003593 NP_003584 C/G A599P minus 703214 1303 SEQUENOM CEPH CEPH (92) 92 0.27 0.27 0 92 1 0.23 0 1496 1 108 "by doubleHit,freq,cluster" conservative 600838 17q11-q12 forkhead box N1 1025 rs532964 DMGDH 29958 5 78376042 NM_013391 NP_037523 C/T S279P minus 24413460 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.44 0 48 1 0.28 0.02 94 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.739 7 Tolerant 1 2.79 17 moderately conservative 605849 5q14.1 dimethylglycine dehydrogenase 1026 rs533617 APOB 338 2 21145624 NM_000384 NP_000375 C/T H1923R plus 704195 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.02 0.04 0.02 260 3 123 "HapMap,submitter,freq" conservative 107730 2p24-p23 apolipoprotein B (including Ag(x) antigen) 1027 rs533617 APOB 338 2 21145624 NM_000384 NP_000375 C/T H1923R plus 704195 1303 SEQUENOM CEPH CEPH (92) 92 0.06 0.04 0.02 260 3 123 "HapMap,submitter,freq" conservative 107730 2p24-p23 apolipoprotein B (including Ag(x) antigen) 1028 rs533617 APOB 338 2 21145624 NM_000384 NP_000375 C/T H1923R plus 24242187 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0.02 260 3 123 "HapMap,submitter,freq" conservative 107730 2p24-p23 apolipoprotein B (including Ag(x) antigen) 1029 rs542998 RTN3 10313 11 63243962 NM_201428 NP_958831 C/T V452A plus 5561507 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.18 0.19 0.03 168 2 0.43 0 46 1 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 604249 11q13 reticulon 3 1030 rs542998 RTN3 10313 11 63243962 NM_201428 NP_958831 C/T V452A plus 23743402 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.19 0.03 168 2 0.43 0 46 1 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 604249 11q13 reticulon 3 1031 rs543355 LAMA1 284217 18 6948609 NM_005559 NP_005550 C/T T2611A plus 714130 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.01 0.01 140 2 0.2 0.26 94 2 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.46 2.77 13 moderately conservative 150320 18p11.23 "laminin, alpha 1" 1032 rs543355 LAMA1 284217 18 6948609 NM_005559 NP_005550 C/T T2611A plus 23585775 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.01 0.01 140 2 0.2 0.26 94 2 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.46 2.77 13 moderately conservative 150320 18p11.23 "laminin, alpha 1" 1033 rs543573 KIAA0625 23064 9 132232383 NM_015046 NP_055861 C/T I1386V plus 714352 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.1 0.12 0.04 168 2 0.27 0.02 1596 3 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 608465 9q34.3 senataxin 1034 rs543573 KIAA0625 23064 9 132232383 NM_015046 NP_055861 C/T I1386V plus 23435974 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.12 0.04 168 2 0.27 0.02 1596 3 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 608465 9q34.3 senataxin 1035 rs544641 ZBTB3 79842 11 62276141 NM_024784 NP_079060 C/G I574M minus 12161398 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.02 0.03 0.01 166 2 0.16 0.08 160 5 123 "HapMap,doubleHit,freq,cluster" conservative 11q12.3 zinc finger and BTB domain containing 3 1036 rs544641 ZBTB3 79842 11 62276141 NM_024784 NP_079060 C/G I574M minus 24183476 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.04 0.03 0.01 166 2 0.16 0.08 160 5 123 "HapMap,doubleHit,freq,cluster" conservative 11q12.3 zinc finger and BTB domain containing 3 1037 rs550252 TCEB3 6924 1 23824246 NM_003198 NP_003189 C/T A490V plus 721179 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.04 0 92 1 119 by freq Borderline 1.097 8 moderately conservative 600786 1p36.1 "transcription elongation factor B (SIII), polypeptide 3 (110kDa, elongin A)" 1038 rs553717 GPC5 2262 13 91143580 NM_004466 NP_004457 A/G A155V minus 724691 1303 SEQUENOM CEPH CEPH (92) 92 0.17 0.17 0 92 1 0.06 0.04 94 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.937 5 Potentially intolerant 0.1 2.78 29 moderately conservative 602446 13q32 glypican 5 1039 rs554202 MOGAT2 80168 11 75106606 NM_025098 NP_079374 A/G M9V plus 1814968 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.37 0.4 0.07 166 2 0.21 0.04 1559 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.385 10 Tolerant 0.61 2.91 21 conservative 11q13.3 monoacylglycerol O-acyltransferase 2 1040 rs554202 MOGAT2 80168 11 75106606 NM_025098 NP_079374 A/G M9V plus 23681355 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.4 0.07 166 2 0.21 0.04 1559 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.385 10 Tolerant 0.61 2.91 21 conservative 11q13.3 monoacylglycerol O-acyltransferase 2 1041 rs554971 IL28A 282616 19 44451175 NM_172138 NP_742150 A/G T10M minus 725976 1303 SEQUENOM CEPH CEPH (92) 92 0.38 0.38 0 92 1 103 by freq moderately conservative 607401 19q13.13 "interleukin 28A (interferon, lambda 2)" 1042 rs556052 PPP1R15A 23645 19 54069248 NM_014330 NP_055145 C/G A316P minus 727083 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.3 0.3 0 118 1 0.13 0 1490 1 120 "HapMap,doubleHit,freq,cluster" conservative 19q13.2 "protein phosphatase 1, regulatory (inhibitor) subunit 15A" 1043 rs557806 PPP1R15A 23645 19 54069054 NM_014330 NP_055145 C/G R251P minus 728867 1303 SEQUENOM CEPH CEPH (92) 92 0.29 0.29 0 92 1 120 "by doubleHit,freq,cluster" Tolerant 0.28 3.14 12 moderately radical 19q13.2 "protein phosphatase 1, regulatory (inhibitor) subunit 15A" 1044 rs558614 LATS2 26524 13 20460948 NM_014572 NP_055387 C/T A324V minus 729690 1303 SEQUENOM CEPH CEPH (92) 92 0.09 0.09 0 92 1 121 "by doubleHit,freq,cluster" Benign 0.45 5 moderately conservative 604861 13q11-q12 "LATS, large tumor suppressor, homolog 2 (Drosophila)" 1045 rs560096 IGHMBP2 3508 11 68435538 NM_002180 NP_002171 C/T L201S plus 76795 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 82 0.07 0.18 0.12 486 8 0.44 0.05 1840 10 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.773 5 moderately radical 600502 11q13.2-q13.4 immunoglobulin mu binding protein 2 1046 rs560096 IGHMBP2 3508 11 68435538 NM_002180 NP_002171 C/T L201S plus 76795 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 22 0.23 0.18 0.12 486 8 0.44 0.05 1840 10 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.773 5 moderately radical 600502 11q13.2-q13.4 immunoglobulin mu binding protein 2 1047 rs560096 IGHMBP2 3508 11 68435538 NM_002180 NP_002171 C/T L201S plus 76795 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 86 0.13 0.18 0.12 486 8 0.44 0.05 1840 10 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.773 5 moderately radical 600502 11q13.2-q13.4 immunoglobulin mu binding protein 2 1048 rs560096 IGHMBP2 3508 11 68435538 NM_002180 NP_002171 C/T L201S plus 76795 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.13 0.18 0.12 486 8 0.44 0.05 1840 10 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.773 5 moderately radical 600502 11q13.2-q13.4 immunoglobulin mu binding protein 2 1049 rs560096 IGHMBP2 3508 11 68435538 NM_002180 NP_002171 C/T L201S plus 76795 902 AFFY Caucasian 24 0.04 0.18 0.12 486 8 0.44 0.05 1840 10 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.773 5 moderately radical 600502 11q13.2-q13.4 immunoglobulin mu binding protein 2 1050 rs560096 IGHMBP2 3508 11 68435538 NM_002180 NP_002171 C/T L201S plus 76795 904 AFFY CEPH 12 0.25 0.18 0.12 486 8 0.44 0.05 1840 10 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.773 5 moderately radical 600502 11q13.2-q13.4 immunoglobulin mu binding protein 2 1051 rs560096 IGHMBP2 3508 11 68435538 NM_002180 NP_002171 C/T L201S plus 76795 1303 SEQUENOM CEPH CEPH (92) 92 0.39 0.18 0.12 486 8 0.44 0.05 1840 10 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.773 5 moderately radical 600502 11q13.2-q13.4 immunoglobulin mu binding protein 2 1052 rs560096 IGHMBP2 3508 11 68435538 NM_002180 NP_002171 C/T L201S plus 24102663 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.18 0.12 486 8 0.44 0.05 1840 10 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.773 5 moderately radical 600502 11q13.2-q13.4 immunoglobulin mu binding protein 2 1053 rs560191 TP53BP1 7158 15 41555066 NM_005657 NP_005648 C/G D353E plus 731297 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 6 0.5 0.37 0.07 266 4 0.26 0.18 136 4 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 1 3.04 12 conservative 605230 15q15-q21 "tumor protein p53 binding protein, 1" 1054 rs560191 TP53BP1 7158 15 41555066 NM_005657 NP_005648 C/G D353E plus 14391011 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.31 0.37 0.07 266 4 0.26 0.18 136 4 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 1 3.04 12 conservative 605230 15q15-q21 "tumor protein p53 binding protein, 1" 1055 rs560191 TP53BP1 7158 15 41555066 NM_005657 NP_005648 C/G D353E plus 14391011 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.37 0.07 266 4 0.26 0.18 136 4 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 1 3.04 12 conservative 605230 15q15-q21 "tumor protein p53 binding protein, 1" 1056 rs560191 TP53BP1 7158 15 41555066 NM_005657 NP_005648 C/G D353E plus 23963802 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.37 0.07 266 4 0.26 0.18 136 4 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 1 3.04 12 conservative 605230 15q15-q21 "tumor protein p53 binding protein, 1" 1057 rs562047 HSPA1A 3303 6 31891842 NM_005345 NP_005336 C/G E110D minus 3172585 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 52 0.04 0.06 0.01 236 2 123 "by doubleHit,freq,cluster" Benign 0.967 479 conservative 140550 6p21.3 heat shock 70kDa protein 1A 1058 rs562047 HSPA1A 3303 6 31891842 NM_005345 NP_005336 C/G E110D minus 24811755 1303 SEQUENOM CEPH CEPH (92) 184 0.06 0.06 0.01 236 2 123 "by doubleHit,freq,cluster" Benign 0.967 479 conservative 140550 6p21.3 heat shock 70kDa protein 1A 1059 rs564196 PPP1R15A 23645 19 54068394 NM_014330 NP_055145 C/T R31H minus 735374 1303 SEQUENOM CEPH CEPH (92) 92 0.46 0.46 0 92 1 120 "by doubleHit,freq,cluster" conservative 19q13.2 "protein phosphatase 1, regulatory (inhibitor) subunit 15A" 1060 rs566655 LAMA1 284217 18 7024508 NM_005559 NP_005550 A/C N674T minus 24554442 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.25 0 48 1 0.19 0.06 94 2 123 "by doubleHit,submitter,freq,cluster" Tolerant 1 2.85 10 moderately conservative 150320 18p11.23 "laminin, alpha 1" 1061 rs567083 MAK 4117 6 10883586 NM_005906 NP_005897 A/G P520S plus 738322 1303 SEQUENOM CEPH CEPH (92) 92 0.05 0.03 0.02 258 4 123 by freq Benign 0.546 14 moderately conservative 154235 6q22 male germ cell-associated kinase 1062 rs567083 MAK 4117 6 10883586 NM_005906 NP_005897 A/G P520S plus 2445066 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 24 0.04 0.03 0.02 258 4 123 by freq Benign 0.546 14 moderately conservative 154235 6q22 male germ cell-associated kinase 1063 rs567083 MAK 4117 6 10883586 NM_005906 NP_005897 A/G P520S plus 2445066 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 94 0.02 0.03 0.02 258 4 123 by freq Benign 0.546 14 moderately conservative 154235 6q22 male germ cell-associated kinase 1064 rs567083 MAK 4117 6 10883586 NM_005906 NP_005897 A/G P520S plus 24373650 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.03 0.02 258 4 123 by freq Benign 0.546 14 moderately conservative 154235 6q22 male germ cell-associated kinase 1065 rs569108 MS4A2 2206 11 59619680 NM_000139 NP_000130 C/T E237G minus 2390014 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.01 0 92 1 0.17 0 1092 1 100 "by cluster,freq" Probably damaging 2.009 6 moderately conservative 147138 11q13 "membrane-spanning 4-domains, subfamily A, member 2 (Fc fragment of IgE, high affinity I, receptor for; beta polypeptide)" 1066 rs573212 FBP2 8789 9 94429221 NM_003837 NP_003828 C/G V86L plus 16336543 902 AFFY Caucasian 22 0.09 0.15 0.04 80 3 0.13 0.11 150 4 123 "by submitter,freq,cluster" Borderline 1.205 53 Tolerant 1 2.79 82 conservative 603027 9q22.3 "fructose-1,6-bisphosphatase 2" 1067 rs573212 FBP2 8789 9 94429221 NM_003837 NP_003828 C/G V86L plus 16336543 904 AFFY CEPH 12 0.17 0.15 0.04 80 3 0.13 0.11 150 4 123 "by submitter,freq,cluster" Borderline 1.205 53 Tolerant 1 2.79 82 conservative 603027 9q22.3 "fructose-1,6-bisphosphatase 2" 1068 rs573212 FBP2 8789 9 94429221 NM_003837 NP_003828 C/G V86L plus 24071709 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.17 0.15 0.04 80 3 0.13 0.11 150 4 123 "by submitter,freq,cluster" Borderline 1.205 53 Tolerant 1 2.79 82 conservative 603027 9q22.3 "fructose-1,6-bisphosphatase 2" 1069 rs578430 MUSK 4593 9 110642698 NM_005592 NP_005583 G/T V829L plus 749904 1303 SEQUENOM CEPH CEPH (92) 92 0.07 0.07 0 92 1 123 by freq Benign 0.675 5 Tolerant 0.37 2.81 27 conservative 601296 9q31.3-q32 "muscle, skeletal, receptor tyrosine kinase" 1070 rs581157 IREM2 342510 17 70125184 NM_181449 NP_852114 G/T K19T plus 752704 885 TSC-CSHL HapMap-CEPH-30-trios 112 0.42 0.44 0.04 160 2 0.38 0.01 94 2 123 "HapMap,doubleHit,freq,cluster" moderately conservative 17q25.2 immune receptor expressed on myeloid cells 2 1071 rs581157 IREM2 342510 17 70125184 NM_181449 NP_852114 G/T K19T plus 24558713 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.44 0.04 160 2 0.38 0.01 94 2 123 "HapMap,doubleHit,freq,cluster" moderately conservative 17q25.2 immune receptor expressed on myeloid cells 2 1072 rs584367 PLA2G2D 26279 1 20187360 NM_012400 NP_036532 C/T S80G plus 1958114 1303 SEQUENOM CEPH CEPH (92) 92 0.22 0.3 0.16 140 2 0.3 0.05 1588 3 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.37 2.8 179 moderately conservative 605630 1p36.12 "phospholipase A2, group IID" 1073 rs584367 PLA2G2D 26279 1 20187360 NM_012400 NP_036532 C/T S80G plus 24236283 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.3 0.16 140 2 0.3 0.05 1588 3 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.37 2.8 179 moderately conservative 605630 1p36.12 "phospholipase A2, group IID" 1074 rs589623 DNCH2 79659 11 102587800 XM_370652 XP_370652 C/T R2871Q minus 23560235 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.23 0 48 1 0.25 0.11 94 2 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.39 2.79 14 conservative 603297 11q21-q22.1 "dynein, cytoplasmic, heavy polypeptide 2" 1075 rs593818 CYP4F12 66002 19 15668884 NM_023944 NP_076433 A/G S522G plus 765638 1303 SEQUENOM CEPH CEPH (92) 92 0.49 0.44 0.09 140 2 0.36 0.13 94 2 123 "by doubleHit,freq,cluster" Benign 0.388 20 moderately conservative 19p13.1 "cytochrome P450, family 4, subfamily F, polypeptide 12" 1076 rs593818 CYP4F12 66002 19 15668884 NM_023944 NP_076433 A/G S522G plus 23580674 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.44 0.09 140 2 0.36 0.13 94 2 123 "by doubleHit,freq,cluster" Benign 0.388 20 moderately conservative 19p13.1 "cytochrome P450, family 4, subfamily F, polypeptide 12" 1077 rs597570 FEZ1 9638 11 124856682 NM_005103 NP_005094 A/T D123E minus 769458 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 10 0.2 0.22 0.08 358 5 0.1 0.03 1618 5 123 "HapMap,doubleHit,submitter,freq,cluster" Borderline 0.12 3.05 21 conservative 604825 11q24.2 fasciculation and elongation protein zeta 1 (zygin I) 1078 rs597570 FEZ1 9638 11 124856682 NM_005103 NP_005094 A/T D123E minus 769458 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 92 0.16 0.22 0.08 358 5 0.1 0.03 1618 5 123 "HapMap,doubleHit,submitter,freq,cluster" Borderline 0.12 3.05 21 conservative 604825 11q24.2 fasciculation and elongation protein zeta 1 (zygin I) 1079 rs597570 FEZ1 9638 11 124856682 NM_005103 NP_005094 A/T D123E minus 769458 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.17 0.22 0.08 358 5 0.1 0.03 1618 5 123 "HapMap,doubleHit,submitter,freq,cluster" Borderline 0.12 3.05 21 conservative 604825 11q24.2 fasciculation and elongation protein zeta 1 (zygin I) 1080 rs597570 FEZ1 9638 11 124856682 NM_005103 NP_005094 A/T D123E minus 16510765 1303 SEQUENOM CEPH CEPH (92) 92 0.34 0.22 0.08 358 5 0.1 0.03 1618 5 123 "HapMap,doubleHit,submitter,freq,cluster" Borderline 0.12 3.05 21 conservative 604825 11q24.2 fasciculation and elongation protein zeta 1 (zygin I) 1081 rs597570 FEZ1 9638 11 124856682 NM_005103 NP_005094 A/T D123E minus 23641456 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.2 0.22 0.08 358 5 0.1 0.03 1618 5 123 "HapMap,doubleHit,submitter,freq,cluster" Borderline 0.12 3.05 21 conservative 604825 11q24.2 fasciculation and elongation protein zeta 1 (zygin I) 1082 rs602990 VAV2 7410 9 133673548 NM_003371 NP_003362 C/T M584V plus 2835292 1303 SEQUENOM CEPH CEPH (92) 92 0.49 0.49 0 92 1 119 "by doubleHit,freq" Borderline 1.062 17 Tolerant 1 3.25 23 conservative 600428 9q34.1 vav 2 oncogene 1083 rs605059 HSD17B1 3292 17 37960432 NM_000413 NP_000404 C/T G313S minus 777110 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.43 0.29 0.05 162 3 0.36 0.04 48 2 121 "by doubleHit,freq,cluster" moderately conservative 109684 17q11-q21 hydroxysteroid (17-beta) dehydrogenase 1 1084 rs605059 HSD17B1 3292 17 37960432 NM_000413 NP_000404 C/T G313S minus 3176234 619 WICVAR MITOGPOP6 CORIELL Mixed 56 0.29 0.29 0.05 162 3 0.36 0.04 48 2 121 "by doubleHit,freq,cluster" moderately conservative 109684 17q11-q21 hydroxysteroid (17-beta) dehydrogenase 1 1085 rs605059 HSD17B1 3292 17 37960432 NM_000413 NP_000404 C/T G313S minus 16745938 1303 SEQUENOM CEPH CEPH (92) 92 0.27 0.29 0.05 162 3 0.36 0.04 48 2 121 "by doubleHit,freq,cluster" moderately conservative 109684 17q11-q21 hydroxysteroid (17-beta) dehydrogenase 1 1086 rs607230 LAMA1 284217 18 6970523 NM_005559 NP_005550 C/T K2002E plus 779323 1303 SEQUENOM CEPH CEPH (92) 92 0.37 0.37 0 92 1 121 "by doubleHit,freq,cluster" Borderline 0.19 2.76 13 moderately conservative 150320 18p11.23 "laminin, alpha 1" 1087 rs607567 MICL 160364 12 10022951 NM_201625 NP_963919 A/C C71G minus 23786563 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.25 0 48 1 0.17 0.18 94 2 123 "by doubleHit,submitter,freq,cluster" radical 12p13.31 myeloid inhibitory C-type lectin-like receptor 1088 rs608433 ZNF236 7776 18 72740115 NM_007345 NP_031371 C/T I613V minus 780552 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.03 0.07 0.04 260 3 0.1 0 48 1 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 604760 18q22-q23 zinc finger protein 236 1089 rs608433 ZNF236 7776 18 72740115 NM_007345 NP_031371 C/T I613V minus 780552 1303 SEQUENOM CEPH CEPH (92) 92 0.11 0.07 0.04 260 3 0.1 0 48 1 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 604760 18q22-q23 zinc finger protein 236 1090 rs608433 ZNF236 7776 18 72740115 NM_007345 NP_031371 C/T I613V minus 24107976 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.07 0.04 260 3 0.1 0 48 1 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 604760 18q22-q23 zinc finger protein 236 1091 rs608620 PCSK7 9159 11 116582219 NM_004716 NP_004707 G/T L688V minus 4079307 1303 SEQUENOM CEPH CEPH (92) 92 0.33 0.33 0 92 1 113 "by doubleHit,freq" conservative 604872 11q23-q24 proprotein convertase subtilisin/kexin type 7 1092 rs609290 CYP4F12 66002 19 15650140 NM_023944 NP_076433 C/T I90V minus 781430 1303 SEQUENOM CEPH CEPH (92) 92 0.09 0.09 0 92 1 83 by freq Benign 0.134 40 conservative 19p13.1 "cytochrome P450, family 4, subfamily F, polypeptide 12" 1093 rs609636 CYP4F12 66002 19 15650098 NM_023944 NP_076433 C/T N76D minus 781784 1303 SEQUENOM CEPH CEPH (92) 92 0.11 0.11 0 92 1 83 by freq Benign 0.358 40 conservative 19p13.1 "cytochrome P450, family 4, subfamily F, polypeptide 12" 1094 rs610308 PPP1R15A 23645 19 54069131 NM_014330 NP_055145 C/T K277E minus 782465 1303 SEQUENOM CEPH CEPH (92) 92 0.22 0.22 0 92 1 0.12 0 1282 1 120 "by doubleHit,freq,cluster" moderately conservative 19q13.2 "protein phosphatase 1, regulatory (inhibitor) subunit 15A" 1095 rs611251 PPP1R15A 23645 19 54068898 NM_014330 NP_055145 A/G V199A minus 5163966 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.16 0 92 1 0.07 0 738 1 120 "by doubleHit,freq,cluster" moderately conservative 19q13.2 "protein phosphatase 1, regulatory (inhibitor) subunit 15A" 1096 rs615942 COASY 80347 17 37968330 NM_025233 NP_079509 G/T S55Y minus 2909636 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.39 0.37 0.05 254 3 0.46 0.04 1578 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.461 7 moderately radical 17q12-q21 Coenzyme A synthase 1097 rs615942 COASY 80347 17 37968330 NM_025233 NP_079509 G/T S55Y minus 2909636 1303 SEQUENOM CEPH CEPH (92) 92 0.32 0.37 0.05 254 3 0.46 0.04 1578 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.461 7 moderately radical 17q12-q21 Coenzyme A synthase 1098 rs615942 COASY 80347 17 37968330 NM_025233 NP_079509 G/T S55Y minus 24587840 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.41 0.37 0.05 254 3 0.46 0.04 1578 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.461 7 moderately radical 17q12-q21 Coenzyme A synthase 1099 rs616114 MEP1B 4225 18 28051919 NM_005925 NP_005916 A/G P695L minus 788399 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.38 0.4 0.04 168 2 0.32 0.01 1580 3 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.917 5 moderately conservative 600389 18q12.2-q12.3 "meprin A, beta" 1100 rs616114 MEP1B 4225 18 28051919 NM_005925 NP_005916 A/G P695L minus 24687373 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.4 0.04 168 2 0.32 0.01 1580 3 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.917 5 moderately conservative 600389 18q12.2-q12.3 "meprin A, beta" 1101 rs619203 ROS1 6098 6 117728877 NM_002944 NP_002935 C/G S2229C minus 791558 1303 SEQUENOM CEPH CEPH (92) 92 0.19 0.19 0 134 2 0.16 0.04 94 2 123 "by doubleHit,freq,cluster" Probably damaging 2.424 5 Tolerant 0.24 3.24 56 moderately radical 165020 6q22 v-ros UR2 sarcoma virus oncogene homolog 1 (avian) 1102 rs619203 ROS1 6098 6 117728877 NM_002944 NP_002935 C/G S2229C minus 24370589 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.19 0.19 0 134 2 0.16 0.04 94 2 123 "by doubleHit,freq,cluster" Probably damaging 2.424 5 Tolerant 0.24 3.24 56 moderately radical 165020 6q22 v-ros UR2 sarcoma virus oncogene homolog 1 (avian) 1103 rs622082 IGHMBP2 3508 11 68460535 NM_002180 NP_002171 A/G T671A plus 3172863 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 54 0.3 0.3 0 54 1 0.21 0 1498 1 120 "by doubleHit,freq,cluster" Borderline 1.238 5 moderately conservative 600502 11q13.2-q13.4 immunoglobulin mu binding protein 2 1104 rs627441 DLAT 1737 11 111413372 NM_001931 NP_001922 A/G V318A minus 799946 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.26 0.31 0.08 212 2 120 "HapMap,doubleHit,submitter,freq" Benign 0.096 17 Tolerant 1 2.82 44 moderately conservative 608770 11q23.1 dihydrolipoamide S-acetyltransferase (E2 component of pyruvate dehydrogenase complex) 1105 rs627441 DLAT 1737 11 111413372 NM_001931 NP_001922 A/G V318A minus 799946 1303 SEQUENOM CEPH CEPH (92) 92 0.38 0.31 0.08 212 2 120 "HapMap,doubleHit,submitter,freq" Benign 0.096 17 Tolerant 1 2.82 44 moderately conservative 608770 11q23.1 dihydrolipoamide S-acetyltransferase (E2 component of pyruvate dehydrogenase complex) 1106 rs627928 RNASEL 6041 1 179282994 NM_021133 NP_066956 G/T D541E minus 19095328 1303 SEQUENOM CEPH CEPH (92) 92 0.4 0.4 0 92 1 121 "by doubleHit,submitter,freq,cluster" Borderline 1.098 5 Tolerant 0.63 3.15 30 conservative 180435 1q25 "ribonuclease L (2',5'-oligoisoadenylate synthetase-dependent)" 1107 rs629682 AOC3 8639 17 38257563 NM_003734 NP_003725 C/T W226X minus 802226 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 83 0.4 0.4 0 83 1 0.39 0.05 166 2 108 HapMap Probably damaging Intolerant radical 603735 17q21 "amine oxidase, copper containing 3 (vascular adhesion protein 1)" 1108 rs629849 IGF2R 3482 6 160464820 NM_000876 NP_000867 A/G R1619G plus 802398 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 86 0.06 0.13 0.05 522 5 0.17 0.03 1864 7 123 "by doubleHit,freq,cluster" Benign 0.565 17 moderately radical 147280 6q26 insulin-like growth factor 2 receptor 1109 rs629849 IGF2R 3482 6 160464820 NM_000876 NP_000867 A/G R1619G plus 959503 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.14 0.13 0.05 522 5 0.17 0.03 1864 7 123 "by doubleHit,freq,cluster" Benign 0.565 17 moderately radical 147280 6q26 insulin-like growth factor 2 receptor 1110 rs629849 IGF2R 3482 6 160464820 NM_000876 NP_000867 A/G R1619G plus 959503 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 182 0.16 0.13 0.05 522 5 0.17 0.03 1864 7 123 "by doubleHit,freq,cluster" Benign 0.565 17 moderately radical 147280 6q26 insulin-like growth factor 2 receptor 1111 rs629849 IGF2R 3482 6 160464820 NM_000876 NP_000867 A/G R1619G plus 8819763 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.2 0.13 0.05 522 5 0.17 0.03 1864 7 123 "by doubleHit,freq,cluster" Benign 0.565 17 moderately radical 147280 6q26 insulin-like growth factor 2 receptor 1112 rs629849 IGF2R 3482 6 160464820 NM_000876 NP_000867 A/G R1619G plus 12585908 693 EGP_SNPS PDR90 NIHPDR 180 0.11 0.13 0.05 522 5 0.17 0.03 1864 7 123 "by doubleHit,freq,cluster" Benign 0.565 17 moderately radical 147280 6q26 insulin-like growth factor 2 receptor 1113 rs629976 IL28B 282617 19 44427365 NM_172139 NP_742151 A/G R28H minus 802528 1303 SEQUENOM CEPH CEPH (92) 92 0.35 0.35 0 92 1 103 by freq conservative 607402 19q13.13 "interleukin 28B (interferon, lambda 3)" 1114 rs630079 AOC3 8639 17 38257494 NM_003734 NP_003725 C/T H203R minus 3311445 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 83 0.42 0.38 0.04 267 2 0.37 0 166 2 123 by freq Benign 0.618 13 Tolerant 0.6 2.9 22 conservative 603735 17q21 "amine oxidase, copper containing 3 (vascular adhesion protein 1)" 1115 rs630079 AOC3 8639 17 38257494 NM_003734 NP_003725 C/T H203R minus 24796535 1303 SEQUENOM CEPH CEPH (92) 184 0.36 0.38 0.04 267 2 0.37 0 166 2 123 by freq Benign 0.618 13 Tolerant 0.6 2.9 22 conservative 603735 17q21 "amine oxidase, copper containing 3 (vascular adhesion protein 1)" 1116 rs637186 CD5 921 11 60649182 NM_014207 NP_055022 A/G H461R plus 809905 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.15 0.11 140 2 0.02 0 46 1 123 "by doubleHit,submitter,freq,cluster" Benign 0.289 7 conservative 153340 11q13 CD5 antigen (p56-62) 1117 rs637186 CD5 921 11 60649182 NM_014207 NP_055022 A/G H461R plus 24569935 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.15 0.11 140 2 0.02 0 46 1 123 "by doubleHit,submitter,freq,cluster" Benign 0.289 7 conservative 153340 11q13 CD5 antigen (p56-62) 1118 rs638043 KRT2A 3849 12 51330534 NM_000423 NP_000414 C/T G219D plus 2200757 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.18 0.05 138 2 0.04 0.04 90 2 123 by freq Benign 0.91 152 Tolerant 0.32 2.93 110 moderately conservative 600194 12q11-q13 keratin 2A (epidermal ichthyosis bullosa of Siemens) 1119 rs638043 KRT2A 3849 12 51330534 NM_000423 NP_000414 C/T G219D plus 24388531 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.13 0.18 0.05 138 2 0.04 0.04 90 2 123 by freq Benign 0.91 152 Tolerant 0.32 2.93 110 moderately conservative 600194 12q11-q13 keratin 2A (epidermal ichthyosis bullosa of Siemens) 1120 rs641153 BF 629 6 32022159 NM_001710 NP_001701 C/T R32Q minus 5606986 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 28 0.11 0.14 0.06 350 4 0.27 0 96 2 123 "by doubleHit,freq,cluster" conservative 138470 6p21.3 "B-factor, properdin" 1121 rs641153 BF 629 6 32022159 NM_001710 NP_001701 C/T R32Q minus 5606986 1303 SEQUENOM CEPH CEPH (92) 92 0.22 0.14 0.06 350 4 0.27 0 96 2 123 "by doubleHit,freq,cluster" conservative 138470 6p21.3 "B-factor, properdin" 1122 rs641153 BF 629 6 32022159 NM_001710 NP_001701 C/T R32Q minus 12674483 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.11 0.14 0.06 350 4 0.27 0 96 2 123 "by doubleHit,freq,cluster" conservative 138470 6p21.3 "B-factor, properdin" 1123 rs641153 BF 629 6 32022159 NM_001710 NP_001701 C/T R32Q minus 24796283 1303 SEQUENOM CEPH CEPH (92) 184 0.11 0.14 0.06 350 4 0.27 0 96 2 123 "by doubleHit,freq,cluster" conservative 138470 6p21.3 "B-factor, properdin" 1124 rs648802 PERP 64065 6 138455026 NM_022121 NP_071404 C/G P143R plus 3070296 1303 SEQUENOM CEPH CEPH (92) 92 0.49 0.49 0 92 1 120 "by doubleHit,submitter,freq,cluster" Tolerant 0.91 3.19 11 moderately radical 6q24 "PERP, TP53 apoptosis effector" 1125 rs649224 ME2 4200 18 46712660 NM_002396 NP_002387 C/T G450E minus 822148 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.03 0.14 0.17 210 2 116 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.055 32 Tolerant 1 2.76 89 moderately conservative 154270 18q21 "malic enzyme 2, NAD(+)-dependent, mitochondrial" 1126 rs649224 ME2 4200 18 46712660 NM_002396 NP_002387 C/T G450E minus 822148 1303 SEQUENOM CEPH CEPH (92) 92 0.27 0.14 0.17 210 2 116 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.055 32 Tolerant 1 2.76 89 moderately conservative 154270 18q21 "malic enzyme 2, NAD(+)-dependent, mitochondrial" 1127 rs662471 LAMA1 284217 18 6998591 NM_005559 NP_005550 A/G M1340V minus 3086161 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.2 0 92 1 120 "by doubleHit,freq,cluster" Intolerant 0.04 2.76 13 conservative 150320 18p11.23 "laminin, alpha 1" 1128 rs663227 UNC93A 54346 6 167699136 NM_018974 NP_061847 C/T Y387H plus 836450 1303 SEQUENOM CEPH CEPH (92) 92 0.32 0.32 0 92 1 83 by freq Possibly damaging 1.716 5 Intolerant 0 2.78 21 moderately conservative 607995 6q27 unc-93 homolog A (C. elegans) 1129 rs663606 UNC93A 54346 6 167699185 NM_018974 NP_061847 C/T M403T plus 836836 1303 SEQUENOM CEPH CEPH (92) 92 0.46 0.46 0 92 1 121 "by submitter,freq,cluster" Benign 0.291 5 Tolerant 1 2.78 21 moderately conservative 607995 6q27 unc-93 homolog A (C. elegans) 1130 rs671871 LAMA1 284217 18 6967844 NM_005559 NP_005550 A/G I2076T plus 845270 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.09 0.13 140 2 0.22 0.11 94 2 123 "by doubleHit,submitter,freq,cluster" Borderline 0.2 2.76 13 moderately conservative 150320 18p11.23 "laminin, alpha 1" 1131 rs671871 LAMA1 284217 18 6967844 NM_005559 NP_005550 A/G I2076T plus 23585965 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.09 0.13 140 2 0.22 0.11 94 2 123 "by doubleHit,submitter,freq,cluster" Borderline 0.2 2.76 13 moderately conservative 150320 18p11.23 "laminin, alpha 1" 1132 rs676210 APOB 338 2 21143176 NM_000384 NP_000375 A/G P2739L plus 2152529 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.2 0.01 154 2 0.27 0.09 438 5 121 "by doubleHit,freq,cluster" moderately conservative 107730 2p24-p23 apolipoprotein B (including Ag(x) antigen) 1133 rs676210 APOB 338 2 21143176 NM_000384 NP_000375 A/G P2739L plus 8819681 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.19 0.2 0.01 154 2 0.27 0.09 438 5 121 "by doubleHit,freq,cluster" moderately conservative 107730 2p24-p23 apolipoprotein B (including Ag(x) antigen) 1134 rs676314 NAPSA 9476 19 55557347 NM_004851 NP_004842 C/T I40T minus 849807 1303 SEQUENOM CEPH CEPH (92) 92 0.25 0.25 0 92 1 120 "by doubleHit,submitter,freq,cluster" Benign 0.332 6 Tolerant 0.67 2.8 67 moderately conservative 605631 19q13.33 napsin A aspartic peptidase 1135 rs676823 GPR109A 338442 12 121712119 NM_177551 NP_808219 C/T F198L minus 850328 1303 SEQUENOM CEPH CEPH (92) 92 0.13 0.13 0 92 1 0.44 0 1496 1 123 "by cluster,freq" Tolerant 1 2.81 27 conservative 12q24.31 G protein-coupled receptor 109A 1136 rs679620 MMP3 4314 11 102218830 NM_002422 NP_002413 A/G K45E minus 4251046 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.33 0.38 0.05 306 4 0.33 0.03 1604 4 123 "HapMap,doubleHit,freq,cluster" Benign 0.012 45 Tolerant 1 2.72 58 moderately conservative 185250 11q22.3 "matrix metalloproteinase 3 (stromelysin 1, progelatinase)" 1137 rs679620 MMP3 4314 11 102218830 NM_002422 NP_002413 A/G K45E minus 4251046 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.43 0.38 0.05 306 4 0.33 0.03 1604 4 123 "HapMap,doubleHit,freq,cluster" Benign 0.012 45 Tolerant 1 2.72 58 moderately conservative 185250 11q22.3 "matrix metalloproteinase 3 (stromelysin 1, progelatinase)" 1138 rs679620 MMP3 4314 11 102218830 NM_002422 NP_002413 A/G K45E minus 4251046 1303 SEQUENOM CEPH CEPH (92) 92 0.36 0.38 0.05 306 4 0.33 0.03 1604 4 123 "HapMap,doubleHit,freq,cluster" Benign 0.012 45 Tolerant 1 2.72 58 moderately conservative 185250 11q22.3 "matrix metalloproteinase 3 (stromelysin 1, progelatinase)" 1139 rs679620 MMP3 4314 11 102218830 NM_002422 NP_002413 A/G K45E minus 24073656 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.38 0.05 306 4 0.33 0.03 1604 4 123 "HapMap,doubleHit,freq,cluster" Benign 0.012 45 Tolerant 1 2.72 58 moderately conservative 185250 11q22.3 "matrix metalloproteinase 3 (stromelysin 1, progelatinase)" 1140 rs679899 APOB 338 2 21162566 NM_000384 NP_000375 A/G A618V plus 2756662 1303 SEQUENOM CEPH CEPH (92) 92 0.49 0.49 0 92 1 0.26 0 94 1 121 "by doubleHit,freq,cluster" moderately conservative 107730 2p24-p23 apolipoprotein B (including Ag(x) antigen) 1141 rs682632 TEK 7010 9 27173463 NM_000459 NP_000450 G/T Q346P minus 1651479 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.02 0 92 1 121 "by cluster,freq" Possibly damaging 1.679 9 moderately conservative 600221 9p21 "TEK tyrosine kinase, endothelial (venous malformations, multiple cutaneous and mucosal)" 1142 rs684535 CDON 50937 11 125336180 NM_016952 NP_058648 A/T I1221N plus 858175 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.21 0.26 0.03 274 4 0.12 0.07 138 4 123 "HapMap,doubleHit,freq,cluster" moderately radical 608707 11q23-q24 cell adhesion molecule-related/down-regulated by oncogenes 1143 rs684535 CDON 50937 11 125336180 NM_016952 NP_058648 A/T I1221N plus 858175 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 92 0.25 0.26 0.03 274 4 0.12 0.07 138 4 123 "HapMap,doubleHit,freq,cluster" moderately radical 608707 11q23-q24 cell adhesion molecule-related/down-regulated by oncogenes 1144 rs684535 CDON 50937 11 125336180 NM_016952 NP_058648 A/T I1221N plus 858175 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.29 0.26 0.03 274 4 0.12 0.07 138 4 123 "HapMap,doubleHit,freq,cluster" moderately radical 608707 11q23-q24 cell adhesion molecule-related/down-regulated by oncogenes 1145 rs684535 CDON 50937 11 125336180 NM_016952 NP_058648 A/T I1221N plus 24597994 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.26 0.03 274 4 0.12 0.07 138 4 123 "HapMap,doubleHit,freq,cluster" moderately radical 608707 11q23-q24 cell adhesion molecule-related/down-regulated by oncogenes 1146 rs688906 DNCH2 79659 11 102534726 XM_370652 XP_370652 C/T K1413R minus 23559641 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.31 0 48 1 0.29 0.17 94 2 123 "by doubleHit,submitter,freq,cluster" Intolerant 0 2.81 12 conservative 603297 11q21-q22.1 "dynein, cytoplasmic, heavy polypeptide 2" 1147 rs689647 TP53BP1 7158 15 41549488 NM_005657 NP_005648 C/T G412S plus 863398 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.07 0.16 0.14 364 5 0.42 0.05 126 4 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 605230 15q15-q21 "tumor protein p53 binding protein, 1" 1148 rs689647 TP53BP1 7158 15 41549488 NM_005657 NP_005648 C/T G412S plus 863398 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 92 0.08 0.16 0.14 364 5 0.42 0.05 126 4 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 605230 15q15-q21 "tumor protein p53 binding protein, 1" 1149 rs689647 TP53BP1 7158 15 41549488 NM_005657 NP_005648 C/T G412S plus 10801045 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.07 0.16 0.14 364 5 0.42 0.05 126 4 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 605230 15q15-q21 "tumor protein p53 binding protein, 1" 1150 rs689647 TP53BP1 7158 15 41549488 NM_005657 NP_005648 C/T G412S plus 10801045 1303 SEQUENOM CEPH CEPH (92) 92 0.37 0.16 0.14 364 5 0.42 0.05 126 4 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 605230 15q15-q21 "tumor protein p53 binding protein, 1" 1151 rs689647 TP53BP1 7158 15 41549488 NM_005657 NP_005648 C/T G412S plus 24038555 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.13 0.16 0.14 364 5 0.42 0.05 126 4 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 605230 15q15-q21 "tumor protein p53 binding protein, 1" 1152 rs696217 GHRL 51738 3 10306457 NM_016362 NP_057446 G/T L72M plus 1598058 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.08 0.08 0 118 1 0.19 0 1522 2 120 "HapMap,doubleHit,freq,cluster" Benign 0.985 16 Borderline 0.11 3.02 26 conservative 605353 3p26-p25 ghrelin precursor 1153 rs699664 GGCX 2677 2 85692194 NM_000821 NP_000812 A/G R325Q minus 81736 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 82 0.29 0.34 0.07 340 4 0.32 0.06 258 4 123 "HapMap,doubleHit,freq" Borderline 1.157 9 Tolerant 0.32 3.19 16 conservative 137167 2p12 gamma-glutamyl carboxylase 1154 rs699664 GGCX 2677 2 85692194 NM_000821 NP_000812 A/G R325Q minus 81736 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.43 0.34 0.07 340 4 0.32 0.06 258 4 123 "HapMap,doubleHit,freq" Borderline 1.157 9 Tolerant 0.32 3.19 16 conservative 137167 2p12 gamma-glutamyl carboxylase 1155 rs699664 GGCX 2677 2 85692194 NM_000821 NP_000812 A/G R325Q minus 81736 1303 SEQUENOM CEPH CEPH (92) 92 0.29 0.34 0.07 340 4 0.32 0.06 258 4 123 "HapMap,doubleHit,freq" Borderline 1.157 9 Tolerant 0.32 3.19 16 conservative 137167 2p12 gamma-glutamyl carboxylase 1156 rs699664 GGCX 2677 2 85692194 NM_000821 NP_000812 A/G R325Q minus 24169475 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.34 0.07 340 4 0.32 0.06 258 4 123 "HapMap,doubleHit,freq" Borderline 1.157 9 Tolerant 0.32 3.19 16 conservative 137167 2p12 gamma-glutamyl carboxylase 1157 rs699738 CD2 914 1 117023189 NM_001767 NP_001758 G/T H266Q minus 3172797 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 22 0.32 0.2 0.06 162 4 0.29 0 1252 1 123 "by doubleHit,freq,cluster" Probably damaging 2.426 8 conservative 186990 1p13 "CD2 antigen (p50), sheep red blood cell receptor" 1158 rs699738 CD2 914 1 117023189 NM_001767 NP_001758 G/T H266Q minus 4385082 649 FHCRC POPU1 USA (20) 12 0.1 0.2 0.06 162 4 0.29 0 1252 1 123 "by doubleHit,freq,cluster" Probably damaging 2.426 8 conservative 186990 1p13 "CD2 antigen (p50), sheep red blood cell receptor" 1159 rs699738 CD2 914 1 117023189 NM_001767 NP_001758 G/T H266Q minus 4385082 649 FHCRC POPU1 USA (20) 36 0.2 0.2 0.06 162 4 0.29 0 1252 1 123 "by doubleHit,freq,cluster" Probably damaging 2.426 8 conservative 186990 1p13 "CD2 antigen (p50), sheep red blood cell receptor" 1160 rs699738 CD2 914 1 117023189 NM_001767 NP_001758 G/T H266Q minus 17337954 1303 SEQUENOM CEPH CEPH (92) 92 0.18 0.2 0.06 162 4 0.29 0 1252 1 123 "by doubleHit,freq,cluster" Probably damaging 2.426 8 conservative 186990 1p13 "CD2 antigen (p50), sheep red blood cell receptor" 1161 rs700241 DAB2 1601 5 39412889 NM_001343 NP_001334 A/G T586I plus 2681857 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.02 0.02 0 116 1 0.02 0 1498 1 108 "HapMap,freq,cluster" Benign 0.675 6 Potentially intolerant 0.06 3.14 33 moderately conservative 601236 5p13 "disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)" 1162 rs701753 CP 1356 3 150398933 NM_000096 NP_000087 A/T E544D plus 887587 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 10 0.2 0.08 0.03 222 3 0.21 0 14 1 123 "HapMap,freq,cluster" Potentially damaging 1.389 11 conservative 117700 3q23-q25 ceruloplasmin (ferroxidase) 1163 rs701753 CP 1356 3 150398933 NM_000096 NP_000087 A/T E544D plus 1914677 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.07 0.08 0.03 222 3 0.21 0 14 1 123 "HapMap,freq,cluster" Potentially damaging 1.389 11 conservative 117700 3q23-q25 ceruloplasmin (ferroxidase) 1164 rs701753 CP 1356 3 150398933 NM_000096 NP_000087 A/T E544D plus 1914677 1303 SEQUENOM CEPH CEPH (92) 92 0.09 0.08 0.03 222 3 0.21 0 14 1 123 "HapMap,freq,cluster" Potentially damaging 1.389 11 conservative 117700 3q23-q25 ceruloplasmin (ferroxidase) 1165 rs701865 PDE6C 5146 10 95371763 NM_006204 NP_006195 A/T S270T plus 1477173 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.43 0.44 0.01 256 3 0.42 0.08 84 2 123 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.051 41 Tolerant 0.81 2.86 45 moderately conservative 600827 10q24 "phosphodiesterase 6C, cGMP-specific, cone, alpha prime" 1166 rs701865 PDE6C 5146 10 95371763 NM_006204 NP_006195 A/T S270T plus 1477173 1303 SEQUENOM CEPH CEPH (92) 92 0.45 0.44 0.01 256 3 0.42 0.08 84 2 123 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.051 41 Tolerant 0.81 2.86 45 moderately conservative 600827 10q24 "phosphodiesterase 6C, cGMP-specific, cone, alpha prime" 1167 rs701865 PDE6C 5146 10 95371763 NM_006204 NP_006195 A/T S270T plus 23580834 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.43 0.44 0.01 256 3 0.42 0.08 84 2 123 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.051 41 Tolerant 0.81 2.86 45 moderately conservative 600827 10q24 "phosphodiesterase 6C, cGMP-specific, cone, alpha prime" 1168 rs702689 MAP3K1 4214 5 56213200 XM_042066 XP_042066 A/G D940N plus 1146310 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.19 0.24 0.1 333 5 0.33 0.09 430 6 123 "by doubleHit,submitter,freq,cluster" conservative 600982 5q11.2 mitogen-activated protein kinase kinase kinase 1 1169 rs702689 MAP3K1 4214 5 56213200 XM_042066 XP_042066 A/G D940N plus 3176945 619 WICVAR MITOGPOP6 CORIELL Mixed 25 0.5 0.24 0.1 333 5 0.33 0.09 430 6 123 "by doubleHit,submitter,freq,cluster" conservative 600982 5q11.2 mitogen-activated protein kinase kinase kinase 1 1170 rs702689 MAP3K1 4214 5 56213200 XM_042066 XP_042066 A/G D940N plus 3576043 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.19 0.24 0.1 333 5 0.33 0.09 430 6 123 "by doubleHit,submitter,freq,cluster" conservative 600982 5q11.2 mitogen-activated protein kinase kinase kinase 1 1171 rs702689 MAP3K1 4214 5 56213200 XM_042066 XP_042066 A/G D940N plus 3576043 1303 SEQUENOM CEPH CEPH (92) 92 0.21 0.24 0.1 333 5 0.33 0.09 430 6 123 "by doubleHit,submitter,freq,cluster" conservative 600982 5q11.2 mitogen-activated protein kinase kinase kinase 1 1172 rs702689 MAP3K1 4214 5 56213200 XM_042066 XP_042066 A/G D940N plus 23358119 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.24 0.1 333 5 0.33 0.09 430 6 123 "by doubleHit,submitter,freq,cluster" conservative 600982 5q11.2 mitogen-activated protein kinase kinase kinase 1 1173 rs707555 PCK1 5105 20 55571301 NM_002591 NP_002582 C/G V184L minus 1507075 1303 SEQUENOM CEPH CEPH (92) 92 0.11 0.11 0.01 140 2 0.15 0.18 94 2 123 "by doubleHit,submitter,freq,cluster" Potentially damaging 1.34 53 conservative 261680 20q13.31 phosphoenolpyruvate carboxykinase 1 (soluble) 1174 rs707555 PCK1 5105 20 55571301 NM_002591 NP_002582 C/G V184L minus 24006946 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.11 0.01 140 2 0.15 0.18 94 2 123 "by doubleHit,submitter,freq,cluster" Potentially damaging 1.34 53 conservative 261680 20q13.31 phosphoenolpyruvate carboxykinase 1 (soluble) 1175 rs707950 HLA-DQA1 3117 6 32717851 NM_002122 NP_002113 C/G Q152H plus 24816100 1303 SEQUENOM CEPH CEPH (92) 184 0.27 0.27 0 184 1 123 by freq Benign 0.479 191 Tolerant 0.97 2.84 306 conservative 146880 6p21.3 "major histocompatibility complex, class II, DQ alpha 1" 1176 rs709012 SN 6614 20 3623498 NM_023068 NP_075556 G/T H919P plus 8345514 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.42 0.42 0.07 214 3 0.23 0.02 1594 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.134 6 Tolerant 0.3 2.78 11 moderately conservative 600751 20p13 sialoadhesin 1177 rs709012 SN 6614 20 3623498 NM_023068 NP_075556 G/T H919P plus 8345514 1303 SEQUENOM CEPH CEPH (92) 46 0.5 0.42 0.07 214 3 0.23 0.02 1594 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.134 6 Tolerant 0.3 2.78 11 moderately conservative 600751 20p13 sialoadhesin 1178 rs709012 SN 6614 20 3623498 NM_023068 NP_075556 G/T H919P plus 24497001 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.42 0.07 214 3 0.23 0.02 1594 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.134 6 Tolerant 0.3 2.78 11 moderately conservative 600751 20p13 sialoadhesin 1179 rs709932 SERPINA1 5265 14 93918954 NM_000295 NP_000286 A/G R125H minus 1487247 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 82 0.17 0.15 0.06 502 7 0.09 0.09 279 5 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.39 2.75 79 conservative 107400 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1" 1180 rs709932 SERPINA1 5265 14 93918954 NM_000295 NP_000286 A/G R125H minus 1487247 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 22 0.09 0.15 0.06 502 7 0.09 0.09 279 5 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.39 2.75 79 conservative 107400 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1" 1181 rs709932 SERPINA1 5265 14 93918954 NM_000295 NP_000286 A/G R125H minus 1487247 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 94 0.11 0.15 0.06 502 7 0.09 0.09 279 5 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.39 2.75 79 conservative 107400 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1" 1182 rs709932 SERPINA1 5265 14 93918954 NM_000295 NP_000286 A/G R125H minus 1487247 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.14 0.15 0.06 502 7 0.09 0.09 279 5 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.39 2.75 79 conservative 107400 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1" 1183 rs709932 SERPINA1 5265 14 93918954 NM_000295 NP_000286 A/G R125H minus 1487247 1303 SEQUENOM CEPH CEPH (92) 92 0.15 0.15 0.06 502 7 0.09 0.09 279 5 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.39 2.75 79 conservative 107400 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1" 1184 rs709932 SERPINA1 5265 14 93918954 NM_000295 NP_000286 A/G R125H minus 3177172 619 WICVAR MITOGPOP6 CORIELL Mixed 44 0.32 0.15 0.06 502 7 0.09 0.09 279 5 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.39 2.75 79 conservative 107400 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1" 1185 rs709932 SERPINA1 5265 14 93918954 NM_000295 NP_000286 A/G R125H minus 24129851 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.15 0.06 502 7 0.09 0.09 279 5 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.39 2.75 79 conservative 107400 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1" 1186 rs710187 GCAT 23464 22 36528589 NM_014291 NP_055106 C/T R39C plus 137242 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 12 0.42 0.47 0.01 224 3 0.26 0.06 34 2 123 "HapMap,doubleHit,freq,cluster" Probably damaging 2.278 7 Intolerant 0 2.8 77 radical 607422 22q13.1 glycine C-acetyltransferase (2-amino-3-ketobutyrate coenzyme A ligase) 1187 rs710187 GCAT 23464 22 36528589 NM_014291 NP_055106 C/T R39C plus 7997788 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.47 0.47 0.01 224 3 0.26 0.06 34 2 123 "HapMap,doubleHit,freq,cluster" Probably damaging 2.278 7 Intolerant 0 2.8 77 radical 607422 22q13.1 glycine C-acetyltransferase (2-amino-3-ketobutyrate coenzyme A ligase) 1188 rs710187 GCAT 23464 22 36528589 NM_014291 NP_055106 C/T R39C plus 7997788 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.47 0.01 224 3 0.26 0.06 34 2 123 "HapMap,doubleHit,freq,cluster" Probably damaging 2.278 7 Intolerant 0 2.8 77 radical 607422 22q13.1 glycine C-acetyltransferase (2-amino-3-ketobutyrate coenzyme A ligase) 1189 rs710193 ST13 6767 22 39547690 NM_003932 NP_003923 C/T M297I plus 2671357 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.15 0.15 0 84 1 0.05 0 168 2 92 "by doubleHit,freq" Benign 0.952 7 Potentially intolerant 0.1 3.06 19 conservative 606796 22q13.2 suppression of tumorigenicity 13 (colon carcinoma) (Hsp70 interacting protein) 1190 rs712665 U2AF1L1 7310 5 112255698 NM_005083 NP_005074 C/T S155G minus 1998868 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.38 0.3 0.09 260 3 0.15 0.06 1588 3 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.581 7 moderately conservative 601079 5q22 U2(RNU2) small nuclear RNA auxillary factor 1-like 1 1191 rs712665 U2AF1L1 7310 5 112255698 NM_005083 NP_005074 C/T S155G minus 1998868 1303 SEQUENOM CEPH CEPH (92) 92 0.21 0.3 0.09 260 3 0.15 0.06 1588 3 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.581 7 moderately conservative 601079 5q22 U2(RNU2) small nuclear RNA auxillary factor 1-like 1 1192 rs712665 U2AF1L1 7310 5 112255698 NM_005083 NP_005074 C/T S155G minus 23418318 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.3 0.09 260 3 0.15 0.06 1588 3 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.581 7 moderately conservative 601079 5q22 U2(RNU2) small nuclear RNA auxillary factor 1-like 1 1193 rs714368 SLC22A16 85413 6 110884821 NM_033125 NP_149116 A/G H49R minus 10328090 1303 SEQUENOM CEPH CEPH (92) 92 0.19 0.24 0.11 140 2 0.39 0.02 92 2 123 "by doubleHit,submitter,freq,cluster" Possibly damaging 1.615 5 Potentially intolerant 0.07 2.78 19 conservative 608276 6q22.1 "solute carrier family 22 (organic cation transporter), member 16" 1194 rs714368 SLC22A16 85413 6 110884821 NM_033125 NP_149116 A/G H49R minus 23456009 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.24 0.11 140 2 0.39 0.02 92 2 123 "by doubleHit,submitter,freq,cluster" Possibly damaging 1.615 5 Potentially intolerant 0.07 2.78 19 conservative 608276 6q22.1 "solute carrier family 22 (organic cation transporter), member 16" 1195 rs721917 SFTPD 6441 10 81696304 NM_003019 NP_003010 C/T M31T minus 63537 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.43 0.43 0.04 336 5 0.41 0.04 1964 9 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 178635 10q22.2-q23.1 "surfactant, pulmonary-associated protein D" 1196 rs721917 SFTPD 6441 10 81696304 NM_003019 NP_003010 C/T M31T minus 63537 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.41 0.43 0.04 336 5 0.41 0.04 1964 9 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 178635 10q22.2-q23.1 "surfactant, pulmonary-associated protein D" 1197 rs721917 SFTPD 6441 10 81696304 NM_003019 NP_003010 C/T M31T minus 63537 1303 SEQUENOM CEPH CEPH (92) 92 0.49 0.43 0.04 336 5 0.41 0.04 1964 9 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 178635 10q22.2-q23.1 "surfactant, pulmonary-associated protein D" 1198 rs721917 SFTPD 6441 10 81696304 NM_003019 NP_003010 C/T M31T minus 8819859 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.4 0.43 0.04 336 5 0.41 0.04 1964 9 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 178635 10q22.2-q23.1 "surfactant, pulmonary-associated protein D" 1199 rs721917 SFTPD 6441 10 81696304 NM_003019 NP_003010 C/T M31T minus 23388886 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.43 0.04 336 5 0.41 0.04 1964 9 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 178635 10q22.2-q23.1 "surfactant, pulmonary-associated protein D" 1200 rs723077 TTC12 54970 11 112699378 NM_017868 NP_060338 A/C M73L plus 65174 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 82 0.48 0.46 0.03 486 8 0.29 0.19 203 6 123 "HapMap,doubleHit,submitter,freq" conservative 11q23.2 tetratricopeptide repeat domain 12 1201 rs723077 TTC12 54970 11 112699378 NM_017868 NP_060338 A/C M73L plus 65174 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.43 0.46 0.03 486 8 0.29 0.19 203 6 123 "HapMap,doubleHit,submitter,freq" conservative 11q23.2 tetratricopeptide repeat domain 12 1202 rs723077 TTC12 54970 11 112699378 NM_017868 NP_060338 A/C M73L plus 65174 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 90 0.47 0.46 0.03 486 8 0.29 0.19 203 6 123 "HapMap,doubleHit,submitter,freq" conservative 11q23.2 tetratricopeptide repeat domain 12 1203 rs723077 TTC12 54970 11 112699378 NM_017868 NP_060338 A/C M73L plus 65174 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.46 0.46 0.03 486 8 0.29 0.19 203 6 123 "HapMap,doubleHit,submitter,freq" conservative 11q23.2 tetratricopeptide repeat domain 12 1204 rs723077 TTC12 54970 11 112699378 NM_017868 NP_060338 A/C M73L plus 65174 902 AFFY Caucasian 24 0.38 0.46 0.03 486 8 0.29 0.19 203 6 123 "HapMap,doubleHit,submitter,freq" conservative 11q23.2 tetratricopeptide repeat domain 12 1205 rs723077 TTC12 54970 11 112699378 NM_017868 NP_060338 A/C M73L plus 65174 904 AFFY CEPH 40 0.43 0.46 0.03 486 8 0.29 0.19 203 6 123 "HapMap,doubleHit,submitter,freq" conservative 11q23.2 tetratricopeptide repeat domain 12 1206 rs723077 TTC12 54970 11 112699378 NM_017868 NP_060338 A/C M73L plus 65174 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.46 0.03 486 8 0.29 0.19 203 6 123 "HapMap,doubleHit,submitter,freq" conservative 11q23.2 tetratricopeptide repeat domain 12 1207 rs723077 TTC12 54970 11 112699378 NM_017868 NP_060338 A/C M73L plus 24565864 1371 PERLEGEN AFD_EUR_PANEL European American (24) 24 0.5 0.46 0.03 486 8 0.29 0.19 203 6 123 "HapMap,doubleHit,submitter,freq" conservative 11q23.2 tetratricopeptide repeat domain 12 1208 rs723685 SLC22A16 85413 6 110870568 NM_033125 NP_149116 C/T V252A minus 66006 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.08 0.06 0.04 210 2 121 "HapMap,doubleHit,freq,cluster" Potentially damaging 1.416 6 Intolerant 0.01 2.79 21 moderately conservative 608276 6q22.1 "solute carrier family 22 (organic cation transporter), member 16" 1209 rs723685 SLC22A16 85413 6 110870568 NM_033125 NP_149116 C/T V252A minus 66006 1303 SEQUENOM CEPH CEPH (92) 92 0.03 0.06 0.04 210 2 121 "HapMap,doubleHit,freq,cluster" Potentially damaging 1.416 6 Intolerant 0.01 2.79 21 moderately conservative 608276 6q22.1 "solute carrier family 22 (organic cation transporter), member 16" 1210 rs724558 SERPINB10 5273 18 59736240 NM_005024 NP_005015 C/T I99T plus 67221 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 82 0.18 0.15 0.04 630 7 0.29 0.13 304 6 123 "HapMap,doubleHit,freq,cluster" Potentially intolerant 0.07 2.76 59 moderately conservative 602058 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10" 1211 rs724558 SERPINB10 5273 18 59736240 NM_005024 NP_005015 C/T I99T plus 67221 766 TSC-CSHL WICGR1_CAUCASIAN WICGR Caucasian (93) 94 0.14 0.15 0.04 630 7 0.29 0.13 304 6 123 "HapMap,doubleHit,freq,cluster" Potentially intolerant 0.07 2.76 59 moderately conservative 602058 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10" 1212 rs724558 SERPINB10 5273 18 59736240 NM_005024 NP_005015 C/T I99T plus 67221 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.07 0.15 0.04 630 7 0.29 0.13 304 6 123 "HapMap,doubleHit,freq,cluster" Potentially intolerant 0.07 2.76 59 moderately conservative 602058 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10" 1213 rs724558 SERPINB10 5273 18 59736240 NM_005024 NP_005015 C/T I99T plus 67221 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 180 0.09 0.15 0.04 630 7 0.29 0.13 304 6 123 "HapMap,doubleHit,freq,cluster" Potentially intolerant 0.07 2.76 59 moderately conservative 602058 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10" 1214 rs724558 SERPINB10 5273 18 59736240 NM_005024 NP_005015 C/T I99T plus 67221 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.19 0.15 0.04 630 7 0.29 0.13 304 6 123 "HapMap,doubleHit,freq,cluster" Potentially intolerant 0.07 2.76 59 moderately conservative 602058 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10" 1215 rs724558 SERPINB10 5273 18 59736240 NM_005024 NP_005015 C/T I99T plus 67221 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.15 0.04 630 7 0.29 0.13 304 6 123 "HapMap,doubleHit,freq,cluster" Potentially intolerant 0.07 2.76 59 moderately conservative 602058 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10" 1216 rs724558 SERPINB10 5273 18 59736240 NM_005024 NP_005015 C/T I99T plus 23531843 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.15 0.04 630 7 0.29 0.13 304 6 123 "HapMap,doubleHit,freq,cluster" Potentially intolerant 0.07 2.76 59 moderately conservative 602058 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10" 1217 rs731170 LILRB4 11006 19 59868074 NM_006847 NP_006838 A/G D223G plus 76395 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.34 0.26 0.14 306 5 0.22 0 1496 1 123 "HapMap,doubleHit,freq,cluster" Benign 0.193 27 moderately conservative 604821 19q13.4 "leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4" 1218 rs731170 LILRB4 11006 19 59868074 NM_006847 NP_006838 A/G D223G plus 76395 1303 SEQUENOM CEPH CEPH (92) 92 0.11 0.26 0.14 306 5 0.22 0 1496 1 123 "HapMap,doubleHit,freq,cluster" Benign 0.193 27 moderately conservative 604821 19q13.4 "leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4" 1219 rs731170 LILRB4 11006 19 59868074 NM_006847 NP_006838 A/G D223G plus 16359984 649 FHCRC POPU1 USA (20) 16 0.05 0.26 0.14 306 5 0.22 0 1496 1 123 "HapMap,doubleHit,freq,cluster" Benign 0.193 27 moderately conservative 604821 19q13.4 "leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4" 1220 rs731170 LILRB4 11006 19 59868074 NM_006847 NP_006838 A/G D223G plus 16359984 649 FHCRC POPU1 USA (20) 38 0.35 0.26 0.14 306 5 0.22 0 1496 1 123 "HapMap,doubleHit,freq,cluster" Benign 0.193 27 moderately conservative 604821 19q13.4 "leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4" 1221 rs731170 LILRB4 11006 19 59868074 NM_006847 NP_006838 A/G D223G plus 16360036 649 FHCRC POPU1 USA (20) 40 0.4 0.26 0.14 306 5 0.22 0 1496 1 123 "HapMap,doubleHit,freq,cluster" Benign 0.193 27 moderately conservative 604821 19q13.4 "leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4" 1222 rs732774 ATP7B 540 13 51421809 NM_000053 NP_000044 A/G R952K minus 78425 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.36 0.47 0.03 274 4 0.38 0.08 130 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.137 20 Tolerant 0.99 2.94 20 conservative 606882 13q14.2-q21 "ATPase, Cu++ transporting, beta polypeptide (Wilson disease)" 1223 rs732774 ATP7B 540 13 51421809 NM_000053 NP_000044 A/G R952K minus 78425 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 92 0.48 0.47 0.03 274 4 0.38 0.08 130 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.137 20 Tolerant 0.99 2.94 20 conservative 606882 13q14.2-q21 "ATPase, Cu++ transporting, beta polypeptide (Wilson disease)" 1224 rs732774 ATP7B 540 13 51421809 NM_000053 NP_000044 A/G R952K minus 78425 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.49 0.47 0.03 274 4 0.38 0.08 130 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.137 20 Tolerant 0.99 2.94 20 conservative 606882 13q14.2-q21 "ATPase, Cu++ transporting, beta polypeptide (Wilson disease)" 1225 rs732774 ATP7B 540 13 51421809 NM_000053 NP_000044 A/G R952K minus 24448176 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.47 0.03 274 4 0.38 0.08 130 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.137 20 Tolerant 0.99 2.94 20 conservative 606882 13q14.2-q21 "ATPase, Cu++ transporting, beta polypeptide (Wilson disease)" 1226 rs733731 PGLYRP2 114770 19 15448185 NM_052890 NP_443122 A/G R99Q minus 24195787 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.35 0.35 0 46 1 0.34 0.12 78 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.084 6 conservative 608199 19p13.12 peptidoglycan recognition protein 2 1227 rs733743 ZNF306 80317 6 28435350 NM_024493 NP_077819 C/G R3T minus 79697 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.12 0.13 0.04 224 3 0.16 0.12 260 4 123 "by submitter,freq,cluster" Possibly damaging 1.807 7 Tolerant 0.81 2.95 19 moderately conservative 6p21.33 zinc finger protein 306 1228 rs733743 ZNF306 80317 6 28435350 NM_024493 NP_077819 C/G R3T minus 79697 1303 SEQUENOM CEPH CEPH (92) 92 0.11 0.13 0.04 224 3 0.16 0.12 260 4 123 "by submitter,freq,cluster" Possibly damaging 1.807 7 Tolerant 0.81 2.95 19 moderately conservative 6p21.33 zinc finger protein 306 1229 rs733743 ZNF306 80317 6 28435350 NM_024493 NP_077819 C/G R3T minus 23916317 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.13 0.04 224 3 0.16 0.12 260 4 123 "by submitter,freq,cluster" Possibly damaging 1.807 7 Tolerant 0.81 2.95 19 moderately conservative 6p21.33 zinc finger protein 306 1230 rs734784 KCNS1 3787 20 43157041 NM_002251 NP_002242 A/G I489V minus 80995 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 80 0.45 0.47 0.02 172 2 0.4 0 84 1 121 "by doubleHit,submitter,freq,cluster" Tolerant 0.38 2.88 41 conservative 602905 20q12 "potassium voltage-gated channel, delayed-rectifier, subfamily S, member 1" 1231 rs734784 KCNS1 3787 20 43157041 NM_002251 NP_002242 A/G I489V minus 12587043 1303 SEQUENOM CEPH CEPH (92) 92 0.48 0.47 0.02 172 2 0.4 0 84 1 121 "by doubleHit,submitter,freq,cluster" Tolerant 0.38 2.88 41 conservative 602905 20q12 "potassium voltage-gated channel, delayed-rectifier, subfamily S, member 1" 1232 rs738792 MMP11 4320 22 22445932 NM_005940 NP_005931 C/T A38V plus 86318 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.05 0.05 0 164 2 0.34 0.02 1563 3 123 "HapMap,doubleHit,freq,cluster" moderately conservative 185261 22q11.23 matrix metalloproteinase 11 (stromelysin 3) 1233 rs738792 MMP11 4320 22 22445932 NM_005940 NP_005931 C/T A38V plus 23607471 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.05 0.05 0 164 2 0.34 0.02 1563 3 123 "HapMap,doubleHit,freq,cluster" moderately conservative 185261 22q11.23 matrix metalloproteinase 11 (stromelysin 3) 1234 rs742493 UNC5CL 222643 6 41106145 NM_173561 NP_775832 A/G R432G minus 91336 1303 SEQUENOM CEPH CEPH (92) 92 0.27 0.24 0.06 132 2 0.06 0.01 1386 3 123 "by cluster,freq" moderately radical 6p21.1 unc-5 homolog C (C. elegans)-like 1235 rs742493 UNC5CL 222643 6 41106145 NM_173561 NP_775832 A/G R432G minus 24435638 1371 PERLEGEN AFD_EUR_PANEL European American (24) 40 0.18 0.24 0.06 132 2 0.06 0.01 1386 3 123 "by cluster,freq" moderately radical 6p21.1 unc-5 homolog C (C. elegans)-like 1236 rs743616 ARSA 410 22 49354183 NM_000487 NP_000478 C/G T391S plus 92782 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.43 0.44 0.02 430 4 0.26 0.03 92 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.948 7 Tolerant 0.96 2.75 21 moderately conservative 607574 22q13.33 arylsulfatase A 1237 rs743616 ARSA 410 22 49354183 NM_000487 NP_000478 C/G T391S plus 92782 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.44 0.02 430 4 0.26 0.03 92 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.948 7 Tolerant 0.96 2.75 21 moderately conservative 607574 22q13.33 arylsulfatase A 1238 rs743616 ARSA 410 22 49354183 NM_000487 NP_000478 C/G T391S plus 8485032 693 EGP_SNPS PDR90 NIHPDR 170 0.44 0.44 0.02 430 4 0.26 0.03 92 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.948 7 Tolerant 0.96 2.75 21 moderately conservative 607574 22q13.33 arylsulfatase A 1239 rs743616 ARSA 410 22 49354183 NM_000487 NP_000478 C/G T391S plus 24706948 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.44 0.02 430 4 0.26 0.03 92 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.948 7 Tolerant 0.96 2.75 21 moderately conservative 607574 22q13.33 arylsulfatase A 1240 rs751141 EPHX2 2053 8 27429782 NM_001979 NP_001970 C/T R287Q minus 103248 1303 SEQUENOM CEPH CEPH (92) 92 0.14 0.14 0.01 140 2 0.11 0.12 90 2 123 "by doubleHit,submitter,freq,cluster" Possibly damaging 1.595 9 Intolerant 0.02 2.71 84 conservative 132811 8p21-p12 "epoxide hydrolase 2, cytoplasmic" 1241 rs751141 EPHX2 2053 8 27429782 NM_001979 NP_001970 C/T R287Q minus 24085004 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.14 0.01 140 2 0.11 0.12 90 2 123 "by doubleHit,submitter,freq,cluster" Possibly damaging 1.595 9 Intolerant 0.02 2.71 84 conservative 132811 8p21-p12 "epoxide hydrolase 2, cytoplasmic" 1242 rs757110 ABCC8 6833 11 17375053 NM_000352 NP_000343 G/T A1369S minus 128868 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 78 0.32 0.37 0.04 1209 5 0.11 0.16 118 3 123 "by doubleHit,freq,cluster" Benign 0.151 18 moderately conservative 600509 11p15.1 "ATP-binding cassette, sub-family C (CFTR/MRP), member 8" 1243 rs757110 ABCC8 6833 11 17375053 NM_000352 NP_000343 G/T A1369S minus 128868 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 24 0.46 0.37 0.04 1209 5 0.11 0.16 118 3 123 "by doubleHit,freq,cluster" Benign 0.151 18 moderately conservative 600509 11p15.1 "ATP-binding cassette, sub-family C (CFTR/MRP), member 8" 1244 rs757110 ABCC8 6833 11 17375053 NM_000352 NP_000343 G/T A1369S minus 128868 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 94 0.46 0.37 0.04 1209 5 0.11 0.16 118 3 123 "by doubleHit,freq,cluster" Benign 0.151 18 moderately conservative 600509 11p15.1 "ATP-binding cassette, sub-family C (CFTR/MRP), member 8" 1245 rs757110 ABCC8 6833 11 17375053 NM_000352 NP_000343 G/T A1369S minus 128868 1303 SEQUENOM CEPH CEPH (92) 92 0.31 0.37 0.04 1209 5 0.11 0.16 118 3 123 "by doubleHit,freq,cluster" Benign 0.151 18 moderately conservative 600509 11p15.1 "ATP-binding cassette, sub-family C (CFTR/MRP), member 8" 1246 rs757110 ABCC8 6833 11 17375053 NM_000352 NP_000343 G/T A1369S minus 12587336 928 IBARROSO ELY UK (Ely region of East Anglia) 921 0.37 0.37 0.04 1209 5 0.11 0.16 118 3 123 "by doubleHit,freq,cluster" Benign 0.151 18 moderately conservative 600509 11p15.1 "ATP-binding cassette, sub-family C (CFTR/MRP), member 8" 1247 rs757660 SEC14L2 23541 22 29117691 NM_012429 NP_036561 A/G R11K plus 129607 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 80 0.19 0.25 0.04 336 4 0.37 0.1 230 4 123 "HapMap,doubleHit,freq,cluster" Benign 0.308 17 Tolerant 1 2.94 29 conservative 607558 22q12.2 SEC14-like 2 (S. cerevisiae) 1248 rs757660 SEC14L2 23541 22 29117691 NM_012429 NP_036561 A/G R11K plus 5184931 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.28 0.25 0.04 336 4 0.37 0.1 230 4 123 "HapMap,doubleHit,freq,cluster" Benign 0.308 17 Tolerant 1 2.94 29 conservative 607558 22q12.2 SEC14-like 2 (S. cerevisiae) 1249 rs757660 SEC14L2 23541 22 29117691 NM_012429 NP_036561 A/G R11K plus 5184931 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.25 0.04 336 4 0.37 0.1 230 4 123 "HapMap,doubleHit,freq,cluster" Benign 0.308 17 Tolerant 1 2.94 29 conservative 607558 22q12.2 SEC14-like 2 (S. cerevisiae) 1250 rs757660 SEC14L2 23541 22 29117691 NM_012429 NP_036561 A/G R11K plus 23665295 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.27 0.25 0.04 336 4 0.37 0.1 230 4 123 "HapMap,doubleHit,freq,cluster" Benign 0.308 17 Tolerant 1 2.94 29 conservative 607558 22q12.2 SEC14-like 2 (S. cerevisiae) 1251 rs760357 TPSG1 25823 16 1213491 NM_012467 NP_036599 A/G V60M minus 133243 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.14 0.27 0.07 106 2 0.14 0.02 1506 2 100 "by cluster,freq" conservative 16p13.3 tryptase gamma 1 1252 rs760357 TPSG1 25823 16 1213491 NM_012467 NP_036599 A/G V60M minus 133243 1303 SEQUENOM CEPH CEPH (92) 92 0.29 0.27 0.07 106 2 0.14 0.02 1506 2 100 "by cluster,freq" conservative 16p13.3 tryptase gamma 1 1253 rs760749 MOV10L1 54456 22 48858143 NM_018995 NP_061868 A/C I454L plus 24214763 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.12 0.11 94 2 123 "by doubleHit,submitter,freq,cluster" conservative 605794 22q13.33 "Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)" 1254 rs763361 CD226 10666 18 65682622 NM_006566 NP_006557 C/T S307G plus 149473 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.48 0.45 0.04 236 3 0.34 0.01 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 605397 18q22.3 CD226 antigen 1255 rs763361 CD226 10666 18 65682622 NM_006566 NP_006557 C/T S307G plus 149473 1303 SEQUENOM CEPH CEPH (92) 92 0.41 0.45 0.04 236 3 0.34 0.01 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 605397 18q22.3 CD226 antigen 1256 rs763361 CD226 10666 18 65682622 NM_006566 NP_006557 C/T S307G plus 24509880 1371 PERLEGEN AFD_EUR_PANEL European American (24) 24 0.5 0.45 0.04 236 3 0.34 0.01 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 605397 18q22.3 CD226 antigen 1257 rs764264 VNN3 55350 6 133097427 NM_078625 NP_523239 C/T H33R plus 150727 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.02 0 92 1 86 by freq conservative 606592 6q23-q24 vanin 3 1258 rs764535 TLR5 7100 1 2901488 NM_003268 NP_003259 A/G T82I plus 151118 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 82 0.04 0.05 0.01 118 2 0.15 0 34 1 86 "by submitter,freq" Tolerant 0.46 2.82 10 moderately conservative 603031 1q41-q42 toll-like receptor 5 1259 rs764535 TLR5 7100 1 2901488 NM_003268 NP_003259 A/G T82I plus 151118 904 AFFY CEPH 36 0.06 0.05 0.01 118 2 0.15 0 34 1 86 "by submitter,freq" Tolerant 0.46 2.82 10 moderately conservative 603031 1q41-q42 toll-like receptor 5 1260 rs765746 ZNF30 90075 19 40126909 NM_194325 NP_919306 C/T Y319C minus 152765 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.14 0.12 0.02 228 4 0.32 0.04 768 2 119 "by doubleHit,freq,cluster" Possibly damaging 1.608 242 Intolerant 0 2.74 95 radical 19q13.13 zinc finger protein 30 (KOX 28) 1261 rs765746 ZNF30 90075 19 40126909 NM_194325 NP_919306 C/T Y319C minus 152765 902 AFFY Caucasian 26 0.12 0.12 0.02 228 4 0.32 0.04 768 2 119 "by doubleHit,freq,cluster" Possibly damaging 1.608 242 Intolerant 0 2.74 95 radical 19q13.13 zinc finger protein 30 (KOX 28) 1262 rs765746 ZNF30 90075 19 40126909 NM_194325 NP_919306 C/T Y319C minus 152765 904 AFFY CEPH 26 0.15 0.12 0.02 228 4 0.32 0.04 768 2 119 "by doubleHit,freq,cluster" Possibly damaging 1.608 242 Intolerant 0 2.74 95 radical 19q13.13 zinc finger protein 30 (KOX 28) 1263 rs765746 ZNF30 90075 19 40126909 NM_194325 NP_919306 C/T Y319C minus 152765 1303 SEQUENOM CEPH CEPH (92) 92 0.1 0.12 0.02 228 4 0.32 0.04 768 2 119 "by doubleHit,freq,cluster" Possibly damaging 1.608 242 Intolerant 0 2.74 95 radical 19q13.13 zinc finger protein 30 (KOX 28) 1264 rs766173 BRCA2 675 13 31804480 NM_000059 NP_000050 G/T N289H minus 5586314 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.03 0.03 0.01 330 3 0.04 0.03 318 4 120 "by cluster,freq" Possibly damaging 1.699 9 moderately conservative 600185 13q12.3 "breast cancer 2, early onset" 1265 rs766173 BRCA2 675 13 31804480 NM_000059 NP_000050 G/T N289H minus 5586314 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.03 0.01 330 3 0.04 0.03 318 4 120 "by cluster,freq" Possibly damaging 1.699 9 moderately conservative 600185 13q12.3 "breast cancer 2, early onset" 1266 rs766173 BRCA2 675 13 31804480 NM_000059 NP_000050 G/T N289H minus 16355779 693 EGP_SNPS PDR90 NIHPDR 178 0.04 0.03 0.01 330 3 0.04 0.03 318 4 120 "by cluster,freq" Possibly damaging 1.699 9 moderately conservative 600185 13q12.3 "breast cancer 2, early onset" 1267 rs769193 MPG 4350 16 75652 NM_002434 NP_002425 C/T A258V plus 4388616 693 EGP_SNPS PDR90 NIHPDR 180 0.01 0.01 0 180 1 106 "by cluster,freq" Benign 0.079 10 Tolerant 0.36 2.73 79 moderately conservative 156565 16p13.3 N-methylpurine-DNA glycosylase 1268 rs769242 CCNA2 890 4 123099822 NM_001237 NP_001228 A/G I163V minus 869797 555 UUGC NIH90 NIHPDR 178 0.03 0.03 0.01 410 3 0.02 0.01 298 3 121 "by cluster,freq" Benign 0.106 18 conservative 123835 4q25-q31 cyclin A2 1269 rs769242 CCNA2 890 4 123099822 NM_001237 NP_001228 A/G I163V minus 4478779 693 EGP_SNPS PDR90 NIHPDR 170 0.04 0.03 0.01 410 3 0.02 0.01 298 3 121 "by cluster,freq" Benign 0.106 18 conservative 123835 4q25-q31 cyclin A2 1270 rs769242 CCNA2 890 4 123099822 NM_001237 NP_001228 A/G I163V minus 5586326 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.02 0.03 0.01 410 3 0.02 0.01 298 3 121 "by cluster,freq" Benign 0.106 18 conservative 123835 4q25-q31 cyclin A2 1271 rs769403 GAD1 2571 2 171539042 NM_000817 NP_000808 G/T V474G plus 870094 506 NCBI NIHPDR NIHPDR 86 0.03 0.03 0 86 1 101 "by cluster,freq" Possibly damaging 1.805 21 Tolerant 0.37 2.8 50 moderately radical 605363 2q31 "glutamate decarboxylase 1 (brain, 67kDa)" 1272 rs769416 NBS1 4683 8 91052633 NM_002485 NP_002476 G/T Q216K plus 870110 506 NCBI NIHPDR NIHPDR 156 0.01 0.01 0 332 2 121 "by cluster,freq" Borderline 1.152 8 Tolerant 1 3.08 20 moderately conservative 602667 8q21 Nijmegen breakage syndrome 1 (nibrin) 1273 rs769416 NBS1 4683 8 91052633 NM_002485 NP_002476 G/T Q216K plus 22970238 693 EGP_SNPS PDR90 NIHPDR 176 0.01 0.01 0 332 2 121 "by cluster,freq" Borderline 1.152 8 Tolerant 1 3.08 20 moderately conservative 602667 8q21 Nijmegen breakage syndrome 1 (nibrin) 1274 rs769420 NBS1 4683 8 91051867 NM_002485 NP_002476 A/G P266L plus 870114 506 NCBI NIHPDR NIHPDR 170 0.03 0.02 0.01 346 2 121 "HapMap,freq,cluster" Probably damaging 2.55 8 Intolerant 0.01 3.24 16 moderately conservative 602667 8q21 Nijmegen breakage syndrome 1 (nibrin) 1275 rs769420 NBS1 4683 8 91051867 NM_002485 NP_002476 A/G P266L plus 22970244 693 EGP_SNPS PDR90 NIHPDR 176 0.02 0.02 0.01 346 2 121 "HapMap,freq,cluster" Probably damaging 2.55 8 Intolerant 0.01 3.24 16 moderately conservative 602667 8q21 Nijmegen breakage syndrome 1 (nibrin) 1276 rs769443 FAU 2197 11 64644854 NM_001997 NP_001988 A/G V93M minus 870145 555 UUGC NIH90 NIHPDR 180 0.01 0.01 0 358 2 119 "by cluster,freq" Potentially damaging 1.438 13 Intolerant 0 3.02 74 conservative 134690 11q13 Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed (fox derived); ribosomal protein S30 1277 rs769443 FAU 2197 11 64644854 NM_001997 NP_001988 A/G V93M minus 12709619 693 EGP_SNPS PDR90 NIHPDR 178 0.01 0.01 0 358 2 119 "by cluster,freq" Potentially damaging 1.438 13 Intolerant 0 3.02 74 conservative 134690 11q13 Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed (fox derived); ribosomal protein S30 1278 rs769452 APOE 348 19 50102950 NM_000041 NP_000032 C/T L46P plus 870160 563 DEBNICK MDECODE-1 European-Americans 48 0.02 0.02 0 48 1 86 by freq Potentially damaging 1.381 27 Tolerant 0.26 2.86 26 moderately conservative 107741 19q13.2 apolipoprotein E 1279 rs770087 DUSP6 1848 12 88247241 NM_001946 NP_001937 G/T S144A minus 1798733 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.2 0.01 140 2 0.05 0.1 964 2 123 "by doubleHit,freq,cluster" Benign 0.134 18 Potentially intolerant 0.1 2.83 45 moderately conservative 602748 12q22-q23 dual specificity phosphatase 6 1280 rs770087 DUSP6 1848 12 88247241 NM_001946 NP_001937 G/T S144A minus 23458622 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.2 0.01 140 2 0.05 0.1 964 2 123 "by doubleHit,freq,cluster" Benign 0.134 18 Potentially intolerant 0.1 2.83 45 moderately conservative 602748 12q22-q23 dual specificity phosphatase 6 1281 rs773123 ERBB3 2065 12 54781265 NM_001982 NP_001973 A/T S1119C minus 1984870 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.47 0 92 1 121 "by doubleHit,freq,cluster" moderately radical 190151 12q13 v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian) 1282 rs774027 TIMELESS 8914 12 55108645 NM_003920 NP_003911 A/T I455L plus 1986181 1303 SEQUENOM CEPH CEPH (92) 92 0.28 0.3 0.03 140 2 0.25 0.04 94 2 123 "by doubleHit,freq" Benign 0.165 6 conservative 603887 12q12-q13 timeless homolog (Drosophila) 1283 rs774027 TIMELESS 8914 12 55108645 NM_003920 NP_003911 A/T I455L plus 24456217 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.3 0.03 140 2 0.25 0.04 94 2 123 "by doubleHit,freq" Benign 0.165 6 conservative 603887 12q12-q13 timeless homolog (Drosophila) 1284 rs774047 TIMELESS 8914 12 55102189 NM_003920 NP_003911 C/T R831Q plus 1986172 1303 SEQUENOM CEPH CEPH (92) 92 0.48 0.43 0.1 140 2 0.38 0.04 1572 3 123 "by doubleHit,freq,cluster" Benign 0.084 6 conservative 603887 12q12-q13 timeless homolog (Drosophila) 1285 rs774047 TIMELESS 8914 12 55102189 NM_003920 NP_003911 C/T R831Q plus 24456190 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.43 0.1 140 2 0.38 0.04 1572 3 123 "by doubleHit,freq,cluster" Benign 0.084 6 conservative 603887 12q12-q13 timeless homolog (Drosophila) 1286 rs782572 PNPT1 87178 2 55823771 NM_033109 NP_149100 C/T I121V plus 3635716 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.48 0.48 0 120 1 123 "HapMap,doubleHit,submitter,freq" Benign 0.148 9 conservative 2p15 polyribonucleotide nucleotidyltransferase 1 1287 rs783396 AIM1 202 6 107094063 XM_166300 XP_166300 A/C E1819A plus 1615915 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.18 0.03 140 2 0.08 0.01 94 2 123 "by submitter,freq,cluster" moderately radical 601797 6q21 absent in melanoma 1 1288 rs783396 AIM1 202 6 107094063 XM_166300 XP_166300 A/C E1819A plus 24360909 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.18 0.03 140 2 0.08 0.01 94 2 123 "by submitter,freq,cluster" moderately radical 601797 6q21 absent in melanoma 1 1289 rs783420 AIM1 202 6 107066629 XM_166300 XP_166300 C/G G530A minus 2281838 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.44 0 92 1 120 "by doubleHit,freq" moderately conservative 601797 6q21 absent in melanoma 1 1290 rs783423 AIM1 202 6 107065437 XM_166300 XP_166300 A/G S311N plus 23324559 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.2 0.18 94 2 123 "by doubleHit,freq,cluster" conservative 601797 6q21 absent in melanoma 1 1291 rs785467 PIK3R3 8503 1 46233579 NM_003629 NP_003620 A/T N283K minus 1927292 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.36 0.36 0.07 318 4 0.31 0.01 1570 3 123 "HapMap,doubleHit,freq,cluster" Potentially damaging 1.26 37 Tolerant 1 3.04 35 moderately conservative 606076 1p34.1 "phosphoinositide-3-kinase, regulatory subunit, polypeptide 3 (p55, gamma)" 1292 rs785467 PIK3R3 8503 1 46233579 NM_003629 NP_003620 A/T N283K minus 1927292 1303 SEQUENOM CEPH CEPH (92) 92 0.42 0.36 0.07 318 4 0.31 0.01 1570 3 123 "HapMap,doubleHit,freq,cluster" Potentially damaging 1.26 37 Tolerant 1 3.04 35 moderately conservative 606076 1p34.1 "phosphoinositide-3-kinase, regulatory subunit, polypeptide 3 (p55, gamma)" 1293 rs785467 PIK3R3 8503 1 46233579 NM_003629 NP_003620 A/T N283K minus 3177818 619 WICVAR MITOGPOP6 CORIELL Mixed 58 0.24 0.36 0.07 318 4 0.31 0.01 1570 3 123 "HapMap,doubleHit,freq,cluster" Potentially damaging 1.26 37 Tolerant 1 3.04 35 moderately conservative 606076 1p34.1 "phosphoinositide-3-kinase, regulatory subunit, polypeptide 3 (p55, gamma)" 1294 rs785467 PIK3R3 8503 1 46233579 NM_003629 NP_003620 A/T N283K minus 24243577 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.36 0.07 318 4 0.31 0.01 1570 3 123 "HapMap,doubleHit,freq,cluster" Potentially damaging 1.26 37 Tolerant 1 3.04 35 moderately conservative 606076 1p34.1 "phosphoinositide-3-kinase, regulatory subunit, polypeptide 3 (p55, gamma)" 1295 rs788908 ADAMTS3 9508 4 73779321 NM_014243 NP_055058 A/G R138K minus 2198837 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.41 0.26 0.19 248 4 0.26 0.03 1568 4 120 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.189 8 conservative 605011 4q21.1 "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3" 1296 rs788908 ADAMTS3 9508 4 73779321 NM_014243 NP_055058 A/G R138K minus 2198837 902 AFFY Caucasian 24 0.33 0.26 0.19 248 4 0.26 0.03 1568 4 120 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.189 8 conservative 605011 4q21.1 "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3" 1297 rs788908 ADAMTS3 9508 4 73779321 NM_014243 NP_055058 A/G R138K minus 2198837 904 AFFY CEPH 12 0.25 0.26 0.19 248 4 0.26 0.03 1568 4 120 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.189 8 conservative 605011 4q21.1 "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3" 1298 rs788908 ADAMTS3 9508 4 73779321 NM_014243 NP_055058 A/G R138K minus 2198837 1303 SEQUENOM CEPH CEPH (92) 92 0.05 0.26 0.19 248 4 0.26 0.03 1568 4 120 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.189 8 conservative 605011 4q21.1 "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3" 1299 rs794001 N4BP2 55728 4 39944128 NM_018177 NP_060647 A/G D611N plus 2193078 760 TSC-CSHL CEL_CAUCASIAN CELERA Caucasians (30) 60 0.28 0.26 0.04 108 2 0.18 0.09 166 3 123 "by doubleHit,submitter,freq,cluster" conservative 4p14 Nedd4 binding protein 2 1300 rs794001 N4BP2 55728 4 39944128 NM_018177 NP_060647 A/G D611N plus 23719790 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.26 0.04 108 2 0.18 0.09 166 3 123 "by doubleHit,submitter,freq,cluster" conservative 4p14 Nedd4 binding protein 2 1301 rs801720 CERK 64781 22 45402678 NM_182661 NP_872602 G/T E113D minus 8305886 1303 SEQUENOM CEPH CEPH (92) 92 0.39 0.39 0 92 1 0.38 0 1492 1 120 "by doubleHit,freq,cluster" conservative 22q13.31 ceramide kinase 1302 rs805657 SLK 9748 10 105752581 NM_014720 NP_055535 A/G C552Y plus 1951606 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.18 0.17 0.02 260 3 0.19 0.22 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Probably damaging 2.6 10 radical 10q25.1 SNF1 sucrose nonfermenting like kinase (yeast) 1303 rs805657 SLK 9748 10 105752581 NM_014720 NP_055535 A/G C552Y plus 1951606 1303 SEQUENOM CEPH CEPH (92) 92 0.15 0.17 0.02 260 3 0.19 0.22 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Probably damaging 2.6 10 radical 10q25.1 SNF1 sucrose nonfermenting like kinase (yeast) 1304 rs805657 SLK 9748 10 105752581 NM_014720 NP_055535 A/G C552Y plus 23510988 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.17 0.02 260 3 0.19 0.22 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Probably damaging 2.6 10 radical 10q25.1 SNF1 sucrose nonfermenting like kinase (yeast) 1305 rs814628 LIPF 8513 10 90419632 NM_004190 NP_004181 A/G T161A plus 1764627 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.14 0.15 0.01 260 3 0.3 0.05 1392 3 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.802 44 Intolerant 0.01 2.79 39 moderately conservative 601980 10q23.31 "lipase, gastric" 1306 rs814628 LIPF 8513 10 90419632 NM_004190 NP_004181 A/G T161A plus 1764627 1303 SEQUENOM CEPH CEPH (92) 92 0.15 0.15 0.01 260 3 0.3 0.05 1392 3 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.802 44 Intolerant 0.01 2.79 39 moderately conservative 601980 10q23.31 "lipase, gastric" 1307 rs814628 LIPF 8513 10 90419632 NM_004190 NP_004181 A/G T161A plus 24081117 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.15 0.01 260 3 0.3 0.05 1392 3 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.802 44 Intolerant 0.01 2.79 39 moderately conservative 601980 10q23.31 "lipase, gastric" 1308 rs820196 RECQL5 9400 17 71139134 NM_004259 NP_004250 C/T D480G plus 1802369 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.22 0.21 0.02 168 2 0.26 0.08 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.103 7 moderately conservative 603781 17q25.2-q25.3 RecQ protein-like 5 1309 rs820196 RECQL5 9400 17 71139134 NM_004259 NP_004250 C/T D480G plus 24098205 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.21 0.02 168 2 0.26 0.08 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.103 7 moderately conservative 603781 17q25.2-q25.3 RecQ protein-like 5 1310 rs827528 FZD6 8323 8 104381608 NM_003506 NP_003497 A/G M33V plus 1989018 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.3 0.26 0.06 212 2 119 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.25 2.79 85 conservative 603409 8q22.3-q23.1 frizzled homolog 6 (Drosophila) 1311 rs827528 FZD6 8323 8 104381608 NM_003506 NP_003497 A/G M33V plus 1989018 1303 SEQUENOM CEPH CEPH (92) 92 0.21 0.26 0.06 212 2 119 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.25 2.79 85 conservative 603409 8q22.3-q23.1 frizzled homolog 6 (Drosophila) 1312 rs832582 MAP3K1 4214 5 56213500 XM_042066 XP_042066 A/G V1040I plus 1317910 1303 SEQUENOM CEPH CEPH (92) 92 0.15 0.16 0.01 140 2 0.35 0.07 94 2 123 "by submitter,freq,cluster" conservative 600982 5q11.2 mitogen-activated protein kinase kinase kinase 1 1313 rs832582 MAP3K1 4214 5 56213500 XM_042066 XP_042066 A/G V1040I plus 23955529 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.16 0.01 140 2 0.35 0.07 94 2 123 "by submitter,freq,cluster" conservative 600982 5q11.2 mitogen-activated protein kinase kinase kinase 1 1314 rs838827 IKBKAP 8518 9 108748207 NM_003640 NP_003631 C/T R525Q plus 1666273 1303 SEQUENOM CEPH CEPH (92) 92 0.03 0.03 0.01 140 2 120 by doubleHit Benign 0.387 9 Tolerant 0.54 2.94 13 conservative 603722 9q31 "inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein" 1315 rs838827 IKBKAP 8518 9 108748207 NM_003640 NP_003631 C/T R525Q plus 3177966 619 WICVAR MITOGPOP6 CORIELL Mixed 48 0.02 0.03 0.01 140 2 120 by doubleHit Benign 0.387 9 Tolerant 0.54 2.94 13 conservative 603722 9q31 "inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein" 1316 rs843358 EIF2B5 8893 3 185343945 NM_003907 NP_003898 C/T I587V minus 2545226 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.26 0 92 1 0.45 0 1494 1 121 "by doubleHit,freq,cluster" Benign 0.3 6 conservative 603945 3q27.3 "eukaryotic translation initiation factor 2B, subunit 5 epsilon, 82kDa" 1317 rs846266 GLI3 2737 7 41861462 NM_000168 NP_000159 A/G T183A minus 1403663 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.45 0.46 0.04 404 4 0.31 0.17 314 5 123 "by doubleHit,freq,cluster" Benign 0.039 5 moderately conservative 165240 7p13 GLI-Kruppel family member GLI3 (Greig cephalopolysyndactyly syndrome) 1318 rs846266 GLI3 2737 7 41861462 NM_000168 NP_000159 A/G T183A minus 1403663 1303 SEQUENOM CEPH CEPH (92) 92 0.45 0.46 0.04 404 4 0.31 0.17 314 5 123 "by doubleHit,freq,cluster" Benign 0.039 5 moderately conservative 165240 7p13 GLI-Kruppel family member GLI3 (Greig cephalopolysyndactyly syndrome) 1319 rs846266 GLI3 2737 7 41861462 NM_000168 NP_000159 A/G T183A minus 24195653 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.39 0.46 0.04 404 4 0.31 0.17 314 5 123 "by doubleHit,freq,cluster" Benign 0.039 5 moderately conservative 165240 7p13 GLI-Kruppel family member GLI3 (Greig cephalopolysyndactyly syndrome) 1320 rs846266 GLI3 2737 7 41861462 NM_000168 NP_000159 A/G T183A minus 24810597 1303 SEQUENOM CEPH CEPH (92) 184 0.49 0.46 0.04 404 4 0.31 0.17 314 5 123 "by doubleHit,freq,cluster" Benign 0.039 5 moderately conservative 165240 7p13 GLI-Kruppel family member GLI3 (Greig cephalopolysyndactyly syndrome) 1321 rs853678 ZNF323 64288 6 28405292 NM_145909 NP_665916 A/T T50S minus 17877537 1303 SEQUENOM CEPH CEPH (92) 92 0.18 0.16 0.05 136 2 0.18 0.03 1556 3 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.21 2.78 28 moderately conservative 6p21.31 zinc finger protein 323 1322 rs853678 ZNF323 64288 6 28405292 NM_145909 NP_665916 A/T T50S minus 23290944 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.11 0.16 0.05 136 2 0.18 0.03 1556 3 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.21 2.78 28 moderately conservative 6p21.31 zinc finger protein 323 1323 rs854524 PPP1R9A 55607 7 94543462 XM_371933 XP_371933 A/G R1017Q plus 1847017 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.46 0.02 140 2 0.4 0.08 90 2 123 "by doubleHit,submitter,freq,cluster" conservative 602468 7q21.3 "protein phosphatase 1, regulatory (inhibitor) subunit 9A" 1324 rs854524 PPP1R9A 55607 7 94543462 XM_371933 XP_371933 A/G R1017Q plus 24194066 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.46 0.02 140 2 0.4 0.08 90 2 123 "by doubleHit,submitter,freq,cluster" conservative 602468 7q21.3 "protein phosphatase 1, regulatory (inhibitor) subunit 9A" 1325 rs855314 PGM1 5236 1 63807132 NM_002633 NP_002624 C/T I88V minus 2583793 902 AFFY Caucasian 24 0.08 0.11 0.06 36 2 0.12 0.04 62 3 116 "by doubleHit,submitter,freq,cluster" Benign 0.155 95 Tolerant 1 2.82 108 conservative 171900 1p31 phosphoglucomutase 1 1326 rs855314 PGM1 5236 1 63807132 NM_002633 NP_002624 C/T I88V minus 2583793 904 AFFY CEPH 12 0.17 0.11 0.06 36 2 0.12 0.04 62 3 116 "by doubleHit,submitter,freq,cluster" Benign 0.155 95 Tolerant 1 2.82 108 conservative 171900 1p31 phosphoglucomutase 1 1327 rs855791 TMPRSS6 164656 22 35787436 NM_153609 NP_705837 C/T V736A minus 24601298 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.41 0.41 0 46 1 0.29 0.17 92 2 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.66 2.78 36 moderately conservative 22q13.1 "transmembrane protease, serine 6" 1328 rs859210 AKR7A2 8574 1 19380011 NM_003689 NP_003680 A/G E180K minus 2040466 1303 SEQUENOM CEPH CEPH (92) 92 0.05 0.05 0 92 1 98 by freq Potentially damaging 1.47 27 Intolerant 0.02 2.77 20 moderately conservative 603418 1p35.1-p36.23 "aldo-keto reductase family 7, member A2 (aflatoxin aldehyde reductase)" 1329 rs861539 XRCC3 7517 14 103235506 NM_005432 NP_005423 C/T T241M minus 1719048 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.35 0.31 0.1 416 4 0.21 0.09 508 6 119 "by cluster,freq" Potentially intolerant 0.07 2.78 11 moderately conservative 600675 14q32.3 X-ray repair complementing defective repair in Chinese hamster cells 3 1330 rs861539 XRCC3 7517 14 103235506 NM_005432 NP_005423 C/T T241M minus 4472483 693 EGP_SNPS PDR90 NIHPDR 180 0.22 0.31 0.1 416 4 0.21 0.09 508 6 119 "by cluster,freq" Potentially intolerant 0.07 2.78 11 moderately conservative 600675 14q32.3 X-ray repair complementing defective repair in Chinese hamster cells 3 1331 rs861539 XRCC3 7517 14 103235506 NM_005432 NP_005423 C/T T241M minus 4472483 1303 SEQUENOM CEPH CEPH (92) 92 0.35 0.31 0.1 416 4 0.21 0.09 508 6 119 "by cluster,freq" Potentially intolerant 0.07 2.78 11 moderately conservative 600675 14q32.3 X-ray repair complementing defective repair in Chinese hamster cells 3 1332 rs861539 XRCC3 7517 14 103235506 NM_005432 NP_005423 C/T T241M minus 5586983 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.45 0.31 0.1 416 4 0.21 0.09 508 6 119 "by cluster,freq" Potentially intolerant 0.07 2.78 11 moderately conservative 600675 14q32.3 X-ray repair complementing defective repair in Chinese hamster cells 3 1333 rs866484 IFI16 3428 1 155799550 NM_005531 NP_005522 C/G S179T minus 1290164 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 12 0.17 0.17 0.03 194 3 0.42 0 48 2 120 "by doubleHit,freq,cluster" Tolerant 1 3.03 31 moderately conservative 147586 1q22 "interferon, gamma-inducible protein 16" 1334 rs866484 IFI16 3428 1 155799550 NM_005531 NP_005522 C/G S179T minus 1290164 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 90 0.2 0.17 0.03 194 3 0.42 0 48 2 120 "by doubleHit,freq,cluster" Tolerant 1 3.03 31 moderately conservative 147586 1q22 "interferon, gamma-inducible protein 16" 1335 rs866484 IFI16 3428 1 155799550 NM_005531 NP_005522 C/G S179T minus 1290164 1303 SEQUENOM CEPH CEPH (92) 92 0.15 0.17 0.03 194 3 0.42 0 48 2 120 "by doubleHit,freq,cluster" Tolerant 1 3.03 31 moderately conservative 147586 1q22 "interferon, gamma-inducible protein 16" 1336 rs867168 ZNF554 115196 19 2784802 NM_152303 NP_689516 C/T E139G minus 1288955 1303 SEQUENOM CEPH CEPH (92) 92 0.29 0.26 0.05 140 2 0.25 0.3 94 2 123 "by doubleHit,freq" Tolerant 0.37 2.79 20 moderately conservative 19p13.3 zinc finger protein 554 1337 rs867168 ZNF554 115196 19 2784802 NM_152303 NP_689516 C/T E139G minus 24190893 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.26 0.05 140 2 0.25 0.3 94 2 123 "by doubleHit,freq" Tolerant 0.37 2.79 20 moderately conservative 19p13.3 zinc finger protein 554 1338 rs867169 ZNF554 115196 19 2784864 NM_152303 NP_689516 C/T V160I minus 1288956 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.2 0.01 140 2 0.29 0.25 94 2 123 "by doubleHit,submitter,freq" Tolerant 0.39 2.79 20 conservative 19p13.3 zinc finger protein 554 1339 rs867169 ZNF554 115196 19 2784864 NM_152303 NP_689516 C/T V160I minus 24190895 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.2 0.01 140 2 0.29 0.25 94 2 123 "by doubleHit,submitter,freq" Tolerant 0.39 2.79 20 conservative 19p13.3 zinc finger protein 554 1340 rs867186 PROCR 10544 20 33228215 NM_006404 NP_006395 A/G S219G plus 2982093 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 44 0.18 0.13 0.06 184 3 0.06 0.01 140 3 123 "by doubleHit,freq" Benign 0.45 5 moderately conservative 600646 20q11.2 "protein C receptor, endothelial (EPCR)" 1341 rs867186 PROCR 10544 20 33228215 NM_006404 NP_006395 A/G S219G plus 8375245 1303 SEQUENOM CEPH CEPH (92) 92 0.08 0.13 0.06 184 3 0.06 0.01 140 3 123 "by doubleHit,freq" Benign 0.45 5 moderately conservative 600646 20q11.2 "protein C receptor, endothelial (EPCR)" 1342 rs867186 PROCR 10544 20 33228215 NM_006404 NP_006395 A/G S219G plus 24537849 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.13 0.06 184 3 0.06 0.01 140 3 123 "by doubleHit,freq" Benign 0.45 5 moderately conservative 600646 20q11.2 "protein C receptor, endothelial (EPCR)" 1343 rs867228 FPR1 2357 19 56941023 NM_002029 NP_002020 A/C E346A minus 1289025 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.22 0.27 0.07 256 3 0.26 0.03 810 3 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.952 21 Tolerant 0.34 3.06 22 moderately radical 136537 19q13.4 formyl peptide receptor 1 1344 rs867228 FPR1 2357 19 56941023 NM_002029 NP_002020 A/C E346A minus 1289025 1303 SEQUENOM CEPH CEPH (92) 92 0.35 0.27 0.07 256 3 0.26 0.03 810 3 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.952 21 Tolerant 0.34 3.06 22 moderately radical 136537 19q13.4 formyl peptide receptor 1 1345 rs867228 FPR1 2357 19 56941023 NM_002029 NP_002020 A/C E346A minus 24198505 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.27 0.07 256 3 0.26 0.03 810 3 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.952 21 Tolerant 0.34 3.06 22 moderately radical 136537 19q13.4 formyl peptide receptor 1 1346 rs869457 LAMC3 10319 9 130954005 NM_006059 NP_006050 A/G P522S minus 1291793 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 82 0.37 0.3 0.09 174 2 0.2 0.01 1572 2 120 "by doubleHit,freq,cluster" Tolerant 0.98 2.83 17 moderately conservative 604349 9q31-q34 "laminin, gamma 3" 1347 rs869457 LAMC3 10319 9 130954005 NM_006059 NP_006050 A/G P522S minus 1291793 1303 SEQUENOM CEPH CEPH (92) 92 0.24 0.3 0.09 174 2 0.2 0.01 1572 2 120 "by doubleHit,freq,cluster" Tolerant 0.98 2.83 17 moderately conservative 604349 9q31-q34 "laminin, gamma 3" 1348 rs871443 ITGB4 3691 17 71265098 NM_000213 NP_000204 C/T L1779P plus 1294606 1303 SEQUENOM CEPH CEPH (92) 92 0.21 0.21 0 92 1 121 "by doubleHit,freq,cluster" Benign 0.377 8 moderately conservative 147557 17q11-qter "integrin, beta 4" 1349 rs871545 ZNF295 49854 21 42286720 NM_020727 NP_065778 A/G N185S minus 1294761 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.16 0 92 1 111 by freq conservative 21q22.3 zinc finger protein 295 1350 rs871546 ZNF295 49854 21 42286622 NM_020727 NP_065778 A/C K218Q minus 1294762 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.38 0.17 140 2 0.04 0.04 94 2 123 "by doubleHit,freq,cluster" moderately conservative 21q22.3 zinc finger protein 295 1351 rs871546 ZNF295 49854 21 42286622 NM_020727 NP_065778 A/C K218Q minus 24605064 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.38 0.17 140 2 0.04 0.04 94 2 123 "by doubleHit,freq,cluster" moderately conservative 21q22.3 zinc finger protein 295 1352 rs874808 DNAH8 1769 6 38881271 NM_001371 NP_001362 C/T G807E minus 1299055 902 AFFY Caucasian 22 0.45 0.42 0.05 174 4 0.37 0.13 156 5 123 "by doubleHit,freq,cluster" Potentially damaging 1.414 13 moderately conservative 603337 6p21.31-p21.1 "dynein, axonemal, heavy polypeptide 8" 1353 rs874808 DNAH8 1769 6 38881271 NM_001371 NP_001362 C/T G807E minus 1299055 904 AFFY CEPH 12 0.33 0.42 0.05 174 4 0.37 0.13 156 5 123 "by doubleHit,freq,cluster" Potentially damaging 1.414 13 moderately conservative 603337 6p21.31-p21.1 "dynein, axonemal, heavy polypeptide 8" 1354 rs874808 DNAH8 1769 6 38881271 NM_001371 NP_001362 C/T G807E minus 1299055 1303 SEQUENOM CEPH CEPH (92) 92 0.4 0.42 0.05 174 4 0.37 0.13 156 5 123 "by doubleHit,freq,cluster" Potentially damaging 1.414 13 moderately conservative 603337 6p21.31-p21.1 "dynein, axonemal, heavy polypeptide 8" 1355 rs874808 DNAH8 1769 6 38881271 NM_001371 NP_001362 C/T G807E minus 24370109 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.42 0.05 174 4 0.37 0.13 156 5 123 "by doubleHit,freq,cluster" Potentially damaging 1.414 13 moderately conservative 603337 6p21.31-p21.1 "dynein, axonemal, heavy polypeptide 8" 1356 rs875379 LAMA5 3911 20 60335381 NM_005560 NP_005551 A/G H1717Y plus 1299815 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.1 0.11 0.02 166 2 0.11 0 46 1 123 "HapMap,freq" Possibly damaging 1.834 6 Tolerant 0.35 2.84 12 moderately conservative 601033 20q13.2-q13.3 "laminin, alpha 5" 1357 rs875379 LAMA5 3911 20 60335381 NM_005560 NP_005551 A/G H1717Y plus 24601596 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.11 0.02 166 2 0.11 0 46 1 123 "HapMap,freq" Possibly damaging 1.834 6 Tolerant 0.35 2.84 12 moderately conservative 601033 20q13.2-q13.3 "laminin, alpha 5" 1358 rs878756 MKL1 57591 22 39139000 NM_020831 NP_065882 A/G S648G minus 7998468 1303 SEQUENOM CEPH CEPH (92) 92 0.46 0.4 0.11 140 2 0.2 0.11 94 2 123 "by doubleHit,freq,cluster" Potentially intolerant 0.07 2.83 20 moderately conservative 606078 22q13 megakaryoblastic leukemia (translocation) 1 1359 rs878756 MKL1 57591 22 39139000 NM_020831 NP_065882 A/G S648G minus 24539613 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.4 0.11 140 2 0.2 0.11 94 2 123 "by doubleHit,freq,cluster" Potentially intolerant 0.07 2.83 20 moderately conservative 606078 22q13 megakaryoblastic leukemia (translocation) 1 1360 rs880303 GJA10 81025 1 39009375 NM_030772 NP_110399 C/T V497I plus 1306346 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.49 0.46 0.05 294 5 0.32 0.11 162 5 123 "HapMap,doubleHit,submitter,freq" conservative 1p34 "gap junction protein, alpha 10, 59kDa" 1361 rs880303 GJA10 81025 1 39009375 NM_030772 NP_110399 C/T V497I plus 1306346 902 AFFY Caucasian 24 0.42 0.46 0.05 294 5 0.32 0.11 162 5 123 "HapMap,doubleHit,submitter,freq" conservative 1p34 "gap junction protein, alpha 10, 59kDa" 1362 rs880303 GJA10 81025 1 39009375 NM_030772 NP_110399 C/T V497I plus 1306346 904 AFFY CEPH 10 0.3 0.46 0.05 294 5 0.32 0.11 162 5 123 "HapMap,doubleHit,submitter,freq" conservative 1p34 "gap junction protein, alpha 10, 59kDa" 1363 rs880303 GJA10 81025 1 39009375 NM_030772 NP_110399 C/T V497I plus 1306346 1303 SEQUENOM CEPH CEPH (92) 92 0.43 0.46 0.05 294 5 0.32 0.11 162 5 123 "HapMap,doubleHit,submitter,freq" conservative 1p34 "gap junction protein, alpha 10, 59kDa" 1364 rs880303 GJA10 81025 1 39009375 NM_030772 NP_110399 C/T V497I plus 24260345 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.46 0.05 294 5 0.32 0.11 162 5 123 "HapMap,doubleHit,submitter,freq" conservative 1p34 "gap junction protein, alpha 10, 59kDa" 1365 rs880633 CHI3L1 1116 1 199884458 NM_001276 NP_001267 C/T R145G plus 1306850 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.43 0.42 0.08 248 4 0.36 0.03 1576 3 123 "by doubleHit,freq,cluster" Probably damaging 2.271 34 Intolerant 0 2.75 66 moderately radical 601525 1q32.1 chitinase 3-like 1 (cartilage glycoprotein-39) 1366 rs880633 CHI3L1 1116 1 199884458 NM_001276 NP_001267 C/T R145G plus 1306850 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 94 0.49 0.42 0.08 248 4 0.36 0.03 1576 3 123 "by doubleHit,freq,cluster" Probably damaging 2.271 34 Intolerant 0 2.75 66 moderately radical 601525 1q32.1 chitinase 3-like 1 (cartilage glycoprotein-39) 1367 rs880633 CHI3L1 1116 1 199884458 NM_001276 NP_001267 C/T R145G plus 1306850 1303 SEQUENOM CEPH CEPH (92) 92 0.33 0.42 0.08 248 4 0.36 0.03 1576 3 123 "by doubleHit,freq,cluster" Probably damaging 2.271 34 Intolerant 0 2.75 66 moderately radical 601525 1q32.1 chitinase 3-like 1 (cartilage glycoprotein-39) 1368 rs880633 CHI3L1 1116 1 199884458 NM_001276 NP_001267 C/T R145G plus 24256121 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.42 0.08 248 4 0.36 0.03 1576 3 123 "by doubleHit,freq,cluster" Probably damaging 2.271 34 Intolerant 0 2.75 66 moderately radical 601525 1q32.1 chitinase 3-like 1 (cartilage glycoprotein-39) 1369 rs882709 KIAA0625 23064 9 132234560 NM_015046 NP_055861 C/G A660G minus 1309695 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.03 0.03 0.01 168 2 0.23 0.17 149 5 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 608465 9q34.3 senataxin 1370 rs882709 KIAA0625 23064 9 132234560 NM_015046 NP_055861 C/G A660G minus 24002655 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.03 0.01 168 2 0.23 0.17 149 5 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 608465 9q34.3 senataxin 1371 rs885479 MC1R 4157 16 88513655 NM_002386 NP_002377 A/G R163Q plus 1313046 1303 SEQUENOM CEPH CEPH (92) 92 0.08 0.06 0.04 138 2 0.02 0 46 1 106 "by doubleHit,freq,cluster" Benign 0.517 210 Tolerant 0.29 2.8 286 conservative 155555 16q24.3 melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor) 1372 rs885479 MC1R 4157 16 88513655 NM_002386 NP_002377 A/G R163Q plus 4472738 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.02 0.06 0.04 138 2 0.02 0 46 1 106 "by doubleHit,freq,cluster" Benign 0.517 210 Tolerant 0.29 2.8 286 conservative 155555 16q24.3 melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor) 1373 rs886016 SARDH 1757 9 133585183 NM_007101 NP_009032 A/G M648V minus 1313716 1303 SEQUENOM CEPH CEPH (92) 92 0.28 0.34 0.12 138 2 0.33 0.15 84 2 123 "by doubleHit,freq,cluster" Tolerant 0.89 2.81 24 conservative 604455 9q33-q34 sarcosine dehydrogenase 1374 rs886016 SARDH 1757 9 133585183 NM_007101 NP_009032 A/G M648V minus 24687247 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.46 0.34 0.12 138 2 0.33 0.15 84 2 123 "by doubleHit,freq,cluster" Tolerant 0.89 2.81 24 conservative 604455 9q33-q34 sarcosine dehydrogenase 1375 rs887241 ALDH3A1 218 17 19586530 NM_000691 NP_000682 G/T S134A minus 1315276 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 6 0.5 0.42 0.06 138 3 0.14 0.1 140 4 123 "by doubleHit,freq,cluster" Benign 0.408 38 Tolerant 0.98 2.79 54 moderately conservative 100660 17p11.2 "aldehyde dehydrogenase 3 family, memberA1" 1376 rs887241 ALDH3A1 218 17 19586530 NM_000691 NP_000682 G/T S134A minus 1315276 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 86 0.45 0.42 0.06 138 3 0.14 0.1 140 4 123 "by doubleHit,freq,cluster" Benign 0.408 38 Tolerant 0.98 2.79 54 moderately conservative 100660 17p11.2 "aldehyde dehydrogenase 3 family, memberA1" 1377 rs887241 ALDH3A1 218 17 19586530 NM_000691 NP_000682 G/T S134A minus 24596928 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.35 0.42 0.06 138 3 0.14 0.1 140 4 123 "by doubleHit,freq,cluster" Benign 0.408 38 Tolerant 0.98 2.79 54 moderately conservative 100660 17p11.2 "aldehyde dehydrogenase 3 family, memberA1" 1378 rs890802 COL23A1 91522 5 177615983 NM_173465 NP_775736 A/G T287A minus 24373538 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.48 0 48 1 0.43 0.08 94 2 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.61 2.77 14 moderately conservative 5q35.3 "collagen, type XXIII, alpha 1" 1379 rs893253 PIP5K3 200576 2 209016034 NM_015040 NP_055855 C/G T998S minus 1323017 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.02 0 92 1 121 "by doubleHit,freq,cluster" moderately conservative 2q34 "phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III" 1380 rs893254 PIP5K3 200576 2 209016025 NM_015040 NP_055855 A/T Q995L minus 1323018 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.05 0.05 0 84 1 0.22 0 82 1 121 "by doubleHit,freq,cluster" moderately radical 2q34 "phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III" 1381 rs897945 THAP9 79725 4 84195441 NM_024672 NP_078948 A/C L299F minus 1328858 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.46 0.43 0.06 260 3 0.29 0.04 1590 3 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 4q21.3 THAP domain containing 9 1382 rs897945 THAP9 79725 4 84195441 NM_024672 NP_078948 A/C L299F minus 1328858 1303 SEQUENOM CEPH CEPH (92) 92 0.36 0.43 0.06 260 3 0.29 0.04 1590 3 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 4q21.3 THAP domain containing 9 1383 rs897945 THAP9 79725 4 84195441 NM_024672 NP_078948 A/C L299F minus 24236182 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.43 0.06 260 3 0.29 0.04 1590 3 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 4q21.3 THAP domain containing 9 1384 rs902790 GPR156 165829 3 121369466 NM_153002 NP_694547 A/T E516D minus 23255540 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.05 0.05 94 2 123 "by cluster,freq" conservative 3q13.33 G protein-coupled receptor 156 1385 rs903365 PPFIA4 8497 1 199776699 XM_046751 XP_046751 C/T C1347R plus 1335657 1303 SEQUENOM CEPH CEPH (92) 92 0.14 0.14 0 92 1 121 "by doubleHit,freq,cluster" radical 603145 1q32.1 "protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4" 1386 rs906807 NDUFV2 4729 18 9107867 NM_021074 NP_066552 A/G V29A minus 1340074 1303 SEQUENOM CEPH CEPH (92) 92 0.23 0.23 0 92 1 121 "by doubleHit,submitter,freq" Benign 0.135 11 moderately conservative 600532 18p11.31-p11.2 "NADH dehydrogenase (ubiquinone) flavoprotein 2, 24kDa" 1387 rs910397 PXMP4 11264 20 31759202 NM_007238 NP_009169 C/T V204I plus 1344491 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 42 0.5 0.43 0.06 182 3 0.28 0.15 262 4 123 "by doubleHit,submitter,freq,cluster" Borderline 1.018 6 conservative 20q11.22 "peroxisomal membrane protein 4, 24kDa" 1388 rs910397 PXMP4 11264 20 31759202 NM_007238 NP_009169 C/T V204I plus 8372329 1303 SEQUENOM CEPH CEPH (92) 92 0.38 0.43 0.06 182 3 0.28 0.15 262 4 123 "by doubleHit,submitter,freq,cluster" Borderline 1.018 6 conservative 20q11.22 "peroxisomal membrane protein 4, 24kDa" 1389 rs910397 PXMP4 11264 20 31759202 NM_007238 NP_009169 C/T V204I plus 24537183 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.43 0.06 182 3 0.28 0.15 262 4 123 "by doubleHit,submitter,freq,cluster" Borderline 1.018 6 conservative 20q11.22 "peroxisomal membrane protein 4, 24kDa" 1390 rs915836 ZNF295 49854 21 42286430 NM_020727 NP_065778 C/T V282I plus 1351111 1303 SEQUENOM CEPH CEPH (92) 92 0.49 0.49 0 92 1 86 by freq conservative 21q22.3 zinc finger protein 295 1391 rs915843 ABCG1 9619 21 42552623 NM_207630 NP_997513 C/T P172L plus 4020640 634 PERLEGEN NCBI|NIHPDR NIHPDR 10 0.4 0.15 0.17 54 2 0.13 0.06 1576 3 123 "by doubleHit,submitter,freq,cluster" moderately conservative 603076 21q22.3 "ATP-binding cassette, sub-family G (WHITE), member 1" 1392 rs915843 ABCG1 9619 21 42552623 NM_207630 NP_997513 C/T P172L plus 23652333 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.09 0.15 0.17 54 2 0.13 0.06 1576 3 123 "by doubleHit,submitter,freq,cluster" moderately conservative 603076 21q22.3 "ATP-binding cassette, sub-family G (WHITE), member 1" 1393 rs917535 PCDHB11 56125 5 140559551 NM_018931 NP_061754 C/T R7H minus 1353203 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 82 0.01 0.05 0.05 222 3 0.12 0 120 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.168 62 Tolerant 0.22 2.82 102 conservative 606337 5q31 protocadherin beta 11 1394 rs917535 PCDHB11 56125 5 140559551 NM_018931 NP_061754 C/T R7H minus 1353203 1303 SEQUENOM CEPH CEPH (92) 92 0.09 0.05 0.05 222 3 0.12 0 120 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.168 62 Tolerant 0.22 2.82 102 conservative 606337 5q31 protocadherin beta 11 1395 rs917535 PCDHB11 56125 5 140559551 NM_018931 NP_061754 C/T R7H minus 23351567 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.05 0.05 222 3 0.12 0 120 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.168 62 Tolerant 0.22 2.82 102 conservative 606337 5q31 protocadherin beta 11 1396 rs922697 SPON2 10417 4 1155571 NM_012445 NP_036577 A/G L40P plus 1359563 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 24 0.04 0.02 0.02 118 2 0.05 0 20 1 121 "HapMap,cluster" Benign 0.519 10 moderately conservative 605918 4p16.3 "spondin 2, extracellular matrix protein" 1397 rs922697 SPON2 10417 4 1155571 NM_012445 NP_036577 A/G L40P plus 1359563 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 94 0.01 0.02 0.02 118 2 0.05 0 20 1 121 "HapMap,cluster" Benign 0.519 10 moderately conservative 605918 4p16.3 "spondin 2, extracellular matrix protein" 1398 rs929387 GLI3 2737 7 41778918 NM_000168 NP_000159 C/T P998L minus 23376218 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.33 0.33 0 46 1 0.25 0.13 88 2 123 "by doubleHit,freq,cluster" Benign 0.2 7 moderately conservative 165240 7p13 GLI-Kruppel family member GLI3 (Greig cephalopolysyndactyly syndrome) 1399 rs930337 SORD 6652 15 43151826 NM_003104 NP_003095 A/C N269T plus 5252928 1303 SEQUENOM CEPH CEPH (92) 92 0.05 0.05 0 276 2 123 "by submitter,freq,cluster" Possibly damaging 1.764 25 moderately conservative 182500 15q15.3 sorbitol dehydrogenase 1400 rs930337 SORD 6652 15 43151826 NM_003104 NP_003095 A/C N269T plus 24802709 1303 SEQUENOM CEPH CEPH (92) 184 0.05 0.05 0 276 2 123 "by submitter,freq,cluster" Possibly damaging 1.764 25 moderately conservative 182500 15q15.3 sorbitol dehydrogenase 1401 rs933135 PLCD1 5333 3 38027729 NM_006225 NP_006216 C/T R257H plus 1372137 765 TSC-CSHL MOT_CAUCASIAN_CEPH MOTOROLA CEPH Caucasians (637) 320 0.02 0.02 0.01 438 3 0.19 0.02 84 2 111 by freq Potentially damaging 1.461 17 Potentially intolerant 0.08 2.77 40 conservative 602142 3p22-p21.3 "phospholipase C, delta 1" 1402 rs933135 PLCD1 5333 3 38027729 NM_006225 NP_006216 C/T R257H plus 1372137 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 24 0.04 0.02 0.01 438 3 0.19 0.02 84 2 111 by freq Potentially damaging 1.461 17 Potentially intolerant 0.08 2.77 40 conservative 602142 3p22-p21.3 "phospholipase C, delta 1" 1403 rs933135 PLCD1 5333 3 38027729 NM_006225 NP_006216 C/T R257H plus 1372137 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 94 0.02 0.02 0.01 438 3 0.19 0.02 84 2 111 by freq Potentially damaging 1.461 17 Potentially intolerant 0.08 2.77 40 conservative 602142 3p22-p21.3 "phospholipase C, delta 1" 1404 rs934945 PER2 8864 2 238937053 NM_022817 NP_073728 A/G G1244E minus 1374311 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.14 0.18 0.07 226 3 0.13 0.08 40 2 86 "HapMap,submitter,freq" moderately conservative 603426 2q37.3 period homolog 2 (Drosophila) 1405 rs934945 PER2 8864 2 238937053 NM_022817 NP_073728 A/G G1244E minus 1374311 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.13 0.18 0.07 226 3 0.13 0.08 40 2 86 "HapMap,submitter,freq" moderately conservative 603426 2q37.3 period homolog 2 (Drosophila) 1406 rs934945 PER2 8864 2 238937053 NM_022817 NP_073728 A/G G1244E minus 1374311 1303 SEQUENOM CEPH CEPH (92) 92 0.25 0.18 0.07 226 3 0.13 0.08 40 2 86 "HapMap,submitter,freq" moderately conservative 603426 2q37.3 period homolog 2 (Drosophila) 1407 rs937838 TGM4 7047 3 44918108 NM_003241 NP_003232 C/G S249T plus 1377860 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.21 0.2 0.04 198 3 0.04 0 1526 2 100 "by cluster,freq" Intolerant 0 2.78 17 moderately conservative 600585 3p22-p21.33 transglutaminase 4 (prostate) 1408 rs937838 TGM4 7047 3 44918108 NM_003241 NP_003232 C/G S249T plus 1377860 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 92 0.17 0.2 0.04 198 3 0.04 0 1526 2 100 "by cluster,freq" Intolerant 0 2.78 17 moderately conservative 600585 3p22-p21.33 transglutaminase 4 (prostate) 1409 rs937838 TGM4 7047 3 44918108 NM_003241 NP_003232 C/G S249T plus 1377860 1303 SEQUENOM CEPH CEPH (92) 92 0.23 0.2 0.04 198 3 0.04 0 1526 2 100 "by cluster,freq" Intolerant 0 2.78 17 moderately conservative 600585 3p22-p21.33 transglutaminase 4 (prostate) 1410 rs938886 TEP1 7011 14 19907541 NM_007110 NP_009041 C/G I2486M plus 1379184 760 TSC-CSHL CEL_CAUCASIAN CELERA Caucasians (30) 58 0.28 0.24 0.06 788 9 0.29 0.11 310 8 123 "HapMap,doubleHit,submitter,freq" conservative 601686 14q11.2 telomerase-associated protein 1 1411 rs938886 TEP1 7011 14 19907541 NM_007110 NP_009041 C/G I2486M plus 1379184 761 TSC-CSHL CEL_CAUCASIAN_CEPH CELERA CEPH Caucasians (661) 318 0.26 0.24 0.06 788 9 0.29 0.11 310 8 123 "HapMap,doubleHit,submitter,freq" conservative 601686 14q11.2 telomerase-associated protein 1 1412 rs938886 TEP1 7011 14 19907541 NM_007110 NP_009041 C/G I2486M plus 1379184 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 10 0.2 0.24 0.06 788 9 0.29 0.11 310 8 123 "HapMap,doubleHit,submitter,freq" conservative 601686 14q11.2 telomerase-associated protein 1 1413 rs938886 TEP1 7011 14 19907541 NM_007110 NP_009041 C/G I2486M plus 1379184 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.25 0.24 0.06 788 9 0.29 0.11 310 8 123 "HapMap,doubleHit,submitter,freq" conservative 601686 14q11.2 telomerase-associated protein 1 1414 rs938886 TEP1 7011 14 19907541 NM_007110 NP_009041 C/G I2486M plus 1379184 1303 SEQUENOM CEPH CEPH (92) 92 0.09 0.24 0.06 788 9 0.29 0.11 310 8 123 "HapMap,doubleHit,submitter,freq" conservative 601686 14q11.2 telomerase-associated protein 1 1415 rs938886 TEP1 7011 14 19907541 NM_007110 NP_009041 C/G I2486M plus 2549686 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.29 0.24 0.06 788 9 0.29 0.11 310 8 123 "HapMap,doubleHit,submitter,freq" conservative 601686 14q11.2 telomerase-associated protein 1 1416 rs938886 TEP1 7011 14 19907541 NM_007110 NP_009041 C/G I2486M plus 2549686 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 94 0.29 0.24 0.06 788 9 0.29 0.11 310 8 123 "HapMap,doubleHit,submitter,freq" conservative 601686 14q11.2 telomerase-associated protein 1 1417 rs938886 TEP1 7011 14 19907541 NM_007110 NP_009041 C/G I2486M plus 3172659 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 34 0.26 0.24 0.06 788 9 0.29 0.11 310 8 123 "HapMap,doubleHit,submitter,freq" conservative 601686 14q11.2 telomerase-associated protein 1 1418 rs938886 TEP1 7011 14 19907541 NM_007110 NP_009041 C/G I2486M plus 23814904 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.24 0.06 788 9 0.29 0.11 310 8 123 "HapMap,doubleHit,submitter,freq" conservative 601686 14q11.2 telomerase-associated protein 1 1419 rs940389 SBLF 11037 2 48719803 NM_006873 NP_006864 C/G R127T plus 1380968 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.38 0.41 0.04 260 3 0.4 0.02 1578 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 605357 2p16.3 stoned B-like factor 1420 rs940389 SBLF 11037 2 48719803 NM_006873 NP_006864 C/G R127T plus 1380968 1303 SEQUENOM CEPH CEPH (92) 92 0.45 0.41 0.04 260 3 0.4 0.02 1578 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 605357 2p16.3 stoned B-like factor 1421 rs940389 SBLF 11037 2 48719803 NM_006873 NP_006864 C/G R127T plus 24156949 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.41 0.04 260 3 0.4 0.02 1578 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 605357 2p16.3 stoned B-like factor 1422 rs947894 GSTP1 2950 11 67109265 NM_000852 NP_000843 A/G I105V plus 1390210 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.39 0.39 0.04 480 5 0.36 0.08 1028 7 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.129 26 Tolerant 0.9 2.8 39 conservative 134660 11q13 glutathione S-transferase pi 1423 rs947894 GSTP1 2950 11 67109265 NM_000852 NP_000843 A/G I105V plus 1390210 1303 SEQUENOM CEPH CEPH (92) 92 0.42 0.39 0.04 480 5 0.36 0.08 1028 7 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.129 26 Tolerant 0.9 2.8 39 conservative 134660 11q13 glutathione S-transferase pi 1424 rs947894 GSTP1 2950 11 67109265 NM_000852 NP_000843 A/G I105V plus 5586573 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.31 0.39 0.04 480 5 0.36 0.08 1028 7 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.129 26 Tolerant 0.9 2.8 39 conservative 134660 11q13 glutathione S-transferase pi 1425 rs947894 GSTP1 2950 11 67109265 NM_000852 NP_000843 A/G I105V plus 12585355 693 EGP_SNPS PDR90 NIHPDR 160 0.4 0.39 0.04 480 5 0.36 0.08 1028 7 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.129 26 Tolerant 0.9 2.8 39 conservative 134660 11q13 glutathione S-transferase pi 1426 rs947894 GSTP1 2950 11 67109265 NM_000852 NP_000843 A/G I105V plus 23600037 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.37 0.39 0.04 480 5 0.36 0.08 1028 7 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.129 26 Tolerant 0.9 2.8 39 conservative 134660 11q13 glutathione S-transferase pi 1427 rs948615 ZNF407 55628 18 70474878 NM_017757 NP_060227 G/T N158T minus 1391313 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.14 0.15 0.01 226 3 0.28 0.25 40 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 18q23 zinc finger protein 407 1428 rs948615 ZNF407 55628 18 70474878 NM_017757 NP_060227 G/T N158T minus 1391313 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 92 0.16 0.15 0.01 226 3 0.28 0.25 40 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 18q23 zinc finger protein 407 1429 rs948615 ZNF407 55628 18 70474878 NM_017757 NP_060227 G/T N158T minus 1391313 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.15 0.15 0.01 226 3 0.28 0.25 40 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 18q23 zinc finger protein 407 1430 rs956748 TAF2 6873 8 120813530 NM_003184 NP_003175 C/T T1139A plus 1402079 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.09 0.06 0.04 260 3 0.45 0 44 1 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 604912 8q24.12 "TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa" 1431 rs956748 TAF2 6873 8 120813530 NM_003184 NP_003175 C/T T1139A plus 1402079 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.06 0.04 260 3 0.45 0 44 1 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 604912 8q24.12 "TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa" 1432 rs956748 TAF2 6873 8 120813530 NM_003184 NP_003175 C/T T1139A plus 23390318 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.06 0.04 260 3 0.45 0 44 1 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 604912 8q24.12 "TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa" 1433 rs956749 TAF2 6873 8 120813580 NM_003184 NP_003175 C/T S1122N plus 1402080 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.09 0.09 0.04 260 3 0.18 0 44 1 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 604912 8q24.12 "TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa" 1434 rs956749 TAF2 6873 8 120813580 NM_003184 NP_003175 C/T S1122N plus 1402080 1303 SEQUENOM CEPH CEPH (92) 92 0.13 0.09 0.04 260 3 0.18 0 44 1 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 604912 8q24.12 "TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa" 1435 rs956749 TAF2 6873 8 120813580 NM_003184 NP_003175 C/T S1122N plus 23390327 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.09 0.04 260 3 0.18 0 44 1 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 604912 8q24.12 "TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa" 1436 rs956868 PRKWNK1 65125 12 861173 NM_018979 NP_061852 A/C T1056P plus 1402227 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.07 0.16 0.07 424 7 0.19 0.07 238 7 123 "HapMap,doubleHit,freq,cluster" conservative 605232 12p13.3 "protein kinase, lysine deficient 1" 1437 rs956868 PRKWNK1 65125 12 861173 NM_018979 NP_061852 A/C T1056P plus 1402227 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 90 0.13 0.16 0.07 424 7 0.19 0.07 238 7 123 "HapMap,doubleHit,freq,cluster" conservative 605232 12p13.3 "protein kinase, lysine deficient 1" 1438 rs956868 PRKWNK1 65125 12 861173 NM_018979 NP_061852 A/C T1056P plus 1402227 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.11 0.16 0.07 424 7 0.19 0.07 238 7 123 "HapMap,doubleHit,freq,cluster" conservative 605232 12p13.3 "protein kinase, lysine deficient 1" 1439 rs956868 PRKWNK1 65125 12 861173 NM_018979 NP_061852 A/C T1056P plus 1402227 902 AFFY Caucasian 40 0.13 0.16 0.07 424 7 0.19 0.07 238 7 123 "HapMap,doubleHit,freq,cluster" conservative 605232 12p13.3 "protein kinase, lysine deficient 1" 1440 rs956868 PRKWNK1 65125 12 861173 NM_018979 NP_061852 A/C T1056P plus 1402227 904 AFFY CEPH 20 0.35 0.16 0.07 424 7 0.19 0.07 238 7 123 "HapMap,doubleHit,freq,cluster" conservative 605232 12p13.3 "protein kinase, lysine deficient 1" 1441 rs956868 PRKWNK1 65125 12 861173 NM_018979 NP_061852 A/C T1056P plus 1402227 1303 SEQUENOM CEPH CEPH (92) 92 0.24 0.16 0.07 424 7 0.19 0.07 238 7 123 "HapMap,doubleHit,freq,cluster" conservative 605232 12p13.3 "protein kinase, lysine deficient 1" 1442 rs956868 PRKWNK1 65125 12 861173 NM_018979 NP_061852 A/C T1056P plus 23344913 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.16 0.07 424 7 0.19 0.07 238 7 123 "HapMap,doubleHit,freq,cluster" conservative 605232 12p13.3 "protein kinase, lysine deficient 1" 1443 rs961360 R3HDM 23518 2 136227390 NM_015361 NP_056176 C/T M270V minus 1408202 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.08 0.11 0.07 262 4 0.47 0.06 1722 6 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 2q21.3 R3H domain (binds single-stranded nucleic acids) containing 1444 rs961360 R3HDM 23518 2 136227390 NM_015361 NP_056176 C/T M270V minus 1408202 902 AFFY Caucasian 40 0.18 0.11 0.07 262 4 0.47 0.06 1722 6 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 2q21.3 R3H domain (binds single-stranded nucleic acids) containing 1445 rs961360 R3HDM 23518 2 136227390 NM_015361 NP_056176 C/T M270V minus 1408202 904 AFFY CEPH 54 0.2 0.11 0.07 262 4 0.47 0.06 1722 6 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 2q21.3 R3H domain (binds single-stranded nucleic acids) containing 1446 rs961360 R3HDM 23518 2 136227390 NM_015361 NP_056176 C/T M270V minus 23874392 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.11 0.07 262 4 0.47 0.06 1722 6 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 2q21.3 R3H domain (binds single-stranded nucleic acids) containing 1447 rs963075 SERPINB10 5273 18 59751364 NM_005024 NP_005015 A/G R246C minus 1410472 766 TSC-CSHL WICGR1_CAUCASIAN WICGR Caucasian (93) 86 0.21 0.26 0.05 454 6 0.36 0.02 1570 5 123 "HapMap,submitter,freq,cluster" Intolerant 0.04 2.87 56 radical 602058 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10" 1448 rs963075 SERPINB10 5273 18 59751364 NM_005024 NP_005015 A/G R246C minus 1410472 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.21 0.26 0.05 454 6 0.36 0.02 1570 5 123 "HapMap,submitter,freq,cluster" Intolerant 0.04 2.87 56 radical 602058 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10" 1449 rs963075 SERPINB10 5273 18 59751364 NM_005024 NP_005015 A/G R246C minus 1410472 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 94 0.23 0.26 0.05 454 6 0.36 0.02 1570 5 123 "HapMap,submitter,freq,cluster" Intolerant 0.04 2.87 56 radical 602058 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10" 1450 rs963075 SERPINB10 5273 18 59751364 NM_005024 NP_005015 A/G R246C minus 1410472 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.3 0.26 0.05 454 6 0.36 0.02 1570 5 123 "HapMap,submitter,freq,cluster" Intolerant 0.04 2.87 56 radical 602058 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10" 1451 rs963075 SERPINB10 5273 18 59751364 NM_005024 NP_005015 A/G R246C minus 1410472 1303 SEQUENOM CEPH CEPH (92) 92 0.33 0.26 0.05 454 6 0.36 0.02 1570 5 123 "HapMap,submitter,freq,cluster" Intolerant 0.04 2.87 56 radical 602058 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10" 1452 rs963075 SERPINB10 5273 18 59751364 NM_005024 NP_005015 A/G R246C minus 24058834 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.26 0.05 454 6 0.36 0.02 1570 5 123 "HapMap,submitter,freq,cluster" Intolerant 0.04 2.87 56 radical 602058 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10" 1453 rs964307 PKHD1L1 93035 8 110482938 NM_177531 NP_803875 A/G Y440H minus 1412128 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.22 0.27 0.08 197 4 0.36 0.16 158 5 123 "HapMap,submitter,freq,cluster" moderately conservative 607843 8q23.2 polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1 1454 rs964307 PKHD1L1 93035 8 110482938 NM_177531 NP_803875 A/G Y440H minus 1412128 902 AFFY Caucasian 24 0.38 0.27 0.08 197 4 0.36 0.16 158 5 123 "HapMap,submitter,freq,cluster" moderately conservative 607843 8q23.2 polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1 1455 rs964307 PKHD1L1 93035 8 110482938 NM_177531 NP_803875 A/G Y440H minus 1412128 904 AFFY CEPH 5 0.5 0.27 0.08 197 4 0.36 0.16 158 5 123 "HapMap,submitter,freq,cluster" moderately conservative 607843 8q23.2 polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1 1456 rs964307 PKHD1L1 93035 8 110482938 NM_177531 NP_803875 A/G Y440H minus 24083373 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.27 0.08 197 4 0.36 0.16 158 5 123 "HapMap,submitter,freq,cluster" moderately conservative 607843 8q23.2 polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1 1457 rs966365 EDARADD 128178 1 232883812 NM_145861 NP_665860 C/T M9I minus 1414869 760 TSC-CSHL CEL_CAUCASIAN CELERA Caucasians (30) 58 0.07 0.15 0.04 500 3 0.23 0.25 112 2 86 "HapMap,doubleHit,submitter,freq" conservative 606603 1q42.3 EDAR-associated death domain 1458 rs966365 EDARADD 128178 1 232883812 NM_145861 NP_665860 C/T M9I minus 1414869 761 TSC-CSHL CEL_CAUCASIAN_CEPH CELERA CEPH Caucasians (661) 322 0.16 0.15 0.04 500 3 0.23 0.25 112 2 86 "HapMap,doubleHit,submitter,freq" conservative 606603 1q42.3 EDAR-associated death domain 1459 rs966365 EDARADD 128178 1 232883812 NM_145861 NP_665860 C/T M9I minus 1414869 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.18 0.15 0.04 500 3 0.23 0.25 112 2 86 "HapMap,doubleHit,submitter,freq" conservative 606603 1q42.3 EDAR-associated death domain 1460 rs967185 EIF3S10 8661 10 120810797 NM_003750 NP_003741 C/T E386K plus 1415941 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 12 0.08 0.08 0 12 1 0.14 0 14 1 86 by freq Potentially damaging 1.267 13 Borderline 0.13 2.88 25 moderately conservative 602039 10q26 "eukaryotic translation initiation factor 3, subunit 10 theta, 150/170kDa" 1461 rs968457 IRF3 3661 19 54858462 NM_001571 NP_001562 A/G R96Q minus 3177821 619 WICVAR MITOGPOP6 CORIELL Mixed 48 0.06 0.06 0 48 1 123 by freq Borderline 1.137 5 Borderline 0.18 2.82 25 conservative 603734 19q13.3-q13.4 interferon regulatory factor 3 1462 rs984274 DCC 1630 18 49190933 NM_005215 NP_005206 C/T M1017V minus 3176064 619 WICVAR MITOGPOP6 CORIELL Mixed 34 0.06 0.06 0 34 1 0.27 0 44 1 123 "HapMap,submitter,freq,cluster" Benign 0.131 6 Tolerant 0.47 2.79 27 conservative 120470 18q21.3 deleted in colorectal carcinoma 1463 rs988574 ITGA1 3672 5 52276567 NM_181501 NP_852478 A/G E1108G plus 1444359 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.03 0.01 140 2 0.2 0.03 1586 3 123 "HapMap,submitter,freq,cluster" Tolerant 0.28 2.76 17 moderately conservative 192968 5q11.2 "integrin, alpha 1" 1464 rs988574 ITGA1 3672 5 52276567 NM_181501 NP_852478 A/G E1108G plus 23403789 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.03 0.01 140 2 0.2 0.03 1586 3 123 "HapMap,submitter,freq,cluster" Tolerant 0.28 2.76 17 moderately conservative 192968 5q11.2 "integrin, alpha 1" 1465 rs997983 MKI67 4288 10 129800465 NM_002417 NP_002408 A/C I631L minus 1456739 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 86 0.09 0.07 0.03 346 4 0.07 0.03 110 3 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 176741 10q25-qter antigen identified by monoclonal antibody Ki-67 1466 rs997983 MKI67 4288 10 129800465 NM_002417 NP_002408 A/C I631L minus 1456739 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.07 0.07 0.03 346 4 0.07 0.03 110 3 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 176741 10q25-qter antigen identified by monoclonal antibody Ki-67 1467 rs997983 MKI67 4288 10 129800465 NM_002417 NP_002408 A/C I631L minus 1456739 1303 SEQUENOM CEPH CEPH (92) 92 0.03 0.07 0.03 346 4 0.07 0.03 110 3 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 176741 10q25-qter antigen identified by monoclonal antibody Ki-67 1468 rs997983 MKI67 4288 10 129800465 NM_002417 NP_002408 A/C I631L minus 24598816 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.07 0.03 346 4 0.07 0.03 110 3 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 176741 10q25-qter antigen identified by monoclonal antibody Ki-67 1469 rs998532 TTF2 8458 1 117329747 NM_003594 NP_003585 A/G K167E plus 1457444 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.45 0.42 0.03 224 3 0.26 0.02 176 3 123 "by doubleHit,submitter,freq,cluster" moderately conservative 604718 1p22 "transcription termination factor, RNA polymerase II" 1470 rs998532 TTF2 8458 1 117329747 NM_003594 NP_003585 A/G K167E plus 1457444 1303 SEQUENOM CEPH CEPH (92) 92 0.39 0.42 0.03 224 3 0.26 0.02 176 3 123 "by doubleHit,submitter,freq,cluster" moderately conservative 604718 1p22 "transcription termination factor, RNA polymerase II" 1471 rs998532 TTF2 8458 1 117329747 NM_003594 NP_003585 A/G K167E plus 24265327 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.42 0.03 224 3 0.26 0.02 176 3 123 "by doubleHit,submitter,freq,cluster" moderately conservative 604718 1p22 "transcription termination factor, RNA polymerase II" 1472 rs999597 KRTAP13-4 284827 21 30724925 NM_181600 NP_853631 C/T R154H minus 1459029 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.02 0.03 0.01 204 2 86 "HapMap,freq" Benign 0.081 7 Borderline 0.11 3.18 11 conservative 21q22.1 keratin associated protein 13-4 1473 rs999597 KRTAP13-4 284827 21 30724925 NM_181600 NP_853631 C/T R154H minus 1459029 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.03 0.03 0.01 204 2 86 "HapMap,freq" Benign 0.081 7 Borderline 0.11 3.18 11 conservative 21q22.1 keratin associated protein 13-4 1474 rs999765 EPHA8 2046 1 22669179 NM_020526 NP_065387 C/G E612Q minus 1459261 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.1 0.1 0.02 224 3 0.09 0.04 258 4 123 "by doubleHit,freq" Benign 0.109 74 Intolerant 0 2.78 83 conservative 176945 1p36.11 EphA8 1475 rs999765 EPHA8 2046 1 22669179 NM_020526 NP_065387 C/G E612Q minus 1459261 1303 SEQUENOM CEPH CEPH (92) 92 0.11 0.1 0.02 224 3 0.09 0.04 258 4 123 "by doubleHit,freq" Benign 0.109 74 Intolerant 0 2.78 83 conservative 176945 1p36.11 EphA8 1476 rs999765 EPHA8 2046 1 22669179 NM_020526 NP_065387 C/G E612Q minus 23181480 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.1 0.02 224 3 0.09 0.04 258 4 123 "by doubleHit,freq" Benign 0.109 74 Intolerant 0 2.78 83 conservative 176945 1p36.11 EphA8 1477 rs999890 PIP5K3 200576 2 209016138 NM_015040 NP_055855 G/T S1033A plus 23215775 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.33 0.18 232 2 0.13 0 46 1 123 "by doubleHit,freq,cluster" moderately conservative 2q34 "phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III" 1478 rs999890 PIP5K3 200576 2 209016138 NM_015040 NP_055855 G/T S1033A plus 24795931 1303 SEQUENOM CEPH CEPH (92) 184 0.39 0.33 0.18 232 2 0.13 0 46 1 123 "by doubleHit,freq,cluster" moderately conservative 2q34 "phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III" 1479 rs1004041 TPSG1 25823 16 1211891 NM_012467 NP_036599 A/C F288L minus 1465449 1303 SEQUENOM CEPH CEPH (92) 92 0.32 0.35 0.07 140 2 0.28 0.13 94 2 123 "by doubleHit,freq,cluster" conservative 16p13.3 tryptase gamma 1 1480 rs1004041 TPSG1 25823 16 1211891 NM_012467 NP_036599 A/C F288L minus 24400155 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.35 0.07 140 2 0.28 0.13 94 2 123 "by doubleHit,freq,cluster" conservative 16p13.3 tryptase gamma 1 1481 rs1004588 DGKG 1608 3 187489320 NM_001346 NP_001337 C/G T142S minus 1466101 1303 SEQUENOM CEPH CEPH (92) 92 0.48 0.42 0.17 118 2 0.34 0 1300 1 102 "by doubleHit,freq,cluster" Benign 0.985 6 moderately conservative 601854 3q27-q28 "diacylglycerol kinase, gamma 90kDa" 1482 rs1004588 DGKG 1608 3 187489320 NM_001346 NP_001337 C/G T142S minus 3175901 619 WICVAR MITOGPOP6 CORIELL Mixed 26 0.19 0.42 0.17 118 2 0.34 0 1300 1 102 "by doubleHit,freq,cluster" Benign 0.985 6 moderately conservative 601854 3q27-q28 "diacylglycerol kinase, gamma 90kDa" 1483 rs1007211 NTRK1 4914 1 153643852 NM_002529 NP_002520 A/G G18E plus 1469256 1303 SEQUENOM CEPH CEPH (92) 92 0.08 0.08 0 92 1 86 by freq moderately conservative 191315 1q21-q22 "neurotrophic tyrosine kinase, receptor, type 1" 1484 rs1009382 TNXB 7148 6 32134085 NM_019105 NP_061978 A/G G2578E minus 1471878 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.38 0.35 0.06 212 2 0.32 0 1488 1 119 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.757 5 moderately conservative 600985 6p21.3 tenascin XB 1485 rs1009382 TNXB 7148 6 32134085 NM_019105 NP_061978 A/G G2578E minus 1471878 1303 SEQUENOM CEPH CEPH (92) 92 0.3 0.35 0.06 212 2 0.32 0 1488 1 119 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.757 5 moderately conservative 600985 6p21.3 tenascin XB 1486 rs1011320 PIK3R2 5296 19 18134047 NM_005027 NP_005018 C/T S313P plus 1474167 760 TSC-CSHL CEL_CAUCASIAN CELERA Caucasians (30) 60 0.05 0.06 0.03 320 4 0.04 0.02 118 2 121 "HapMap,doubleHit,freq,cluster" Benign 0.629 6 moderately conservative 603157 19q13.2-q13.4 "phosphoinositide-3-kinase, regulatory subunit, polypeptide 2 (p85 beta)" 1487 rs1011320 PIK3R2 5296 19 18134047 NM_005027 NP_005018 C/T S313P plus 1474167 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.08 0.06 0.03 320 4 0.04 0.02 118 2 121 "HapMap,doubleHit,freq,cluster" Benign 0.629 6 moderately conservative 603157 19q13.2-q13.4 "phosphoinositide-3-kinase, regulatory subunit, polypeptide 2 (p85 beta)" 1488 rs1011320 PIK3R2 5296 19 18134047 NM_005027 NP_005018 C/T S313P plus 1474167 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.06 0.03 320 4 0.04 0.02 118 2 121 "HapMap,doubleHit,freq,cluster" Benign 0.629 6 moderately conservative 603157 19q13.2-q13.4 "phosphoinositide-3-kinase, regulatory subunit, polypeptide 2 (p85 beta)" 1489 rs1011320 PIK3R2 5296 19 18134047 NM_005027 NP_005018 C/T S313P plus 3177906 619 WICVAR MITOGPOP6 CORIELL Mixed 50 0.08 0.06 0.03 320 4 0.04 0.02 118 2 121 "HapMap,doubleHit,freq,cluster" Benign 0.629 6 moderately conservative 603157 19q13.2-q13.4 "phosphoinositide-3-kinase, regulatory subunit, polypeptide 2 (p85 beta)" 1490 rs1017219 KCNA7 3743 19 54265250 NM_031886 NP_114092 A/G M418T plus 1481085 1303 SEQUENOM CEPH CEPH (92) 92 0.18 0.21 0.07 138 2 0.39 0.08 92 2 123 "by doubleHit,submitter,freq,cluster" Potentially damaging 1.293 31 moderately conservative 176268 19q13.3 "potassium voltage-gated channel, shaker-related subfamily, member 7" 1491 rs1017219 KCNA7 3743 19 54265250 NM_031886 NP_114092 A/G M418T plus 23812958 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.28 0.21 0.07 138 2 0.39 0.08 92 2 123 "by doubleHit,submitter,freq,cluster" Potentially damaging 1.293 31 moderately conservative 176268 19q13.3 "potassium voltage-gated channel, shaker-related subfamily, member 7" 1492 rs1017842 BUB1B 701 15 38276149 NM_001211 NP_001202 C/G E390D minus 23454880 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.02 0.02 0 46 1 0.11 0 46 1 123 "by cluster,freq" conservative 602860 15q15 BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast) 1493 rs1018448 ARFGAP3 26286 22 41531448 NM_014570 NP_055385 A/C S355R plus 24550315 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.42 0 48 1 0.26 0.21 94 2 123 "by submitter,freq,cluster" Benign 0.478 18 moderately radical 22q13.2-q13.3 ADP-ribosylation factor GTPase activating protein 3 1494 rs1020694 SERPINB13 5275 18 59415278 NM_012397 NP_036529 C/T G293S minus 1484999 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.43 0.23 0.06 274 4 0.12 0.06 140 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.084 19 Tolerant 1 2.76 74 moderately conservative 604445 18q21.3-q22 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 13" 1495 rs1020694 SERPINB13 5275 18 59415278 NM_012397 NP_036529 C/T G293S minus 1484999 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 92 0.25 0.23 0.06 274 4 0.12 0.06 140 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.084 19 Tolerant 1 2.76 74 moderately conservative 604445 18q21.3-q22 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 13" 1496 rs1020694 SERPINB13 5275 18 59415278 NM_012397 NP_036529 C/T G293S minus 1484999 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.19 0.23 0.06 274 4 0.12 0.06 140 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.084 19 Tolerant 1 2.76 74 moderately conservative 604445 18q21.3-q22 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 13" 1497 rs1020694 SERPINB13 5275 18 59415278 NM_012397 NP_036529 C/T G293S minus 24494086 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.23 0.06 274 4 0.12 0.06 140 4 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.084 19 Tolerant 1 2.76 74 moderately conservative 604445 18q21.3-q22 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 13" 1498 rs1023783 LASS3 204219 15 98760568 NM_178842 NP_849164 C/T D342G plus 1488440 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.02 0.02 140 2 123 by freq Tolerant 0.39 2.92 11 moderately conservative 15q26.3 LAG1 longevity assurance homolog 3 (S. cerevisiae) 1499 rs1023783 LASS3 204219 15 98760568 NM_178842 NP_849164 C/T D342G plus 24594334 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.02 0.02 140 2 123 by freq Tolerant 0.39 2.92 11 moderately conservative 15q26.3 LAG1 longevity assurance homolog 3 (S. cerevisiae) 1500 rs1026128 COG1 9382 17 68708404 NM_018714 NP_061184 A/G N392S plus 24706885 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.42 0 48 1 0.37 0.01 1582 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.242 5 Tolerant 0.46 2.92 7 conservative 606973 17q25.1 component of oligomeric golgi complex 1 1501 rs1027392 USP29 57663 19 62332958 NM_020903 NP_065954 A/G N368S plus 1492423 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.4 0.42 0.01 344 4 0.19 0.12 178 3 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.52 2.79 101 conservative 19q13.43 ubiquitin specific protease 29 1502 rs1027392 USP29 57663 19 62332958 NM_020903 NP_065954 A/G N368S plus 1492423 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.42 0.42 0.01 344 4 0.19 0.12 178 3 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.52 2.79 101 conservative 19q13.43 ubiquitin specific protease 29 1503 rs1027392 USP29 57663 19 62332958 NM_020903 NP_065954 A/G N368S plus 1492423 1303 SEQUENOM CEPH CEPH (92) 92 0.43 0.42 0.01 344 4 0.19 0.12 178 3 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.52 2.79 101 conservative 19q13.43 ubiquitin specific protease 29 1504 rs1027392 USP29 57663 19 62332958 NM_020903 NP_065954 A/G N368S plus 24719701 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.42 0.01 344 4 0.19 0.12 178 3 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.52 2.79 101 conservative 19q13.43 ubiquitin specific protease 29 1505 rs1029871 NEK4 6787 3 52772674 NM_003157 NP_003148 C/G P225A minus 1495161 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 10 0.1 0.29 0.13 216 4 0.3 0.16 132 4 123 "HapMap,doubleHit,submitter,freq" conservative 601959 3p21.1 NIMA (never in mitosis gene a)-related kinase 4 1506 rs1029871 NEK4 6787 3 52772674 NM_003157 NP_003148 C/G P225A minus 1495161 885 TSC-CSHL HapMap-CEPH-30-trios 102 0.3 0.29 0.13 216 4 0.3 0.16 132 4 123 "HapMap,doubleHit,submitter,freq" conservative 601959 3p21.1 NIMA (never in mitosis gene a)-related kinase 4 1507 rs1029871 NEK4 6787 3 52772674 NM_003157 NP_003148 C/G P225A minus 3177674 619 WICVAR MITOGPOP6 CORIELL Mixed 56 0.16 0.29 0.13 216 4 0.3 0.16 132 4 123 "HapMap,doubleHit,submitter,freq" conservative 601959 3p21.1 NIMA (never in mitosis gene a)-related kinase 4 1508 rs1029871 NEK4 6787 3 52772674 NM_003157 NP_003148 C/G P225A minus 24349523 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.29 0.13 216 4 0.3 0.16 132 4 123 "HapMap,doubleHit,submitter,freq" conservative 601959 3p21.1 NIMA (never in mitosis gene a)-related kinase 4 1509 rs1035539 BCAR1 9564 16 73834276 NM_014567 NP_055382 A/G P76S plus 1501489 1303 SEQUENOM CEPH CEPH (92) 92 0.13 0.13 0 92 1 0.38 0 1468 1 121 "by doubleHit,freq,cluster" Possibly damaging 1.8 6 Tolerant 0.23 3.04 11 moderately conservative 602941 16q22-q23 breast cancer anti-estrogen resistance 1 1510 rs1036199 HAVCR2 84868 5 156464314 NM_032782 NP_116171 A/C R140L plus 23304691 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.17 0.17 0 46 1 0.03 0.04 1548 2 123 "by cluster,freq" Borderline 0.2 2.93 21 moderately radical 606652 5q33.3 hepatitis A virus cellular receptor 2 1511 rs1037921 ARNTL2 56938 12 27444833 NM_020183 NP_064568 C/T N340S minus 1504123 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.07 0.04 0.03 260 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.03 11 Tolerant 0.59 2.89 85 conservative 12p12.2-p11.2 aryl hydrocarbon receptor nuclear translocator-like 2 1512 rs1037921 ARNTL2 56938 12 27444833 NM_020183 NP_064568 C/T N340S minus 1504123 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.04 0.03 260 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.03 11 Tolerant 0.59 2.89 85 conservative 12p12.2-p11.2 aryl hydrocarbon receptor nuclear translocator-like 2 1513 rs1037921 ARNTL2 56938 12 27444833 NM_020183 NP_064568 C/T N340S minus 24451963 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.04 0.03 260 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.03 11 Tolerant 0.59 2.89 85 conservative 12p12.2-p11.2 aryl hydrocarbon receptor nuclear translocator-like 2 1514 rs1040835 GOLGA5 9950 14 92346407 NM_005113 NP_005104 A/G F350L minus 1507380 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.33 0.3 0.06 260 3 0.15 0.03 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.255 8 Tolerant 1 2.87 11 conservative 606918 14q32.12-q32.13 "golgi autoantigen, golgin subfamily a, 5" 1515 rs1040835 GOLGA5 9950 14 92346407 NM_005113 NP_005104 A/G F350L minus 1507380 1303 SEQUENOM CEPH CEPH (92) 92 0.23 0.3 0.06 260 3 0.15 0.03 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.255 8 Tolerant 1 2.87 11 conservative 606918 14q32.12-q32.13 "golgi autoantigen, golgin subfamily a, 5" 1516 rs1040835 GOLGA5 9950 14 92346407 NM_005113 NP_005104 A/G F350L minus 24600610 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.3 0.06 260 3 0.15 0.03 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.255 8 Tolerant 1 2.87 11 conservative 606918 14q32.12-q32.13 "golgi autoantigen, golgin subfamily a, 5" 1517 rs1041981 LTA 4049 6 31648763 NM_000595 NP_000586 A/C T60N plus 4328795 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 42 0.36 0.37 0.03 338 5 0.37 0.03 1596 4 123 "by doubleHit,freq,cluster" Benign 0.111 15 Tolerant 0.41 2.8 86 moderately conservative 153440 6p21.3 "lymphotoxin alpha (TNF superfamily, member 1)" 1518 rs1041981 LTA 4049 6 31648763 NM_000595 NP_000586 A/C T60N plus 6312883 693 EGP_SNPS PDR90 NIHPDR 172 0.38 0.37 0.03 338 5 0.37 0.03 1596 4 123 "by doubleHit,freq,cluster" Benign 0.111 15 Tolerant 0.41 2.8 86 moderately conservative 153440 6p21.3 "lymphotoxin alpha (TNF superfamily, member 1)" 1519 rs1041981 LTA 4049 6 31648763 NM_000595 NP_000586 A/C T60N plus 16360682 649 FHCRC POPU1 USA (20) 40 0.38 0.37 0.03 338 5 0.37 0.03 1596 4 123 "by doubleHit,freq,cluster" Benign 0.111 15 Tolerant 0.41 2.8 86 moderately conservative 153440 6p21.3 "lymphotoxin alpha (TNF superfamily, member 1)" 1520 rs1041981 LTA 4049 6 31648763 NM_000595 NP_000586 A/C T60N plus 16360732 649 FHCRC POPU1 USA (20) 40 0.38 0.37 0.03 338 5 0.37 0.03 1596 4 123 "by doubleHit,freq,cluster" Benign 0.111 15 Tolerant 0.41 2.8 86 moderately conservative 153440 6p21.3 "lymphotoxin alpha (TNF superfamily, member 1)" 1521 rs1041981 LTA 4049 6 31648763 NM_000595 NP_000586 A/C T60N plus 23323156 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.3 0.37 0.03 338 5 0.37 0.03 1596 4 123 "by doubleHit,freq,cluster" Benign 0.111 15 Tolerant 0.41 2.8 86 moderately conservative 153440 6p21.3 "lymphotoxin alpha (TNF superfamily, member 1)" 1522 rs1042007 DNM1 1759 9 128092101 NM_004408 NP_004399 A/G D744N plus 1508887 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.47 0 92 1 106 by freq Possibly damaging 1.593 37 conservative 602377 9q34 dynamin 1 1523 rs1042017 SREBF1 6720 17 17657712 NM_004176 NP_004167 A/G T1000A minus 1508900 1303 SEQUENOM CEPH CEPH (92) 92 0.45 0.45 0 92 1 86 by freq Benign 0.472 14 Tolerant 0.79 2.82 21 moderately conservative 184756 17p11.2 sterol regulatory element binding transcription factor 1 1524 rs1042031 APOB 338 2 21137405 NM_000384 NP_000375 A/G E4181K minus 6312533 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.21 0.19 0.02 260 3 0.23 0.12 602 5 123 "HapMap,freq,cluster" moderately conservative 107730 2p24-p23 apolipoprotein B (including Ag(x) antigen) 1525 rs1042031 APOB 338 2 21137405 NM_000384 NP_000375 A/G E4181K minus 6312533 1303 SEQUENOM CEPH CEPH (92) 92 0.18 0.19 0.02 260 3 0.23 0.12 602 5 123 "HapMap,freq,cluster" moderately conservative 107730 2p24-p23 apolipoprotein B (including Ag(x) antigen) 1526 rs1042031 APOB 338 2 21137405 NM_000384 NP_000375 A/G E4181K minus 24242162 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.19 0.02 260 3 0.23 0.12 602 5 123 "HapMap,freq,cluster" moderately conservative 107730 2p24-p23 apolipoprotein B (including Ag(x) antigen) 1527 rs1042034 APOB 338 2 21136933 NM_000384 NP_000375 A/G S4338N minus 3290027 1303 SEQUENOM CEPH CEPH (92) 92 0.14 0.18 0.04 202 3 0.26 0.09 528 7 123 "by doubleHit,freq,cluster" conservative 107730 2p24-p23 apolipoprotein B (including Ag(x) antigen) 1528 rs1042034 APOB 338 2 21136933 NM_000384 NP_000375 A/G S4338N minus 8819680 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.19 0.18 0.04 202 3 0.26 0.09 528 7 123 "by doubleHit,freq,cluster" conservative 107730 2p24-p23 apolipoprotein B (including Ag(x) antigen) 1529 rs1042034 APOB 338 2 21136933 NM_000384 NP_000375 A/G S4338N minus 23841045 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.18 0.04 202 3 0.26 0.09 528 7 123 "by doubleHit,freq,cluster" conservative 107730 2p24-p23 apolipoprotein B (including Ag(x) antigen) 1530 rs1042038 PSCDBP 9595 2 158125932 NM_004288 NP_004279 A/G D37N minus 1508934 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.2 0 92 1 86 by freq conservative 604448 2q11.2 "pleckstrin homology, Sec7 and coiled-coil domains, binding protein" 1531 rs1042057 TYRO3 7301 15 39657537 NM_006293 NP_006284 C/T A815V plus 1508967 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.04 0 92 1 86 by freq Borderline 1.048 10 Borderline 0.14 2.84 25 moderately conservative 600341 15q15.1-q21.1 TYRO3 protein tyrosine kinase 1532 rs1042206 FCGR3A 2214 1 158326014 NM_000569 NP_000560 C/T F239S minus 16417111 1303 SEQUENOM CEPH CEPH (92) 92 0.48 0.48 0 92 1 120 "by doubleHit,freq,cluster" Benign 0.982 20 Tolerant 0.22 3.03 30 radical 146740 1q23 "Fc fragment of IgG, low affinity IIIa, receptor for (CD16)" 1533 rs1042229 FPR1 2357 19 56941484 NM_002029 NP_002020 G/T N192K minus 14699224 1303 SEQUENOM CEPH CEPH (92) 92 0.48 0.48 0 92 1 0.42 0 1456 1 119 "by submitter,freq,cluster" Benign 0.032 28 Tolerant 0.92 2.94 30 moderately conservative 136537 19q13.4 formyl peptide receptor 1 1534 rs1042303 GPLD1 2822 6 24545437 NM_001503 NP_001494 C/T M694V plus 2632160 1303 SEQUENOM CEPH CEPH (92) 92 0.24 0.3 0.12 140 2 0.24 0.01 1582 3 123 "by doubleHit,freq,cluster" Borderline 1.001 10 Tolerant 0.53 2.98 38 conservative 602515 6p22.3-p22.2 glycosylphosphatidylinositol specific phospholipase D1 1535 rs1042303 GPLD1 2822 6 24545437 NM_001503 NP_001494 C/T M694V plus 24425828 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.3 0.12 140 2 0.24 0.01 1582 3 123 "by doubleHit,freq,cluster" Borderline 1.001 10 Tolerant 0.53 2.98 38 conservative 602515 6p22.3-p22.2 glycosylphosphatidylinositol specific phospholipase D1 1536 rs1042364 ADH4 127 4 100402752 NM_000670 NP_000661 A/G R388G minus 10157120 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.32 0.31 0.02 212 2 121 "HapMap,submitter,freq,cluster" moderately radical 103740 4q22 "alcohol dehydrogenase 4 (class II), pi polypeptide" 1537 rs1042364 ADH4 127 4 100402752 NM_000670 NP_000661 A/G R388G minus 10157120 1303 SEQUENOM CEPH CEPH (92) 92 0.29 0.31 0.02 212 2 121 "HapMap,submitter,freq,cluster" moderately radical 103740 4q22 "alcohol dehydrogenase 4 (class II), pi polypeptide" 1538 rs1042391 GMPR 2766 6 16398740 NM_006877 NP_006868 A/T F256I plus 10319972 885 TSC-CSHL HapMap-CEPH-30-trios 112 0.37 0.38 0.05 252 3 0.17 0.04 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.509 38 conservative 139265 6p23 guanosine monophosphate reductase 1539 rs1042391 GMPR 2766 6 16398740 NM_006877 NP_006868 A/T F256I plus 10319972 1303 SEQUENOM CEPH CEPH (92) 92 0.43 0.38 0.05 252 3 0.17 0.04 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.509 38 conservative 139265 6p23 guanosine monophosphate reductase 1540 rs1042391 GMPR 2766 6 16398740 NM_006877 NP_006868 A/T F256I plus 24374803 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.38 0.05 252 3 0.17 0.04 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.509 38 conservative 139265 6p23 guanosine monophosphate reductase 1541 rs1042445 HRG 3273 3 187878138 NM_000412 NP_000403 C/T R448C plus 1509688 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.21 0.18 0.03 258 3 0.31 0.01 92 2 123 "HapMap,submitter,freq,cluster" radical 142640 3q27 histidine-rich glycoprotein 1542 rs1042445 HRG 3273 3 187878138 NM_000412 NP_000403 C/T R448C plus 1509688 1303 SEQUENOM CEPH CEPH (92) 92 0.15 0.18 0.03 258 3 0.31 0.01 92 2 123 "HapMap,submitter,freq,cluster" radical 142640 3q27 histidine-rich glycoprotein 1543 rs1042445 HRG 3273 3 187878138 NM_000412 NP_000403 C/T R448C plus 23287771 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.17 0.18 0.03 258 3 0.31 0.01 92 2 123 "HapMap,submitter,freq,cluster" radical 142640 3q27 histidine-rich glycoprotein 1544 rs1042464 HRG 3273 3 187878274 NM_000412 NP_000403 A/T N493I plus 3172905 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 52 0.37 0.35 0.06 222 5 0.29 0.1 158 5 123 "by doubleHit,freq,cluster" moderately radical 142640 3q27 histidine-rich glycoprotein 1545 rs1042464 HRG 3273 3 187878274 NM_000412 NP_000403 A/T N493I plus 10078370 902 AFFY Caucasian 22 0.41 0.35 0.06 222 5 0.29 0.1 158 5 123 "by doubleHit,freq,cluster" moderately radical 142640 3q27 histidine-rich glycoprotein 1546 rs1042464 HRG 3273 3 187878274 NM_000412 NP_000403 A/T N493I plus 10078370 904 AFFY CEPH 10 0.2 0.35 0.06 222 5 0.29 0.1 158 5 123 "by doubleHit,freq,cluster" moderately radical 142640 3q27 histidine-rich glycoprotein 1547 rs1042464 HRG 3273 3 187878274 NM_000412 NP_000403 A/T N493I plus 10078370 1303 SEQUENOM CEPH CEPH (92) 92 0.3 0.35 0.06 222 5 0.29 0.1 158 5 123 "by doubleHit,freq,cluster" moderately radical 142640 3q27 histidine-rich glycoprotein 1548 rs1042464 HRG 3273 3 187878274 NM_000412 NP_000403 A/T N493I plus 24333187 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.41 0.35 0.06 222 5 0.29 0.1 158 5 123 "by doubleHit,freq,cluster" moderately radical 142640 3q27 histidine-rich glycoprotein 1549 rs1042522 TP53 7157 17 7520197 NM_000546 NP_000537 C/G P72R minus 2463129 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.23 0.32 0.12 338 4 0.41 0.08 346 4 121 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.821 51 moderately radical 191170 17p13.1 tumor protein p53 (Li-Fraumeni syndrome) 1550 rs1042522 TP53 7157 17 7520197 NM_000546 NP_000537 C/G P72R minus 2463129 1303 SEQUENOM CEPH CEPH (92) 92 0.48 0.32 0.12 338 4 0.41 0.08 346 4 121 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.821 51 moderately radical 191170 17p13.1 tumor protein p53 (Li-Fraumeni syndrome) 1551 rs1042522 TP53 7157 17 7520197 NM_000546 NP_000537 C/G P72R minus 3176059 619 WICVAR MITOGPOP6 CORIELL Mixed 64 0.33 0.32 0.12 338 4 0.41 0.08 346 4 121 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.821 51 moderately radical 191170 17p13.1 tumor protein p53 (Li-Fraumeni syndrome) 1552 rs1042522 TP53 7157 17 7520197 NM_000546 NP_000537 C/G P72R minus 5586947 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.27 0.32 0.12 338 4 0.41 0.08 346 4 121 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.821 51 moderately radical 191170 17p13.1 tumor protein p53 (Li-Fraumeni syndrome) 1553 rs1042589 TPO 7173 2 1525334 NM_175720 NP_783651 C/G P918R plus 23877133 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.42 0 232 2 0.31 0.19 94 2 123 "by doubleHit,freq,cluster" moderately radical 606765 2p25 thyroid peroxidase 1554 rs1042589 TPO 7173 2 1525334 NM_175720 NP_783651 C/G P918R plus 24815828 1303 SEQUENOM CEPH CEPH (92) 184 0.42 0.42 0 232 2 0.31 0.19 94 2 123 "by doubleHit,freq,cluster" moderately radical 606765 2p25 thyroid peroxidase 1555 rs1042602 TYR 7299 11 88551344 NM_000372 NP_000363 A/C S192Y plus 1509962 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.42 0.42 0.08 369 5 0.05 0.03 282 4 123 "HapMap,freq" Possibly damaging 1.634 41 Intolerant 0 2.81 166 moderately radical 606933 11q14-q21 tyrosinase (oculocutaneous albinism IA) 1556 rs1042602 TYR 7299 11 88551344 NM_000372 NP_000363 A/C S192Y plus 1509962 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.42 0.08 369 5 0.05 0.03 282 4 123 "HapMap,freq" Possibly damaging 1.634 41 Intolerant 0 2.81 166 moderately radical 606933 11q14-q21 tyrosinase (oculocutaneous albinism IA) 1557 rs1042602 TYR 7299 11 88551344 NM_000372 NP_000363 A/C S192Y plus 4387030 705 PSU-ANTH GERMANY German 30 0.41 0.42 0.08 369 5 0.05 0.03 282 4 123 "HapMap,freq" Possibly damaging 1.634 41 Intolerant 0 2.81 166 moderately radical 606933 11q14-q21 tyrosinase (oculocutaneous albinism IA) 1558 rs1042602 TYR 7299 11 88551344 NM_000372 NP_000363 A/C S192Y plus 4387030 706 PSU-ANTH SPAIN Spanish 79 0.49 0.42 0.08 369 5 0.05 0.03 282 4 123 "HapMap,freq" Possibly damaging 1.634 41 Intolerant 0 2.81 166 moderately radical 606933 11q14-q21 tyrosinase (oculocutaneous albinism IA) 1559 rs1042602 TYR 7299 11 88551344 NM_000372 NP_000363 A/C S192Y plus 24427553 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.42 0.08 369 5 0.05 0.03 282 4 123 "HapMap,freq" Possibly damaging 1.634 41 Intolerant 0 2.81 166 moderately radical 606933 11q14-q21 tyrosinase (oculocutaneous albinism IA) 1560 rs1042636 CASR 846 3 123486459 NM_000388 NP_000379 A/G R990G plus 5606249 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.07 0.08 0.04 200 3 0.39 0.13 1938 7 123 "by cluster,freq" Possibly damaging 1.575 6 moderately radical 601199 3q21-q24 "calcium-sensing receptor (hypocalciuric hypercalcemia 1, severe neonatal hyperparathyroidism)" 1561 rs1042636 CASR 846 3 123486459 NM_000388 NP_000379 A/G R990G plus 22030142 1303 SEQUENOM CEPH CEPH (92) 92 0.11 0.08 0.04 200 3 0.39 0.13 1938 7 123 "by cluster,freq" Possibly damaging 1.575 6 moderately radical 601199 3q21-q24 "calcium-sensing receptor (hypocalciuric hypercalcemia 1, severe neonatal hyperparathyroidism)" 1562 rs1042636 CASR 846 3 123486459 NM_000388 NP_000379 A/G R990G plus 23901762 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.08 0.04 200 3 0.39 0.13 1938 7 123 "by cluster,freq" Possibly damaging 1.575 6 moderately radical 601199 3q21-q24 "calcium-sensing receptor (hypocalciuric hypercalcemia 1, severe neonatal hyperparathyroidism)" 1563 rs1042703 MMP14 4323 14 22375888 NM_004995 NP_004986 C/T P8S plus 2414700 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.13 0.05 140 2 0.05 0.05 94 2 123 "by doubleHit,freq,cluster" moderately conservative 600754 14q11-q12 matrix metalloproteinase 14 (membrane-inserted) 1564 rs1042703 MMP14 4323 14 22375888 NM_004995 NP_004986 C/T P8S plus 23815139 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.13 0.05 140 2 0.05 0.05 94 2 123 "by doubleHit,freq,cluster" moderately conservative 600754 14q11-q12 matrix metalloproteinase 14 (membrane-inserted) 1565 rs1042704 MMP14 4323 14 22382434 NM_004995 NP_004986 A/G D273N plus 1510165 1303 SEQUENOM CEPH CEPH (92) 92 0.49 0.49 0 92 1 106 by freq Benign 0.344 33 Tolerant 0.41 2.83 48 conservative 600754 14q11-q12 matrix metalloproteinase 14 (membrane-inserted) 1566 rs1042779 ITIH1 3697 3 52796051 NM_002215 NP_002206 A/G Q595R plus 19520909 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.28 0.35 0.08 260 3 0.48 0.02 1564 3 123 "HapMap,doubleHit,freq,cluster" Borderline 1.147 19 conservative 147270 3p21.2-p21.1 inter-alpha (globulin) inhibitor H1 1567 rs1042779 ITIH1 3697 3 52796051 NM_002215 NP_002206 A/G Q595R plus 19520909 1303 SEQUENOM CEPH CEPH (92) 92 0.38 0.35 0.08 260 3 0.48 0.02 1564 3 123 "HapMap,doubleHit,freq,cluster" Borderline 1.147 19 conservative 147270 3p21.2-p21.1 inter-alpha (globulin) inhibitor H1 1568 rs1042779 ITIH1 3697 3 52796051 NM_002215 NP_002206 A/G Q595R plus 24349623 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.35 0.08 260 3 0.48 0.02 1564 3 123 "HapMap,doubleHit,freq,cluster" Borderline 1.147 19 conservative 147270 3p21.2-p21.1 inter-alpha (globulin) inhibitor H1 1569 rs1042780 ME3 10873 11 85839036 NM_006680 NP_006671 C/G K324N minus 1510291 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.34 0.37 0.06 212 2 120 "HapMap,submitter,freq" Benign 0.202 39 moderately conservative 604626 11cen-q22.3 "malic enzyme 3, NADP(+)-dependent, mitochondrial" 1570 rs1042780 ME3 10873 11 85839036 NM_006680 NP_006671 C/G K324N minus 1510291 1303 SEQUENOM CEPH CEPH (92) 92 0.42 0.37 0.06 212 2 120 "HapMap,submitter,freq" Benign 0.202 39 moderately conservative 604626 11cen-q22.3 "malic enzyme 3, NADP(+)-dependent, mitochondrial" 1571 rs1042821 MSH6 2956 2 47922139 NM_000179 NP_000170 C/T G39E minus 4384481 693 EGP_SNPS PDR90 NIHPDR 152 0.16 0.16 0 152 1 123 "by cluster,freq" Benign 0.06 7 moderately conservative 600678 2p16 mutS homolog 6 (E. coli) 1572 rs1042838 PGR 5241 11 100438622 NM_000926 NP_000917 G/T V660L minus 16343470 693 EGP_SNPS PDR90 NIHPDR 180 0.1 0.17 0.1 318 3 0.03 0.01 94 2 123 "by submitter,freq,cluster" Borderline 1.07 10 conservative 607311 11q22-q23 progesterone receptor 1573 rs1042838 PGR 5241 11 100438622 NM_000926 NP_000917 G/T V660L minus 16343470 1303 SEQUENOM CEPH CEPH (92) 92 0.27 0.17 0.1 318 3 0.03 0.01 94 2 123 "by submitter,freq,cluster" Borderline 1.07 10 conservative 607311 11q22-q23 progesterone receptor 1574 rs1042838 PGR 5241 11 100438622 NM_000926 NP_000917 G/T V660L minus 24586705 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.24 0.17 0.1 318 3 0.03 0.01 94 2 123 "by submitter,freq,cluster" Borderline 1.07 10 conservative 607311 11q22-q23 progesterone receptor 1575 rs1043261 IL17RB 55540 3 53874316 NM_018725 NP_061195 C/T Q484X plus 10050330 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.09 0.08 0.02 168 2 0.1 0.03 1570 3 123 "HapMap,doubleHit,freq,cluster" Probably damaging Intolerant radical 605458 3p21.1 interleukin 17 receptor B 1576 rs1043261 IL17RB 55540 3 53874316 NM_018725 NP_061195 C/T Q484X plus 23945774 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.08 0.02 168 2 0.1 0.03 1570 3 123 "HapMap,doubleHit,freq,cluster" Probably damaging Intolerant radical 605458 3p21.1 interleukin 17 receptor B 1577 rs1043307 PSMD9 5715 12 120816516 NM_002813 NP_002804 A/G E197G plus 1511360 1303 SEQUENOM CEPH CEPH (92) 92 0.19 0.22 0.05 140 2 0.29 0.28 90 2 123 "by cluster,freq" Possibly damaging 1.576 8 Borderline 0.16 2.91 13 moderately conservative 603146 12q24.31-q24.32 "proteasome (prosome, macropain) 26S subunit, non-ATPase, 9" 1578 rs1043307 PSMD9 5715 12 120816516 NM_002813 NP_002804 A/G E197G plus 23934828 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.22 0.05 140 2 0.29 0.28 90 2 123 "by cluster,freq" Possibly damaging 1.576 8 Borderline 0.16 2.91 13 moderately conservative 603146 12q24.31-q24.32 "proteasome (prosome, macropain) 26S subunit, non-ATPase, 9" 1579 rs1043424 PINK1 65018 1 20722306 NM_032409 NP_115785 A/C N521T plus 1511554 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.34 0.34 0.08 260 3 0.26 0.08 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.319 8 Borderline 0.13 2.8 62 moderately conservative 608309 1p36 PTEN induced putative kinase 1 1580 rs1043424 PINK1 65018 1 20722306 NM_032409 NP_115785 A/C N521T plus 15414508 1303 SEQUENOM CEPH CEPH (92) 92 0.4 0.34 0.08 260 3 0.26 0.08 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.319 8 Borderline 0.13 2.8 62 moderately conservative 608309 1p36 PTEN induced putative kinase 1 1581 rs1043424 PINK1 65018 1 20722306 NM_032409 NP_115785 A/C N521T plus 23842660 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.34 0.08 260 3 0.26 0.08 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.319 8 Borderline 0.13 2.8 62 moderately conservative 608309 1p36 PTEN induced putative kinase 1 1582 rs1043963 USHBP1 83878 19 17222116 NM_031941 NP_114147 C/T A677V minus 1512609 1303 SEQUENOM CEPH CEPH (92) 92 0.31 0.31 0 92 1 120 by freq moderately conservative 19p13 Usher syndrome 1C binding protein 1 1583 rs1044009 NOTCH3 4854 19 15132771 NM_000435 NP_000426 C/T A2223V minus 2990861 1303 SEQUENOM CEPH CEPH (92) 92 0.3 0.27 0.06 140 2 0.4 0.02 1580 3 123 "by cluster,freq" moderately conservative 600276 19p13.2-p13.1 Notch homolog 3 (Drosophila) 1584 rs1044009 NOTCH3 4854 19 15132771 NM_000435 NP_000426 C/T A2223V minus 23538988 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.27 0.06 140 2 0.4 0.02 1580 3 123 "by cluster,freq" moderately conservative 600276 19p13.2-p13.1 Notch homolog 3 (Drosophila) 1585 rs1044057 STX7 8417 6 132866329 NM_003569 NP_003560 A/G A12T minus 1512787 1303 SEQUENOM CEPH CEPH (92) 92 0.24 0.24 0 92 1 86 by freq Benign 0.667 16 moderately conservative 603217 6q23.1 syntaxin 7 1586 rs1044141 STK17A 9263 7 43437520 NM_004760 NP_004751 A/G K362E plus 10414990 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.37 0.13 140 2 0.28 0.05 1580 3 123 "by doubleHit,freq,cluster" Borderline 1.053 5 moderately conservative 604726 7p12-p14 serine/threonine kinase 17a (apoptosis-inducing) 1587 rs1044141 STK17A 9263 7 43437520 NM_004760 NP_004751 A/G K362E plus 23968531 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.37 0.13 140 2 0.28 0.05 1580 3 123 "by doubleHit,freq,cluster" Borderline 1.053 5 moderately conservative 604726 7p12-p14 serine/threonine kinase 17a (apoptosis-inducing) 1588 rs1044240 ALCAM 214 3 106741551 NM_001627 NP_001618 A/G N258S plus 24796196 1303 SEQUENOM CEPH CEPH (92) 184 0.16 0.16 0 184 1 123 by freq Benign 0.226 12 Tolerant 1 2.79 21 conservative 601662 3q13.1 activated leukocyte cell adhesion molecule 1589 rs1044243 ALCAM 214 3 106743210 NM_001627 NP_001618 C/T T301M plus 14169589 1303 SEQUENOM CEPH CEPH (92) 92 0.24 0.19 0.09 140 2 0.06 0.03 86 2 123 "by cluster,freq" Possibly damaging 1.873 12 moderately conservative 601662 3q13.1 activated leukocyte cell adhesion molecule 1590 rs1044243 ALCAM 214 3 106743210 NM_001627 NP_001618 C/T T301M plus 24308750 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.19 0.09 140 2 0.06 0.03 86 2 123 "by cluster,freq" Possibly damaging 1.873 12 moderately conservative 601662 3q13.1 activated leukocyte cell adhesion molecule 1591 rs1044261 IDI2 91734 10 1055710 NM_033261 NP_150286 C/T W144X plus 12109295 1303 SEQUENOM CEPH CEPH (92) 92 0.15 0.13 0.05 140 2 0.07 0 44 1 123 "by cluster,freq" Probably damaging Intolerant radical 10p15.3 isopentenyl-diphosphate delta isomerase 2 1592 rs1044261 IDI2 91734 10 1055710 NM_033261 NP_150286 C/T W144X plus 24623784 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.13 0.05 140 2 0.07 0 44 1 123 "by cluster,freq" Probably damaging Intolerant radical 10p15.3 isopentenyl-diphosphate delta isomerase 2 1593 rs1044463 SNX2 6643 5 122182555 NM_003100 NP_003091 G/T A384S plus 1513662 1303 SEQUENOM CEPH CEPH (92) 92 0.41 0.23 0.18 276 2 123 by freq Benign 0.218 20 Tolerant 0.78 2.86 24 moderately conservative 605929 5q23 sorting nexin 2 1594 rs1044463 SNX2 6643 5 122182555 NM_003100 NP_003091 G/T A384S plus 24812816 1303 SEQUENOM CEPH CEPH (92) 184 0.14 0.23 0.18 276 2 123 by freq Benign 0.218 20 Tolerant 0.78 2.86 24 moderately conservative 605929 5q23 sorting nexin 2 1595 rs1044498 ENPP1 5167 6 132214061 NM_006208 NP_006199 A/C K121Q plus 12587306 928 IBARROSO ELY UK (Ely region of East Anglia) 921 0.15 0.16 0.02 1061 3 0.13 0.13 92 2 123 "by doubleHit,freq,cluster" Benign 0.943 10 moderately conservative 173335 6q22-q23 ectonucleotide pyrophosphatase/phosphodiesterase 1 1596 rs1044498 ENPP1 5167 6 132214061 NM_006208 NP_006199 A/C K121Q plus 22481659 1303 SEQUENOM CEPH CEPH (92) 92 0.22 0.16 0.02 1061 3 0.13 0.13 92 2 123 "by doubleHit,freq,cluster" Benign 0.943 10 moderately conservative 173335 6q22-q23 ectonucleotide pyrophosphatase/phosphodiesterase 1 1597 rs1044498 ENPP1 5167 6 132214061 NM_006208 NP_006199 A/C K121Q plus 23404875 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.16 0.02 1061 3 0.13 0.13 92 2 123 "by doubleHit,freq,cluster" Benign 0.943 10 moderately conservative 173335 6q22-q23 ectonucleotide pyrophosphatase/phosphodiesterase 1 1598 rs1045102 CNKSR1 10256 1 26199991 NM_006314 NP_006305 A/T K651M plus 1514971 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 83 0.06 0.06 0 83 1 0.06 0 83 1 86 by freq moderately conservative 603272 1p35.3 connector enhancer of kinase suppressor of Ras 1 1599 rs1045105 CNKSR1 10256 1 26200098 NM_006314 NP_006305 A/C H687N plus 1514976 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 83 0.18 0.11 0.06 295 3 0.28 0.04 166 2 106 "HapMap,submitter,freq" moderately conservative 603272 1p35.3 connector enhancer of kinase suppressor of Ras 1 1600 rs1045105 CNKSR1 10256 1 26200098 NM_006314 NP_006305 A/C H687N plus 1514976 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.08 0.11 0.06 295 3 0.28 0.04 166 2 106 "HapMap,submitter,freq" moderately conservative 603272 1p35.3 connector enhancer of kinase suppressor of Ras 1 1601 rs1045105 CNKSR1 10256 1 26200098 NM_006314 NP_006305 A/C H687N plus 1514976 1303 SEQUENOM CEPH CEPH (92) 92 0.08 0.11 0.06 295 3 0.28 0.04 166 2 106 "HapMap,submitter,freq" moderately conservative 603272 1p35.3 connector enhancer of kinase suppressor of Ras 1 1602 rs1045142 ROCK1 6093 18 16788810 NM_005406 NP_005397 A/G R1262Q minus 3757429 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.02 0 92 1 106 by freq Possibly damaging 1.583 15 conservative 601702 18q11.2 "Rho-associated, coiled-coil containing protein kinase 1" 1603 rs1045288 PSMD13 5719 11 227087 NM_002817 NP_002808 A/G N13S plus 15814939 1303 SEQUENOM CEPH CEPH (92) 92 0.37 0.37 0 92 1 0.16 0 718 1 121 "by doubleHit,freq,cluster" conservative 603481 11p15.5 "proteasome (prosome, macropain) 26S subunit, non-ATPase, 13" 1604 rs1045332 CGI-105 51011 2 95498556 NM_016044 NP_057128 C/T M198T plus 3270027 1303 SEQUENOM CEPH CEPH (92) 92 0.21 0.21 0 92 1 100 by freq Probably damaging 2.505 8 Tolerant 0.47 2.78 37 moderately conservative 2p24.3-p11.2 CGI-105 protein 1605 rs1045546 TAPBPL 55080 12 6438168 NM_018009 NP_060479 A/G T334M minus 1515844 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.21 0.02 140 2 0.03 0.01 94 2 123 by freq Tolerant 0.21 2.78 34 moderately conservative 607081 12p13.31 TAP binding protein-like 1606 rs1045546 TAPBPL 55080 12 6438168 NM_018009 NP_060479 A/G T334M minus 24697367 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.21 0.02 140 2 0.03 0.01 94 2 123 by freq Tolerant 0.21 2.78 34 moderately conservative 607081 12p13.31 TAP binding protein-like 1607 rs1045922 RNASE6 6039 14 20319964 NM_005615 NP_005606 A/G R89Q plus 1516639 1303 SEQUENOM CEPH CEPH (92) 46 0.5 0.5 0 46 1 123 by freq conservative 601981 14q11.2 "ribonuclease, RNase A family, k6" 1608 rs1046088 EP300 2033 22 39898883 NM_001429 NP_001420 A/C Q2223P plus 13361762 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.2 0 92 1 119 by freq moderately conservative 602700 22q13.2 E1A binding protein p300 1609 rs1046097 TUBG2 27175 17 38072225 NM_016437 NP_057521 A/G M413V plus 10856512 1303 SEQUENOM CEPH CEPH (92) 92 0.41 0.41 0 92 1 0.47 0 1500 1 121 "by doubleHit,freq,cluster" Borderline 1.151 60 conservative 605785 17q21 "tubulin, gamma 2" 1610 rs1046116 PKP2 5318 12 32913201 NM_004572 NP_004563 C/T L366P minus 12223634 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.24 0.18 0.09 212 2 120 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 602861 12p11 plakophilin 2 1611 rs1046116 PKP2 5318 12 32913201 NM_004572 NP_004563 C/T L366P minus 12223634 1303 SEQUENOM CEPH CEPH (92) 92 0.11 0.18 0.09 212 2 120 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 602861 12p11 plakophilin 2 1612 rs1046248 BDKRB2 624 14 95773237 NM_000623 NP_000614 C/T R14C plus 1517248 1303 SEQUENOM CEPH CEPH (92) 92 0.17 0.15 0.03 370 4 0.07 0 90 2 123 by freq radical 113503 14q32.1-q32.2 bradykinin receptor B2 1613 rs1046248 BDKRB2 624 14 95773237 NM_000623 NP_000614 C/T R14C plus 2981655 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.17 0.15 0.03 370 4 0.07 0 90 2 123 by freq radical 113503 14q32.1-q32.2 bradykinin receptor B2 1614 rs1046248 BDKRB2 624 14 95773237 NM_000623 NP_000614 C/T R14C plus 24607243 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.15 0.03 370 4 0.07 0 90 2 123 by freq radical 113503 14q32.1-q32.2 bradykinin receptor B2 1615 rs1046248 BDKRB2 624 14 95773237 NM_000623 NP_000614 C/T R14C plus 24795976 1303 SEQUENOM CEPH CEPH (92) 184 0.12 0.15 0.03 370 4 0.07 0 90 2 123 by freq radical 113503 14q32.1-q32.2 bradykinin receptor B2 1616 rs1046268 TJP3 27134 19 3701615 NM_014428 NP_055243 C/T M931T plus 12469289 1303 SEQUENOM CEPH CEPH (92) 92 0.49 0.49 0 92 1 120 "by doubleHit,freq,cluster" Possibly damaging 1.711 5 moderately conservative 19p13.3 tight junction protein 3 (zona occludens 3) 1617 rs1046658 RECK 8434 9 36073430 NM_021111 NP_066934 C/T R170X plus 1518040 1303 SEQUENOM CEPH CEPH (92) 92 0.08 0.08 0 92 1 106 by freq Probably damaging Intolerant radical 605227 9p13-p12 reversion-inducing-cysteine-rich protein with kazal motifs 1618 rs1046668 TNFAIP6 7130 2 152052078 NM_007115 NP_009046 A/G Q144R plus 3296528 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.13 0.16 0.08 258 3 0.21 0.09 94 2 123 "HapMap,doubleHit,freq,cluster" Tolerant 0.45 2.98 121 conservative 600410 2q24.1 "tumor necrosis factor, alpha-induced protein 6" 1619 rs1046668 TNFAIP6 7130 2 152052078 NM_007115 NP_009046 A/G Q144R plus 3296528 1303 SEQUENOM CEPH CEPH (92) 92 0.25 0.16 0.08 258 3 0.21 0.09 94 2 123 "HapMap,doubleHit,freq,cluster" Tolerant 0.45 2.98 121 conservative 600410 2q24.1 "tumor necrosis factor, alpha-induced protein 6" 1620 rs1046668 TNFAIP6 7130 2 152052078 NM_007115 NP_009046 A/G Q144R plus 23253087 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.16 0.08 258 3 0.21 0.09 94 2 123 "HapMap,doubleHit,freq,cluster" Tolerant 0.45 2.98 121 conservative 600410 2q24.1 "tumor necrosis factor, alpha-induced protein 6" 1621 rs1046974 SAG 6295 2 234037547 NM_000541 NP_000532 A/G V403I plus 16874051 1303 SEQUENOM CEPH CEPH (92) 92 0.34 0.34 0 92 1 120 "by doubleHit,submitter,freq,cluster" conservative 181031 2q37.1 S-antigen; retina and pineal gland (arrestin) 1622 rs1046984 BRCA2 675 13 31805411 NM_000059 NP_000050 C/T S599F plus 1518650 1303 SEQUENOM CEPH CEPH (92) 92 0.14 0.14 0 92 1 86 by freq Probably damaging 1.998 9 radical 600185 13q12.3 "breast cancer 2, early onset" 1623 rs1047286 C3 718 19 6664262 NM_000064 NP_000055 C/T P314L minus 3177315 619 WICVAR MITOGPOP6 CORIELL Mixed 52 0.19 0.19 0 52 1 102 by freq Possibly damaging 1.514 9 moderately conservative 120700 19p13.3-p13.2 complement component 3 1624 rs1047303 HSD3B1 3283 1 119769288 NM_000862 NP_000853 A/C T367N plus 6413600 1303 SEQUENOM CEPH CEPH (92) 92 0.48 0.48 0 92 1 0.06 0 1378 1 121 "by doubleHit,freq,cluster" Possibly damaging 1.503 29 Tolerant 0.3 3.19 29 moderately conservative 109715 1p13.1 "hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1" 1625 rs1047325 S100A2 6273 1 150347100 NM_005978 NP_005969 A/G S61N minus 15433527 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.13 0.05 140 2 0.21 0.28 90 2 123 "by cluster,freq" Potentially damaging 1.279 7 Tolerant 0.33 2.79 44 conservative 176993 1q21 S100 calcium binding protein A2 1626 rs1047325 S100A2 6273 1 150347100 NM_005978 NP_005969 A/G S61N minus 23213597 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.13 0.05 140 2 0.21 0.28 90 2 123 "by cluster,freq" Potentially damaging 1.279 7 Tolerant 0.33 2.79 44 conservative 176993 1q21 S100 calcium binding protein A2 1627 rs1047372 PCDHB2 56133 5 140456837 NM_018936 NP_061759 A/G G760D plus 24815868 1303 SEQUENOM CEPH CEPH (92) 184 0.38 0.38 0 184 1 123 "by cluster,freq" Benign 0.231 98 Tolerant 1 2.77 127 moderately conservative 606328 5q31 protocadherin beta 2 1628 rs1047626 SLC30A9 10463 4 41844599 NM_006345 NP_006336 A/G M50V plus 24655325 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.38 0 48 1 0.16 0.14 94 2 123 "by doubleHit,freq,cluster" Benign 0.86 5 conservative 604604 4p13-p12 "solute carrier family 30 (zinc transporter), member 9" 1629 rs1047640 SP3 6670 2 174646257 NM_003111 NP_003102 A/G T164A minus 16844292 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.16 0 92 1 0.32 0 1492 1 121 "by doubleHit,freq,cluster" Tolerant 1 3.04 23 moderately conservative 601804 2q31 Sp3 transcription factor 1630 rs1047769 ERCC5 2073 13 102311945 NM_000123 NP_000114 A/G M254V plus 5605242 693 EGP_SNPS PDR90 NIHPDR 178 0.03 0.03 0.01 330 3 0.04 0.02 240 2 118 "by cluster,freq" Possibly damaging 1.528 7 Tolerant 0.25 2.9 8 conservative 133530 13q22 "excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))" 1631 rs1047769 ERCC5 2073 13 102311945 NM_000123 NP_000114 A/G M254V plus 5605242 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.03 0.01 330 3 0.04 0.02 240 2 118 "by cluster,freq" Possibly damaging 1.528 7 Tolerant 0.25 2.9 8 conservative 133530 13q22 "excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))" 1632 rs1047769 ERCC5 2073 13 102311945 NM_000123 NP_000114 A/G M254V plus 12675394 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.05 0.03 0.01 330 3 0.04 0.02 240 2 118 "by cluster,freq" Possibly damaging 1.528 7 Tolerant 0.25 2.9 8 conservative 133530 13q22 "excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))" 1633 rs1047855 ENTPD3 956 3 40443900 NM_001248 NP_001239 C/T A496V plus 16972678 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.27 0.27 0 120 1 120 "HapMap,freq,cluster" moderately conservative 603161 3p21.3 ectonucleoside triphosphate diphosphohydrolase 3 1634 rs1047991 PAPD1 55149 10 30669232 NM_018109 NP_060579 A/G R162C plus 20687231 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.35 0.39 0.08 260 3 0.2 0.07 94 2 123 "HapMap,doubleHit,freq" Possibly damaging 1.744 5 Intolerant 0.03 2.94 16 radical 10p12.1 PAP associated domain containing 1 1635 rs1047991 PAPD1 55149 10 30669232 NM_018109 NP_060579 A/G R162C plus 20687231 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.39 0.08 260 3 0.2 0.07 94 2 123 "HapMap,doubleHit,freq" Possibly damaging 1.744 5 Intolerant 0.03 2.94 16 radical 10p12.1 PAP associated domain containing 1 1636 rs1047991 PAPD1 55149 10 30669232 NM_018109 NP_060579 A/G R162C plus 24624214 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.39 0.08 260 3 0.2 0.07 94 2 123 "HapMap,doubleHit,freq" Possibly damaging 1.744 5 Intolerant 0.03 2.94 16 radical 10p12.1 PAP associated domain containing 1 1637 rs1048108 BARD1 580 2 215499730 NM_000465 NP_000456 C/T P24S minus 1520704 1303 SEQUENOM CEPH CEPH (92) 92 0.42 0.41 0.03 140 2 0.33 0.13 94 2 123 "by cluster,freq" moderately conservative 601593 2q34-q35 BRCA1 associated RING domain 1 1638 rs1048108 BARD1 580 2 215499730 NM_000465 NP_000456 C/T P24S minus 23927969 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.41 0.03 140 2 0.33 0.13 94 2 123 "by cluster,freq" moderately conservative 601593 2q34-q35 BRCA1 associated RING domain 1 1639 rs1048135 NMI 9111 2 151964924 NM_004688 NP_004679 C/T S16L minus 21598065 1303 SEQUENOM CEPH CEPH (92) 92 0.46 0.43 0.05 140 2 0.2 0.17 92 2 123 by freq moderately radical 603525 2p24.3-q21.3 N-myc (and STAT) interactor 1640 rs1048135 NMI 9111 2 151964924 NM_004688 NP_004679 C/T S16L minus 24309331 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.43 0.05 140 2 0.2 0.17 92 2 123 by freq moderately radical 603525 2p24.3-q21.3 N-myc (and STAT) interactor 1641 rs1048197 SMPD2 6610 6 109869025 NM_003080 NP_003071 A/G P3L minus 1520899 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.04 0.03 0.02 212 2 123 "HapMap,submitter,freq" moderately conservative 603498 6q21 "sphingomyelin phosphodiesterase 2, neutral membrane (neutral sphingomyelinase)" 1642 rs1048197 SMPD2 6610 6 109869025 NM_003080 NP_003071 A/G P3L minus 1520899 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.03 0.02 212 2 123 "HapMap,submitter,freq" moderately conservative 603498 6q21 "sphingomyelin phosphodiesterase 2, neutral membrane (neutral sphingomyelinase)" 1643 rs1048430 HLA-DQA1 3117 6 32718465 NM_002122 NP_002113 C/G F238L plus 24816176 1303 SEQUENOM CEPH CEPH (92) 184 0.43 0.43 0 184 1 123 by freq Benign 0.414 162 Tolerant 1 2.84 257 conservative 146880 6p21.3 "major histocompatibility complex, class II, DQ alpha 1" 1644 rs1048661 LOXL1 4016 15 72006599 NM_005576 NP_005567 G/T R141L plus 4929216 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.04 0 92 1 0.44 0 1496 1 108 "by cluster,freq" moderately radical 153456 15q22 lysyl oxidase-like 1 1645 rs1048889 DDX54 79039 12 112059586 NM_024072 NP_076977 C/T P822L minus 1522193 1303 SEQUENOM CEPH CEPH (92) 92 0.39 0.39 0 92 1 123 by freq Benign 0.225 7 moderately conservative 12q24.21 DEAD (Asp-Glu-Ala-Asp) box polypeptide 54 1646 rs1048943 CYP1A1 1543 15 72800038 NM_000499 NP_000490 A/G I462V minus 3176140 619 WICVAR MITOGPOP6 CORIELL Mixed 60 0.02 0.07 0.07 118 2 0.17 0.07 370 4 116 "by cluster,freq" Benign 0.906 90 Borderline 0.11 2.81 88 conservative 108330 15q22-q24 "cytochrome P450, family 1, subfamily A, polypeptide 1" 1647 rs1048943 CYP1A1 1543 15 72800038 NM_000499 NP_000490 A/G I462V minus 5586386 775 SNP500CANCER CAUC1 Caucasian (31) 58 0.12 0.07 0.07 118 2 0.17 0.07 370 4 116 "by cluster,freq" Benign 0.906 90 Borderline 0.11 2.81 88 conservative 108330 15q22-q24 "cytochrome P450, family 1, subfamily A, polypeptide 1" 1648 rs1049125 PNLIPRP1 5407 10 118358596 NM_006229 NP_006220 C/T L461P plus 19174353 1303 SEQUENOM CEPH CEPH (92) 92 0.12 0.12 0.01 140 2 0.07 0.04 94 2 123 "by cluster,freq" Probably damaging 2.033 40 Intolerant 0.01 3.09 28 moderately conservative 604422 10q26.12 pancreatic lipase-related protein 1 1649 rs1049125 PNLIPRP1 5407 10 118358596 NM_006229 NP_006220 C/T L461P plus 24600233 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.12 0.01 140 2 0.07 0.04 94 2 123 "by cluster,freq" Probably damaging 2.033 40 Intolerant 0.01 3.09 28 moderately conservative 604422 10q26.12 pancreatic lipase-related protein 1 1650 rs1049254 CYBA 1535 16 87237329 NM_000101 NP_000092 C/T V174A minus 24694530 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.48 0.48 0 46 1 0.25 0.1 84 2 123 "by doubleHit,freq,cluster" Benign 0.116 9 moderately conservative 608508 16q24 "cytochrome b-245, alpha polypeptide" 1651 rs1049296 TF 7018 3 134977052 NM_001063 NP_001054 C/T P589S plus 8820437 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.04 0.09 0.05 138 2 0.07 0 46 1 120 "by cluster,freq" Borderline 1.244 83 Borderline 0.11 2.82 93 moderately conservative 190000 3q22.1 transferrin 1652 rs1049296 TF 7018 3 134977052 NM_001063 NP_001054 C/T P589S plus 8820437 1303 SEQUENOM CEPH CEPH (92) 92 0.12 0.09 0.05 138 2 0.07 0 46 1 120 "by cluster,freq" Borderline 1.244 83 Borderline 0.11 2.82 93 moderately conservative 190000 3q22.1 transferrin 1653 rs1049306 PDHX 8050 11 34894845 NM_003477 NP_003468 C/T R23C plus 12148948 1303 SEQUENOM CEPH CEPH (92) 92 0.36 0.17 0.12 460 3 123 "by doubleHit,freq,cluster" radical 608769 11p13 "pyruvate dehydrogenase complex, component X" 1654 rs1049306 PDHX 8050 11 34894845 NM_003477 NP_003468 C/T R23C plus 24797023 1303 SEQUENOM CEPH CEPH (92) 184 0.12 0.17 0.12 460 3 123 "by doubleHit,freq,cluster" radical 608769 11p13 "pyruvate dehydrogenase complex, component X" 1655 rs1049306 PDHX 8050 11 34894845 NM_003477 NP_003468 C/T R23C plus 24816514 1303 SEQUENOM CEPH CEPH (92) 184 0.12 0.17 0.12 460 3 123 "by doubleHit,freq,cluster" radical 608769 11p13 "pyruvate dehydrogenase complex, component X" 1656 rs1049544 SPARCL1 8404 4 88772815 NM_004684 NP_004675 C/G H106D minus 4949430 1303 SEQUENOM CEPH CEPH (92) 92 0.33 0.35 0.05 140 2 0.37 0.11 88 2 123 "by doubleHit,freq,cluster" Possibly damaging 1.575 5 moderately conservative 606041 4q22.1 "SPARC-like 1 (mast9, hevin)" 1657 rs1049544 SPARCL1 8404 4 88772815 NM_004684 NP_004675 C/G H106D minus 23881462 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.35 0.05 140 2 0.37 0.11 88 2 123 "by doubleHit,freq,cluster" Possibly damaging 1.575 5 moderately conservative 606041 4q22.1 "SPARC-like 1 (mast9, hevin)" 1658 rs1049564 NP 4860 14 20010446 NM_000270 NP_000261 C/T G51S minus 23617308 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.27 0.2 94 2 123 "by doubleHit,freq,cluster" Potentially damaging 1.411 31 moderately conservative 164050 14q13.1 nucleoside phosphorylase 1659 rs1049742 ABP1 26 7 149992201 NM_001091 NP_001082 C/T S332F plus 17939745 1303 SEQUENOM CEPH CEPH (92) 92 0.09 0.09 0 92 1 121 "by doubleHit,freq,cluster" Possibly damaging 1.954 11 Intolerant 0 2.76 26 radical 104610 7q34-q36 amiloride binding protein 1 (amine oxidase (copper-containing)) 1660 rs1049925 PHC1 1911 12 8978165 NM_004426 NP_004417 C/T T693A minus 24698787 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.26 0.14 232 2 0.24 0.16 94 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.222 12 Tolerant 1 3.03 23 moderately conservative 602978 12p13 polyhomeotic-like 1 (Drosophila) 1661 rs1049925 PHC1 1911 12 8978165 NM_004426 NP_004417 C/T T693A minus 24796441 1303 SEQUENOM CEPH CEPH (92) 184 0.21 0.26 0.14 232 2 0.24 0.16 94 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.222 12 Tolerant 1 3.03 23 moderately conservative 602978 12p13 polyhomeotic-like 1 (Drosophila) 1662 rs1049970 CDH5 1003 16 64989924 NM_001795 NP_001786 C/T I517T plus 14254569 1303 SEQUENOM CEPH CEPH (92) 92 0.39 0.39 0 92 1 120 "by doubleHit,freq,cluster" Benign 0.675 7 moderately conservative 601120 16q22.1 "cadherin 5, type 2, VE-cadherin (vascular epithelium)" 1663 rs1050110 ADPRTL1 143 13 23907485 NM_006437 NP_006428 C/G G1265A minus 5586211 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.47 0.44 0.11 190 4 0.31 0.07 1710 8 116 "by doubleHit,freq,cluster" moderately conservative 607519 13q11 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1 1664 rs1050110 ADPRTL1 143 13 23907485 NM_006437 NP_006428 C/G G1265A minus 5586211 902 AFFY Caucasian 24 0.25 0.44 0.11 190 4 0.31 0.07 1710 8 116 "by doubleHit,freq,cluster" moderately conservative 607519 13q11 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1 1665 rs1050110 ADPRTL1 143 13 23907485 NM_006437 NP_006428 C/G G1265A minus 5586211 904 AFFY CEPH 12 0.25 0.44 0.11 190 4 0.31 0.07 1710 8 116 "by doubleHit,freq,cluster" moderately conservative 607519 13q11 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1 1666 rs1050110 ADPRTL1 143 13 23907485 NM_006437 NP_006428 C/G G1265A minus 5586211 1303 SEQUENOM CEPH CEPH (92) 92 0.49 0.44 0.11 190 4 0.31 0.07 1710 8 116 "by doubleHit,freq,cluster" moderately conservative 607519 13q11 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1 1667 rs1050112 ADPRTL1 143 13 23907297 NM_006437 NP_006428 A/C P1328T minus 5586216 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.47 0.48 0.02 108 2 0.32 0.07 1838 5 120 "by doubleHit,freq,cluster" conservative 607519 13q11 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1 1668 rs1050112 ADPRTL1 143 13 23907297 NM_006437 NP_006428 A/C P1328T minus 5586216 1303 SEQUENOM CEPH CEPH (92) 46 0.5 0.48 0.02 108 2 0.32 0.07 1838 5 120 "by doubleHit,freq,cluster" conservative 607519 13q11 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1 1669 rs1050114 ADPRTL1 143 13 23907288 NM_006437 NP_006428 A/G A1331T minus 5586217 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.02 0.04 0.03 154 2 0.08 0.05 298 3 113 "by cluster,freq" moderately conservative 607519 13q11 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1 1670 rs1050114 ADPRTL1 143 13 23907288 NM_006437 NP_006428 A/G A1331T minus 5586217 1303 SEQUENOM CEPH CEPH (92) 92 0.06 0.04 0.03 154 2 0.08 0.05 298 3 113 "by cluster,freq" moderately conservative 607519 13q11 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1 1671 rs1050152 SLC22A4 6583 5 131704219 NM_003059 NP_003050 C/T L503F plus 24379843 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.42 0 48 1 0.18 0.06 596 2 123 "by cluster,freq" Benign 0.132 12 Potentially intolerant 0.06 2.81 21 conservative 604190 5q31.1 "solute carrier family 22 (organic cation transporter), member 4" 1672 rs1050160 GLUD1 2746 10 88844232 NM_005271 NP_005262 A/G R92Q minus 24797030 1303 SEQUENOM CEPH CEPH (92) 184 0.28 0.28 0 184 1 123 by freq Potentially damaging 1.247 32 Tolerant 0.7 3.07 55 conservative 138130 10q23.3 glutamate dehydrogenase 1 1673 rs1050348 LAMA4 3910 6 112600565 NM_002290 NP_002281 C/T Y491H minus 3156356 1303 SEQUENOM CEPH CEPH (92) 92 0.38 0.37 0.02 140 2 0.22 0.02 94 2 123 "by doubleHit,freq,cluster" Possibly damaging 1.711 6 moderately conservative 600133 6q21 "laminin, alpha 4" 1674 rs1050348 LAMA4 3910 6 112600565 NM_002290 NP_002281 C/T Y491H minus 24413213 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.37 0.02 140 2 0.22 0.02 94 2 123 "by doubleHit,freq,cluster" Possibly damaging 1.711 6 moderately conservative 600133 6q21 "laminin, alpha 4" 1675 rs1050349 LAMA4 3910 6 112564076 NM_002290 NP_002281 C/G P1112R minus 2941526 1303 SEQUENOM CEPH CEPH (92) 92 0.15 0.15 0 92 1 116 "by doubleHit,submitter,cluster" Benign 0.521 8 moderately radical 600133 6q21 "laminin, alpha 4" 1676 rs1050354 PPIG 9360 2 170318610 NM_004792 NP_004783 A/T D445E plus 11496510 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.48 0.44 0.05 260 3 0.33 0.1 90 2 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.77 3.02 8 conservative 606093 2q31.1 peptidyl-prolyl isomerase G (cyclophilin G) 1677 rs1050354 PPIG 9360 2 170318610 NM_004792 NP_004783 A/T D445E plus 11496510 1303 SEQUENOM CEPH CEPH (92) 92 0.41 0.44 0.05 260 3 0.33 0.1 90 2 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.77 3.02 8 conservative 606093 2q31.1 peptidyl-prolyl isomerase G (cyclophilin G) 1678 rs1050354 PPIG 9360 2 170318610 NM_004792 NP_004783 A/T D445E plus 24369174 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.44 0.05 260 3 0.33 0.1 90 2 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.77 3.02 8 conservative 606093 2q31.1 peptidyl-prolyl isomerase G (cyclophilin G) 1679 rs1050450 GPX1 2876 3 49369838 NM_000581 NP_000572 C/T P200L minus 5586547 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.19 0.15 0.03 424 3 0.16 0.06 346 4 123 "by doubleHit,freq,cluster" Benign 0.486 12 Borderline 0.12 3.16 23 moderately conservative 138320 3p21.3 glutathione peroxidase 1 1680 rs1050450 GPX1 2876 3 49369838 NM_000581 NP_000572 C/T P200L minus 12568572 693 EGP_SNPS PDR90 NIHPDR 178 0.17 0.15 0.03 424 3 0.16 0.06 346 4 123 "by doubleHit,freq,cluster" Benign 0.486 12 Borderline 0.12 3.16 23 moderately conservative 138320 3p21.3 glutathione peroxidase 1 1681 rs1050450 GPX1 2876 3 49369838 NM_000581 NP_000572 C/T P200L minus 24787925 1303 SEQUENOM CEPH CEPH (92) 184 0.12 0.15 0.03 424 3 0.16 0.06 346 4 123 "by doubleHit,freq,cluster" Benign 0.486 12 Borderline 0.12 3.16 23 moderately conservative 138320 3p21.3 glutathione peroxidase 1 1682 rs1050501 FCGR2B 2213 1 158375465 NM_004001 NP_003992 C/T I225T plus 19838944 1303 SEQUENOM CEPH CEPH (92) 92 0.11 0.12 0.03 140 2 0.28 0.02 94 2 123 "by doubleHit,freq,cluster" Benign 0.237 40 Tolerant 0.22 2.75 39 moderately conservative 604590 1q23 "Fc fragment of IgG, low affinity IIb, receptor for (CD32)" 1683 rs1050501 FCGR2B 2213 1 158375465 NM_004001 NP_003992 C/T I225T plus 23842385 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.12 0.03 140 2 0.28 0.02 94 2 123 "by doubleHit,freq,cluster" Benign 0.237 40 Tolerant 0.22 2.75 39 moderately conservative 604590 1q23 "Fc fragment of IgG, low affinity IIb, receptor for (CD32)" 1684 rs1050565 BLMH 642 17 25600202 NM_000386 NP_000377 A/G I443V minus 3217070 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.3 0.3 0.04 258 3 0.18 0.03 1596 3 123 "HapMap,freq,cluster" Benign 0.986 12 Tolerant 1 2.82 33 conservative 602403 17q11.2 bleomycin hydrolase 1685 rs1050565 BLMH 642 17 25600202 NM_000386 NP_000377 A/G I443V minus 3217070 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.3 0.04 258 3 0.18 0.03 1596 3 123 "HapMap,freq,cluster" Benign 0.986 12 Tolerant 1 2.82 33 conservative 602403 17q11.2 bleomycin hydrolase 1686 rs1050565 BLMH 642 17 25600202 NM_000386 NP_000377 A/G I443V minus 24705757 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.3 0.04 258 3 0.18 0.03 1596 3 123 "HapMap,freq,cluster" Benign 0.986 12 Tolerant 1 2.82 33 conservative 602403 17q11.2 bleomycin hydrolase 1687 rs1050767 MKI67 4288 10 129791936 NM_002417 NP_002408 A/C T2720P minus 14315599 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.16 0 92 1 121 "by doubleHit,freq,cluster" Tolerant 0.23 2.84 10 conservative 176741 10q25-qter antigen identified by monoclonal antibody Ki-67 1688 rs1050916 BLVRA 644 7 43604120 NM_000712 NP_000703 A/G Q56R plus 1525956 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.03 0.03 0 118 1 106 "HapMap,freq" Potentially damaging 1.432 7 Tolerant 0.51 2.75 15 conservative 109750 7p14-cen biliverdin reductase A 1689 rs1050998 CXCL16 58191 17 4585486 NM_022059 NP_071342 C/T I142T minus 12391137 1303 SEQUENOM CEPH CEPH (92) 92 0.28 0.3 0.05 140 2 0.41 0.03 1588 3 123 "by doubleHit,freq,cluster" moderately conservative 605398 17p13 chemokine (C-X-C motif) ligand 16 1690 rs1050998 CXCL16 58191 17 4585486 NM_022059 NP_071342 C/T I142T minus 24213400 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.3 0.05 140 2 0.41 0.03 1588 3 123 "by doubleHit,freq,cluster" moderately conservative 605398 17p13 chemokine (C-X-C motif) ligand 16 1691 rs1051042 OAS1 4938 12 111819957 NM_016816 NP_058132 C/G R361T plus 16591428 1303 SEQUENOM CEPH CEPH (92) 92 0.24 0.3 0.13 138 2 0.17 0.08 94 2 123 "by doubleHit,freq,cluster" moderately conservative 164350 12q24.1 "2',5'-oligoadenylate synthetase 1, 40/46kDa" 1692 rs1051042 OAS1 4938 12 111819957 NM_016816 NP_058132 C/G R361T plus 24415249 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.43 0.3 0.13 138 2 0.17 0.08 94 2 123 "by doubleHit,freq,cluster" moderately conservative 164350 12q24.1 "2',5'-oligoadenylate synthetase 1, 40/46kDa" 1693 rs1051061 VRK2 7444 2 58228465 NM_006296 NP_006287 A/G I167V plus 4474748 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.34 0.33 0.01 260 3 0.42 0.07 1584 3 123 "HapMap,submitter,freq,cluster" Benign 0.3 8 conservative 602169 2p16-p15 vaccinia related kinase 2 1694 rs1051061 VRK2 7444 2 58228465 NM_006296 NP_006287 A/G I167V plus 4474748 1303 SEQUENOM CEPH CEPH (92) 92 0.32 0.33 0.01 260 3 0.42 0.07 1584 3 123 "HapMap,submitter,freq,cluster" Benign 0.3 8 conservative 602169 2p16-p15 vaccinia related kinase 2 1695 rs1051061 VRK2 7444 2 58228465 NM_006296 NP_006287 A/G I167V plus 23899502 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.33 0.01 260 3 0.42 0.07 1584 3 123 "HapMap,submitter,freq,cluster" Benign 0.3 8 conservative 602169 2p16-p15 vaccinia related kinase 2 1696 rs1051130 CCND3 896 6 42011760 NM_001760 NP_001751 G/T S259A minus 3177789 619 WICVAR MITOGPOP6 CORIELL Mixed 26 0.23 0.33 0.05 288 3 0.46 0 1290 1 121 "by doubleHit,freq,cluster" Benign 0.162 26 Tolerant 0.4 3.13 29 moderately conservative 123834 6p21 cyclin D3 1697 rs1051130 CCND3 896 6 42011760 NM_001760 NP_001751 G/T S259A minus 4479170 693 EGP_SNPS PDR90 NIHPDR 170 0.36 0.33 0.05 288 3 0.46 0 1290 1 121 "by doubleHit,freq,cluster" Benign 0.162 26 Tolerant 0.4 3.13 29 moderately conservative 123834 6p21 cyclin D3 1698 rs1051130 CCND3 896 6 42011760 NM_001760 NP_001751 G/T S259A minus 4479170 1303 SEQUENOM CEPH CEPH (92) 92 0.3 0.33 0.05 288 3 0.46 0 1290 1 121 "by doubleHit,freq,cluster" Benign 0.162 26 Tolerant 0.4 3.13 29 moderately conservative 123834 6p21 cyclin D3 1699 rs1051193 SEL1L 6400 14 81015744 NM_005065 NP_005056 A/G V714I minus 1526538 1303 SEQUENOM CEPH CEPH (92) 92 0.03 0.03 0 92 1 86 by freq Benign 0.225 6 Tolerant 0.57 2.85 25 conservative 602329 14q24.3-q31 sel-1 suppressor of lin-12-like (C. elegans) 1700 rs1051266 SLC19A1 6573 21 45782222 NM_194255 NP_919231 A/G H27R minus 3177864 619 WICVAR MITOGPOP6 CORIELL Mixed 54 0.13 0.26 0.14 146 2 0.44 0 598 1 121 "by doubleHit,freq,cluster" Tolerant 0.35 2.83 35 conservative 600424 21q22.3 "solute carrier family 19 (folate transporter), member 1" 1701 rs1051266 SLC19A1 6573 21 45782222 NM_194255 NP_919231 A/G H27R minus 21819753 1303 SEQUENOM CEPH CEPH (92) 92 0.33 0.26 0.14 146 2 0.44 0 598 1 121 "by doubleHit,freq,cluster" Tolerant 0.35 2.83 35 conservative 600424 21q22.3 "solute carrier family 19 (folate transporter), member 1" 1702 rs1051309 ANKHD1 54882 5 139886028 NM_017747 NP_060217 A/G G1586S plus 1526754 1303 SEQUENOM CEPH CEPH (92) 92 0.03 0.03 0 92 1 106 by freq moderately conservative 5q31.3 ankyrin repeat and KH domain containing 1 1703 rs1051338 LIPA 3988 10 90997340 NM_000235 NP_000226 A/C T16P minus 3176256 619 WICVAR MITOGPOP6 CORIELL Mixed 46 0.3 0.3 0.05 300 4 0.21 0.16 86 2 123 "HapMap,submitter,freq,cluster" Benign 0.45 7 Tolerant 0.21 2.98 24 conservative 278000 10q23.2-q23.3 "lipase A, lysosomal acid, cholesterol esterase (Wolman disease)" 1704 rs1051338 LIPA 3988 10 90997340 NM_000235 NP_000226 A/C T16P minus 3500320 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.33 0.3 0.05 300 4 0.21 0.16 86 2 123 "HapMap,submitter,freq,cluster" Benign 0.45 7 Tolerant 0.21 2.98 24 conservative 278000 10q23.2-q23.3 "lipase A, lysosomal acid, cholesterol esterase (Wolman disease)" 1705 rs1051338 LIPA 3988 10 90997340 NM_000235 NP_000226 A/C T16P minus 3500320 1303 SEQUENOM CEPH CEPH (92) 92 0.31 0.3 0.05 300 4 0.21 0.16 86 2 123 "HapMap,submitter,freq,cluster" Benign 0.45 7 Tolerant 0.21 2.98 24 conservative 278000 10q23.2-q23.3 "lipase A, lysosomal acid, cholesterol esterase (Wolman disease)" 1706 rs1051338 LIPA 3988 10 90997340 NM_000235 NP_000226 A/C T16P minus 24085876 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.19 0.3 0.05 300 4 0.21 0.16 86 2 123 "HapMap,submitter,freq,cluster" Benign 0.45 7 Tolerant 0.21 2.98 24 conservative 278000 10q23.2-q23.3 "lipase A, lysosomal acid, cholesterol esterase (Wolman disease)" 1707 rs1051484 PREP 5550 6 105832729 NM_002726 NP_002717 C/T V706I plus 1673280 1303 SEQUENOM CEPH CEPH (92) 92 0.29 0.16 0.11 242 4 0.3 0.04 1618 5 123 "by doubleHit,freq,cluster" Benign 0.337 16 Tolerant 0.88 2.94 21 conservative 600400 6q22 prolyl endopeptidase 1708 rs1051484 PREP 5550 6 105832729 NM_002726 NP_002717 C/T V706I plus 2588301 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.07 0.16 0.11 242 4 0.3 0.04 1618 5 123 "by doubleHit,freq,cluster" Benign 0.337 16 Tolerant 0.88 2.94 21 conservative 600400 6q22 prolyl endopeptidase 1709 rs1051484 PREP 5550 6 105832729 NM_002726 NP_002717 C/T V706I plus 2588301 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 90 0.09 0.16 0.11 242 4 0.3 0.04 1618 5 123 "by doubleHit,freq,cluster" Benign 0.337 16 Tolerant 0.88 2.94 21 conservative 600400 6q22 prolyl endopeptidase 1710 rs1051484 PREP 5550 6 105832729 NM_002726 NP_002717 C/T V706I plus 23495927 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.09 0.16 0.11 242 4 0.3 0.04 1618 5 123 "by doubleHit,freq,cluster" Benign 0.337 16 Tolerant 0.88 2.94 21 conservative 600400 6q22 prolyl endopeptidase 1711 rs1051489 ZFR 51663 5 32436023 NM_016107 NP_057191 C/T I520T minus 3249658 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.29 0.26 0.04 212 2 121 "HapMap,submitter,freq,cluster" Benign 0.066 7 moderately conservative 5p13.3 zinc finger RNA binding protein 1712 rs1051489 ZFR 51663 5 32436023 NM_016107 NP_057191 C/T I520T minus 22301778 1303 SEQUENOM CEPH CEPH (92) 92 0.23 0.26 0.04 212 2 121 "HapMap,submitter,freq,cluster" Benign 0.066 7 moderately conservative 5p13.3 zinc finger RNA binding protein 1713 rs1051505 ARID3A 1820 19 922949 NM_005224 NP_005215 A/G G556S plus 12474446 1303 SEQUENOM CEPH CEPH (92) 92 0.13 0.13 0 92 1 121 "by doubleHit,freq,cluster" moderately conservative 603265 19p13.3 AT rich interactive domain 3A (BRIGHT- like) 1714 rs1051566 GSTA1 2938 6 52771991 NM_145740 NP_665683 A/G A12T minus 1527223 1303 SEQUENOM CEPH CEPH (92) 92 0.28 0.28 0 92 1 106 by freq Benign 0.009 57 Tolerant 0.34 2.85 64 moderately conservative 138359 6p12.1 glutathione S-transferase A1 1715 rs1051578 GSTA1 2938 6 52771969 NM_145740 NP_665683 C/T T19I minus 1527259 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.04 0 92 1 106 by freq Borderline 1.074 59 Tolerant 1 2.85 67 moderately conservative 138359 6p12.1 glutathione S-transferase A1 1716 rs1051612 POU1F1 5449 3 87408292 NM_000306 NP_000297 C/T Q4R plus 1527313 1303 SEQUENOM CEPH CEPH (92) 92 0.12 0.12 0 92 1 106 by freq Possibly damaging 1.696 22 conservative 173110 3p11 "POU domain, class 1, transcription factor 1 (Pit1, growth hormone factor 1)" 1717 rs1051623 CDH17 1015 8 95212362 NM_004063 NP_004054 C/G E734D minus 3523876 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.35 0.18 140 2 0.22 0.02 94 2 123 "by submitter,freq,cluster" Tolerant 0.23 3.03 13 conservative 603017 8q22.1 "cadherin 17, LI cadherin (liver-intestine)" 1718 rs1051623 CDH17 1015 8 95212362 NM_004063 NP_004054 C/G E734D minus 24044309 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.35 0.18 140 2 0.22 0.02 94 2 123 "by submitter,freq,cluster" Tolerant 0.23 3.03 13 conservative 603017 8q22.1 "cadherin 17, LI cadherin (liver-intestine)" 1719 rs1051624 CDH17 1015 8 95212348 NM_004063 NP_004054 A/C E739A minus 3525064 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.44 0.41 0.04 260 3 0.33 0.13 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.3 2.79 21 moderately radical 603017 8q22.1 "cadherin 17, LI cadherin (liver-intestine)" 1720 rs1051624 CDH17 1015 8 95212348 NM_004063 NP_004054 A/C E739A minus 3525064 1303 SEQUENOM CEPH CEPH (92) 92 0.37 0.41 0.04 260 3 0.33 0.13 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.3 2.79 21 moderately radical 603017 8q22.1 "cadherin 17, LI cadherin (liver-intestine)" 1721 rs1051624 CDH17 1015 8 95212348 NM_004063 NP_004054 A/C E739A minus 24497817 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.41 0.04 260 3 0.33 0.13 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.3 2.79 21 moderately radical 603017 8q22.1 "cadherin 17, LI cadherin (liver-intestine)" 1722 rs1051738 PDE4A 5141 19 10438843 NM_006202 NP_006193 A/C A497E plus 1527521 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.17 0.22 0.07 254 3 0.28 0.18 82 2 123 "HapMap,submitter,freq,cluster" Borderline 1.06 40 moderately radical 600126 19p13.2 "phosphodiesterase 4A, cAMP-specific (phosphodiesterase E2 dunce homolog, Drosophila)" 1723 rs1051738 PDE4A 5141 19 10438843 NM_006202 NP_006193 A/C A497E plus 14728683 1303 SEQUENOM CEPH CEPH (92) 92 0.29 0.22 0.07 254 3 0.28 0.18 82 2 123 "HapMap,submitter,freq,cluster" Borderline 1.06 40 moderately radical 600126 19p13.2 "phosphodiesterase 4A, cAMP-specific (phosphodiesterase E2 dunce homolog, Drosophila)" 1724 rs1051738 PDE4A 5141 19 10438843 NM_006202 NP_006193 A/C A497E plus 23646751 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.19 0.22 0.07 254 3 0.28 0.18 82 2 123 "HapMap,submitter,freq,cluster" Borderline 1.06 40 moderately radical 600126 19p13.2 "phosphodiesterase 4A, cAMP-specific (phosphodiesterase E2 dunce homolog, Drosophila)" 1725 rs1051740 EPHX1 2052 1 222326368 NM_000120 NP_000111 C/T Y113H plus 1527524 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.29 0.33 0.04 314 4 0.34 0.1 604 8 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.928 14 Intolerant 0 2.81 24 moderately conservative 132810 1q42.1 "epoxide hydrolase 1, microsomal (xenobiotic)" 1726 rs1051740 EPHX1 2052 1 222326368 NM_000120 NP_000111 C/T Y113H plus 4041372 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.33 0.33 0.04 314 4 0.34 0.1 604 8 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.928 14 Intolerant 0 2.81 24 moderately conservative 132810 1q42.1 "epoxide hydrolase 1, microsomal (xenobiotic)" 1727 rs1051740 EPHX1 2052 1 222326368 NM_000120 NP_000111 C/T Y113H plus 5586496 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.39 0.33 0.04 314 4 0.34 0.1 604 8 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.928 14 Intolerant 0 2.81 24 moderately conservative 132810 1q42.1 "epoxide hydrolase 1, microsomal (xenobiotic)" 1728 rs1051740 EPHX1 2052 1 222326368 NM_000120 NP_000111 C/T Y113H plus 23857114 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.33 0.04 314 4 0.34 0.1 604 8 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.928 14 Intolerant 0 2.81 24 moderately conservative 132810 1q42.1 "epoxide hydrolase 1, microsomal (xenobiotic)" 1729 rs1051881 EXOSC9 5393 4 123095570 NM_005033 NP_005024 C/G S341T plus 4478804 693 EGP_SNPS PDR90 NIHPDR 174 0.07 0.05 0.03 342 3 0.26 0.31 94 2 123 "HapMap,freq,cluster" moderately conservative 606180 4q27 "polymyositis/scleroderma autoantigen 1, 75kDa" 1730 rs1051881 EXOSC9 5393 4 123095570 NM_005033 NP_005024 C/G S341T plus 4478804 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.02 0.05 0.03 342 3 0.26 0.31 94 2 123 "HapMap,freq,cluster" moderately conservative 606180 4q27 "polymyositis/scleroderma autoantigen 1, 75kDa" 1731 rs1051881 EXOSC9 5393 4 123095570 NM_005033 NP_005024 C/G S341T plus 23305762 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.05 0.03 342 3 0.26 0.31 94 2 123 "HapMap,freq,cluster" moderately conservative 606180 4q27 "polymyositis/scleroderma autoantigen 1, 75kDa" 1732 rs1051931 PLA2G7 7941 6 46780902 NM_005084 NP_005075 A/G V379A plus 2226119 1303 SEQUENOM CEPH CEPH (92) 92 0.24 0.23 0.02 140 2 0.1 0.03 1390 3 123 "by doubleHit,freq,cluster" Possibly damaging 1.51 7 moderately conservative 601690 6p21.2-p12 "phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)" 1733 rs1051931 PLA2G7 7941 6 46780902 NM_005084 NP_005075 A/G V379A plus 23675802 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.23 0.02 140 2 0.1 0.03 1390 3 123 "by doubleHit,freq,cluster" Possibly damaging 1.51 7 moderately conservative 601690 6p21.2-p12 "phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)" 1734 rs1051992 PRKCDBP 112464 11 6297282 NM_145040 NP_659477 C/T L158P minus 16104065 1303 SEQUENOM CEPH CEPH (92) 92 0.4 0.41 0.01 140 2 0.37 0.02 94 2 123 "by doubleHit,freq,cluster" moderately conservative 11p15.4 "protein kinase C, delta binding protein" 1735 rs1051992 PRKCDBP 112464 11 6297282 NM_145040 NP_659477 C/T L158P minus 24514153 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.41 0.01 140 2 0.37 0.02 94 2 123 "by doubleHit,freq,cluster" moderately conservative 11p15.4 "protein kinase C, delta binding protein" 1736 rs1052576 CASP9 842 1 15577849 NM_001229 NP_001220 A/G Q221R minus 2924012 506 NCBI NIHPDR NIHPDR 826 0.45 0.45 0.02 1054 3 0.44 0.09 342 4 121 "by doubleHit,freq,cluster" Borderline 1.1 10 Tolerant 0.88 2.83 20 conservative 602234 1p36.3-p36.1 "caspase 9, apoptosis-related cysteine protease" 1737 rs1052576 CASP9 842 1 15577849 NM_001229 NP_001220 A/G Q221R minus 6310866 693 EGP_SNPS PDR90 NIHPDR 170 0.48 0.45 0.02 1054 3 0.44 0.09 342 4 121 "by doubleHit,freq,cluster" Borderline 1.1 10 Tolerant 0.88 2.83 20 conservative 602234 1p36.3-p36.1 "caspase 9, apoptosis-related cysteine protease" 1738 rs1052576 CASP9 842 1 15577849 NM_001229 NP_001220 A/G Q221R minus 6903699 775 SNP500CANCER CAUC1 Caucasian (31) 58 0.43 0.45 0.02 1054 3 0.44 0.09 342 4 121 "by doubleHit,freq,cluster" Borderline 1.1 10 Tolerant 0.88 2.83 20 conservative 602234 1p36.3-p36.1 "caspase 9, apoptosis-related cysteine protease" 1739 rs1052763 STK22B 23617 22 17494305 NM_053006 NP_443732 C/T T280M plus 3195626 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.19 0.24 0.09 258 3 0.24 0.03 1562 3 123 "HapMap,freq,cluster" Possibly damaging 1.749 8 Borderline 0.16 2.93 86 moderately conservative 22q11.21 serine/threonine kinase 22B (spermiogenesis associated) 1740 rs1052763 STK22B 23617 22 17494305 NM_053006 NP_443732 C/T T280M plus 3195626 1303 SEQUENOM CEPH CEPH (92) 92 0.33 0.24 0.09 258 3 0.24 0.03 1562 3 123 "HapMap,freq,cluster" Possibly damaging 1.749 8 Borderline 0.16 2.93 86 moderately conservative 22q11.21 serine/threonine kinase 22B (spermiogenesis associated) 1741 rs1052763 STK22B 23617 22 17494305 NM_053006 NP_443732 C/T T280M plus 24701578 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.17 0.24 0.09 258 3 0.24 0.03 1562 3 123 "HapMap,freq,cluster" Possibly damaging 1.749 8 Borderline 0.16 2.93 86 moderately conservative 22q11.21 serine/threonine kinase 22B (spermiogenesis associated) 1742 rs1053228 CIDE-3 63924 3 9883875 NM_022094 NP_071377 G/T Q220H minus 24817567 1303 SEQUENOM CEPH CEPH (92) 184 0.11 0.11 0 184 1 123 by freq Possibly damaging 1.599 6 Borderline 0.14 3.09 17 conservative 3p25.3 cell death activator CIDE-3 1743 rs1053230 KMO 8564 1 238081389 NM_003679 NP_003670 A/G R452C minus 11391586 1303 SEQUENOM CEPH CEPH (92) 92 0.3 0.3 0 92 1 116 "by submitter,freq,cluster" radical 603538 1q42-q44 kynurenine 3-monooxygenase (kynurenine 3-hydroxylase) 1744 rs1053312 COL6A1 1291 21 46247817 NM_001848 NP_001839 A/G R850H plus 1530395 1303 SEQUENOM CEPH CEPH (92) 92 0.28 0.29 0.01 276 2 123 "by doubleHit,freq" Potentially damaging 1.489 6 Tolerant 0.24 2.85 19 conservative 120220 21q22.3 "collagen, type VI, alpha 1" 1745 rs1053312 COL6A1 1291 21 46247817 NM_001848 NP_001839 A/G R850H plus 24817592 1303 SEQUENOM CEPH CEPH (92) 184 0.3 0.29 0.01 276 2 123 "by doubleHit,freq" Potentially damaging 1.489 6 Tolerant 0.24 2.85 19 conservative 120220 21q22.3 "collagen, type VI, alpha 1" 1746 rs1053655 ERF 2077 19 47445490 NM_006494 NP_006485 A/G R205H minus 1531069 1303 SEQUENOM CEPH CEPH (92) 92 0.06 0.06 0 92 1 86 by freq Intolerant 0 3.06 28 conservative 19q13 Ets2 repressor factor 1747 rs1053874 DNASE1 1773 16 3647748 NM_005223 NP_005214 A/G R244Q plus 8819957 506 NCBI NIHPDR NIHPDR 146 0.42 0.34 0.1 286 3 0.43 0.03 1746 4 123 "by doubleHit,freq,cluster" Benign 0.28 28 Tolerant 0.4 2.81 44 conservative 125505 16p13.3 deoxyribonuclease I 1748 rs1053874 DNASE1 1773 16 3647748 NM_005223 NP_005214 A/G R244Q plus 14265220 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.34 0.1 286 3 0.43 0.03 1746 4 123 "by doubleHit,freq,cluster" Benign 0.28 28 Tolerant 0.4 2.81 44 conservative 125505 16p13.3 deoxyribonuclease I 1749 rs1053874 DNASE1 1773 16 3647748 NM_005223 NP_005214 A/G R244Q plus 24217047 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.34 0.1 286 3 0.43 0.03 1746 4 123 "by doubleHit,freq,cluster" Benign 0.28 28 Tolerant 0.4 2.81 44 conservative 125505 16p13.3 deoxyribonuclease I 1750 rs1054423 IPO8 10526 12 30739833 NM_006390 NP_006381 A/T I6F minus 1532365 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.04 0 92 1 86 by freq Potentially damaging 1.434 12 Intolerant 0.03 2.81 16 conservative 605600 12p11.22 importin 8 1751 rs1054480 ADAMTS2 9509 5 178473581 NM_014244 NP_055059 C/T P1177S minus 3250293 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.2 0.26 0.07 260 3 0.35 0.08 816 3 123 "HapMap,submitter,freq,cluster" Probably damaging 2.1 9 moderately conservative 604539 5qter "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2" 1752 rs1054480 ADAMTS2 9509 5 178473581 NM_014244 NP_055059 C/T P1177S minus 3250293 1303 SEQUENOM CEPH CEPH (92) 92 0.29 0.26 0.07 260 3 0.35 0.08 816 3 123 "HapMap,submitter,freq,cluster" Probably damaging 2.1 9 moderately conservative 604539 5qter "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2" 1753 rs1054480 ADAMTS2 9509 5 178473581 NM_014244 NP_055059 C/T P1177S minus 24377049 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.26 0.07 260 3 0.35 0.08 816 3 123 "HapMap,submitter,freq,cluster" Probably damaging 2.1 9 moderately conservative 604539 5qter "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2" 1754 rs1054565 TAF1B 9014 2 10001558 NM_005680 NP_005671 A/G T351A plus 1532622 902 AFFY Caucasian 20 0.45 0.38 0.1 168 4 0.36 0.08 144 5 123 "by cluster,freq" Tolerant 0.79 3.11 9 moderately conservative 604904 2p25 "TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa" 1755 rs1054565 TAF1B 9014 2 10001558 NM_005680 NP_005671 A/G T351A plus 1532622 904 AFFY CEPH 10 0.2 0.38 0.1 168 4 0.36 0.08 144 5 123 "by cluster,freq" Tolerant 0.79 3.11 9 moderately conservative 604904 2p25 "TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa" 1756 rs1054565 TAF1B 9014 2 10001558 NM_005680 NP_005671 A/G T351A plus 17649564 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.38 0.1 168 4 0.36 0.08 144 5 123 "by cluster,freq" Tolerant 0.79 3.11 9 moderately conservative 604904 2p25 "TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa" 1757 rs1054565 TAF1B 9014 2 10001558 NM_005680 NP_005671 A/G T351A plus 24162633 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.28 0.38 0.1 168 4 0.36 0.08 144 5 123 "by cluster,freq" Tolerant 0.79 3.11 9 moderately conservative 604904 2p25 "TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa" 1758 rs1054627 IBSP 3381 4 89089871 NM_004967 NP_004958 A/G G195E plus 22189279 1303 SEQUENOM CEPH CEPH (92) 92 0.34 0.37 0.07 140 2 0.14 0.07 94 2 123 by freq Potentially damaging 1.481 9 Tolerant 0.27 3.18 12 moderately conservative 147563 4q21-q25 "integrin-binding sialoprotein (bone sialoprotein, bone sialoprotein II)" 1759 rs1054627 IBSP 3381 4 89089871 NM_004967 NP_004958 A/G G195E plus 24294784 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.37 0.07 140 2 0.14 0.07 94 2 123 by freq Potentially damaging 1.481 9 Tolerant 0.27 3.18 12 moderately conservative 147563 4q21-q25 "integrin-binding sialoprotein (bone sialoprotein, bone sialoprotein II)" 1760 rs1054628 IBSP 3381 4 89090090 NM_004967 NP_004958 C/T A268V plus 11648131 1303 SEQUENOM CEPH CEPH (92) 92 0.23 0.2 0.07 140 2 0.26 0.08 88 2 123 "by cluster,freq" Borderline 1.243 9 moderately conservative 147563 4q21-q25 "integrin-binding sialoprotein (bone sialoprotein, bone sialoprotein II)" 1761 rs1054628 IBSP 3381 4 89090090 NM_004967 NP_004958 C/T A268V plus 23231610 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.2 0.07 140 2 0.26 0.08 88 2 123 "by cluster,freq" Borderline 1.243 9 moderately conservative 147563 4q21-q25 "integrin-binding sialoprotein (bone sialoprotein, bone sialoprotein II)" 1762 rs1054629 IBSP 3381 4 89090097 NM_004967 NP_004958 A/T E270D plus 22189524 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.29 0.28 0.1 254 3 0.12 0.05 90 2 123 "HapMap,submitter,freq" Potentially damaging 1.245 9 conservative 147563 4q21-q25 "integrin-binding sialoprotein (bone sialoprotein, bone sialoprotein II)" 1763 rs1054629 IBSP 3381 4 89090097 NM_004967 NP_004958 A/T E270D plus 22189524 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.28 0.1 254 3 0.12 0.05 90 2 123 "HapMap,submitter,freq" Potentially damaging 1.245 9 conservative 147563 4q21-q25 "integrin-binding sialoprotein (bone sialoprotein, bone sialoprotein II)" 1764 rs1054629 IBSP 3381 4 89090097 NM_004967 NP_004958 A/T E270D plus 24294822 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.43 0.28 0.1 254 3 0.12 0.05 90 2 123 "HapMap,submitter,freq" Potentially damaging 1.245 9 conservative 147563 4q21-q25 "integrin-binding sialoprotein (bone sialoprotein, bone sialoprotein II)" 1765 rs1055246 BCAS1 8537 20 51994876 NM_003657 NP_003648 C/T S583P minus 1533817 1303 SEQUENOM CEPH CEPH (92) 92 0.22 0.17 0.09 140 2 0.13 0.06 94 2 123 "by cluster,freq" moderately conservative 602968 20q13.2-q13.3 breast carcinoma amplified sequence 1 1766 rs1055246 BCAS1 8537 20 51994876 NM_003657 NP_003648 C/T S583P minus 24094423 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.17 0.09 140 2 0.13 0.06 94 2 123 "by cluster,freq" moderately conservative 602968 20q13.2-q13.3 breast carcinoma amplified sequence 1 1767 rs1055851 ERO1LB 56605 1 232707866 NM_019891 NP_063944 C/G H465Q plus 2812728 1303 SEQUENOM CEPH CEPH (92) 92 0.48 0.48 0 92 1 0.22 0 84 1 123 "by doubleHit,freq,cluster" Benign 0.049 9 conservative 1q42.2-q43 ERO1-like beta (S. cerevisiae) 1768 rs1056104 GEMIN6 79833 2 38920600 NM_024775 NP_079051 A/G G140D plus 5007571 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.05 0.07 0.03 260 3 0.32 0.06 1596 3 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.501 7 moderately conservative 607006 2p22.3 gem (nuclear organelle) associated protein 6 1769 rs1056104 GEMIN6 79833 2 38920600 NM_024775 NP_079051 A/G G140D plus 19418274 1303 SEQUENOM CEPH CEPH (92) 92 0.1 0.07 0.03 260 3 0.32 0.06 1596 3 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.501 7 moderately conservative 607006 2p22.3 gem (nuclear organelle) associated protein 6 1770 rs1056104 GEMIN6 79833 2 38920600 NM_024775 NP_079051 A/G G140D plus 23892436 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.07 0.03 260 3 0.32 0.06 1596 3 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.501 7 moderately conservative 607006 2p22.3 gem (nuclear organelle) associated protein 6 1771 rs1056148 GLI4 2738 8 144429756 NM_138465 NP_612474 A/G A180T plus 1535681 1303 SEQUENOM CEPH CEPH (92) 92 0.37 0.37 0 92 1 120 "by doubleHit,freq" Intolerant 0 2.89 398 moderately conservative 165280 8q24.3 GLI-Kruppel family member GLI4 1772 rs1056185 ZNF83 55769 19 57809343 NM_018300 NP_060770 A/G S96N minus 4972848 1303 SEQUENOM CEPH CEPH (92) 92 0.38 0.38 0 92 1 108 "by submitter,freq,cluster" Probably damaging 2.045 154 conservative 194558 19q13.3 zinc finger protein 83 (HPF1) 1773 rs1056445 MTIF2 4528 2 55402470 NM_002453 NP_002444 A/C T59N minus 3638821 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.25 0.23 0.04 212 2 120 "HapMap,doubleHit,freq,cluster" Benign 0.131 6 Tolerant 0.41 2.98 18 moderately conservative 603766 2p14-p16 mitochondrial translational initiation factor 2 1774 rs1056445 MTIF2 4528 2 55402470 NM_002453 NP_002444 A/C T59N minus 14514046 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.23 0.04 212 2 120 "HapMap,doubleHit,freq,cluster" Benign 0.131 6 Tolerant 0.41 2.98 18 moderately conservative 603766 2p14-p16 mitochondrial translational initiation factor 2 1775 rs1056464 KCNA5 3741 12 5024256 NM_002234 NP_002225 C/T P228S plus 1536243 1303 SEQUENOM CEPH CEPH (92) 92 0.05 0.05 0 92 1 106 by freq Probably damaging 2.604 75 Potentially intolerant 0.07 2.78 143 moderately conservative 176267 12p13 "potassium voltage-gated channel, shaker-related subfamily, member 5" 1776 rs1056522 CHST13 166012 3 127744043 NM_152889 NP_690849 C/T R317Q minus 21995839 1303 SEQUENOM CEPH CEPH (92) 92 0.4 0.4 0 92 1 121 "by doubleHit,freq,cluster" Potentially damaging 1.389 7 Tolerant 1 2.82 36 conservative 3q21.3 carbohydrate (chondroitin 4) sulfotransferase 13 1777 rs1056787 CENPC1 1060 4 68208836 NM_001812 NP_001803 A/G G389D minus 1536890 902 AFFY Caucasian 24 0.08 0.13 0.03 116 2 0.05 0.02 60 2 106 by freq moderately conservative 117141 4q12-q13.3 centromere protein C 1 1778 rs1056787 CENPC1 1060 4 68208836 NM_001812 NP_001803 A/G G389D minus 1536890 1303 SEQUENOM CEPH CEPH (92) 92 0.14 0.13 0.03 116 2 0.05 0.02 60 2 106 by freq moderately conservative 117141 4q12-q13.3 centromere protein C 1 1779 rs1056820 ELF1 1997 13 40413286 NM_172373 NP_758961 A/T T343S minus 11071279 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.28 0.29 0.04 258 3 0.12 0.04 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.261 7 Tolerant 0.28 2.93 18 moderately conservative 189973 13q13 E74-like factor 1 (ets domain transcription factor) 1780 rs1056820 ELF1 1997 13 40413286 NM_172373 NP_758961 A/T T343S minus 11071279 1303 SEQUENOM CEPH CEPH (92) 92 0.27 0.29 0.04 258 3 0.12 0.04 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.261 7 Tolerant 0.28 2.93 18 moderately conservative 189973 13q13 E74-like factor 1 (ets domain transcription factor) 1781 rs1056820 ELF1 1997 13 40413286 NM_172373 NP_758961 A/T T343S minus 24655863 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.35 0.29 0.04 258 3 0.12 0.04 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.261 7 Tolerant 0.28 2.93 18 moderately conservative 189973 13q13 E74-like factor 1 (ets domain transcription factor) 1782 rs1056827 CYP1B1 1545 2 38213828 NM_000104 NP_000095 G/T A119S minus 12675382 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.23 0.29 0.08 276 3 0.36 0.05 346 4 123 "by doubleHit,freq,cluster" Benign 0.27 9 Intolerant 0.03 2.79 90 moderately conservative 601771 2p21 "cytochrome P450, family 1, subfamily B, polypeptide 1" 1783 rs1056827 CYP1B1 1545 2 38213828 NM_000104 NP_000095 G/T A119S minus 12675382 1303 SEQUENOM CEPH CEPH (92) 92 0.23 0.29 0.08 276 3 0.36 0.05 346 4 123 "by doubleHit,freq,cluster" Benign 0.27 9 Intolerant 0.03 2.79 90 moderately conservative 601771 2p21 "cytochrome P450, family 1, subfamily B, polypeptide 1" 1784 rs1056827 CYP1B1 1545 2 38213828 NM_000104 NP_000095 G/T A119S minus 12724382 693 EGP_SNPS PDR90 NIHPDR 122 0.36 0.29 0.08 276 3 0.36 0.05 346 4 123 "by doubleHit,freq,cluster" Benign 0.27 9 Intolerant 0.03 2.79 90 moderately conservative 601771 2p21 "cytochrome P450, family 1, subfamily B, polypeptide 1" 1785 rs1056836 CYP1B1 1545 2 38209854 NM_000104 NP_000095 C/G V432L minus 5586405 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.45 0.42 0.03 370 4 0.19 0.09 1940 7 123 "by doubleHit,freq,cluster" Benign 0.993 11 Borderline 0.18 2.79 90 conservative 601771 2p21 "cytochrome P450, family 1, subfamily B, polypeptide 1" 1786 rs1056836 CYP1B1 1545 2 38209854 NM_000104 NP_000095 C/G V432L minus 12724397 693 EGP_SNPS PDR90 NIHPDR 168 0.4 0.42 0.03 370 4 0.19 0.09 1940 7 123 "by doubleHit,freq,cluster" Benign 0.993 11 Borderline 0.18 2.79 90 conservative 601771 2p21 "cytochrome P450, family 1, subfamily B, polypeptide 1" 1787 rs1056836 CYP1B1 1545 2 38209854 NM_000104 NP_000095 C/G V432L minus 12724397 1303 SEQUENOM CEPH CEPH (92) 92 0.41 0.42 0.03 370 4 0.19 0.09 1940 7 123 "by doubleHit,freq,cluster" Benign 0.993 11 Borderline 0.18 2.79 90 conservative 601771 2p21 "cytochrome P450, family 1, subfamily B, polypeptide 1" 1788 rs1056836 CYP1B1 1545 2 38209854 NM_000104 NP_000095 C/G V432L minus 24639455 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.42 0.03 370 4 0.19 0.09 1940 7 123 "by doubleHit,freq,cluster" Benign 0.993 11 Borderline 0.18 2.79 90 conservative 601771 2p21 "cytochrome P450, family 1, subfamily B, polypeptide 1" 1789 rs1056892 CBR3 874 21 36440576 NM_001236 NP_001227 A/G V244M plus 3375972 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.28 0.31 0.06 276 4 0.36 0.07 592 8 123 "by doubleHit,freq,cluster" Benign 0.981 32 Intolerant 0.03 2.83 36 conservative 603608 21q22.2 carbonyl reductase 3 1790 rs1056892 CBR3 874 21 36440576 NM_001236 NP_001227 A/G V244M plus 3375972 1303 SEQUENOM CEPH CEPH (92) 92 0.37 0.31 0.06 276 4 0.36 0.07 592 8 123 "by doubleHit,freq,cluster" Benign 0.981 32 Intolerant 0.03 2.83 36 conservative 603608 21q22.2 carbonyl reductase 3 1791 rs1056892 CBR3 874 21 36440576 NM_001236 NP_001227 A/G V244M plus 6903700 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.25 0.31 0.06 276 4 0.36 0.07 592 8 123 "by doubleHit,freq,cluster" Benign 0.981 32 Intolerant 0.03 2.83 36 conservative 603608 21q22.2 carbonyl reductase 3 1792 rs1056892 CBR3 874 21 36440576 NM_001236 NP_001227 A/G V244M plus 23802318 1371 PERLEGEN AFD_EUR_PANEL European American (24) 40 0.33 0.31 0.06 276 4 0.36 0.07 592 8 123 "by doubleHit,freq,cluster" Benign 0.981 32 Intolerant 0.03 2.83 36 conservative 603608 21q22.2 carbonyl reductase 3 1793 rs1056899 KIAA0625 23064 9 132169455 NM_015046 NP_055861 A/G I2587V minus 14367213 1303 SEQUENOM CEPH CEPH (92) 92 0.31 0.31 0 92 1 0.27 0 1484 1 121 "by doubleHit,freq,cluster" conservative 608465 9q34.3 senataxin 1794 rs1057027 IFI16 3428 1 155815450 NM_005531 NP_005522 A/C R409S plus 24818921 1303 SEQUENOM CEPH CEPH (92) 184 0.06 0.06 0 184 1 123 "by doubleHit,freq" moderately radical 147586 1q22 "interferon, gamma-inducible protein 16" 1795 rs1057028 IFI16 3428 1 155815462 NM_005531 NP_005522 A/T Y413N plus 20450122 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.16 0 92 1 121 "by doubleHit,freq" moderately radical 147586 1q22 "interferon, gamma-inducible protein 16" 1796 rs1057037 PFKL 5211 21 44558295 NM_002626 NP_002617 A/T D284V plus 1537373 1303 SEQUENOM CEPH CEPH (92) 92 0.06 0.09 0.03 276 2 123 by freq Benign 0.842 49 radical 171860 21q22.3 "phosphofructokinase, liver" 1797 rs1057037 PFKL 5211 21 44558295 NM_002626 NP_002617 A/T D284V plus 24796628 1303 SEQUENOM CEPH CEPH (92) 184 0.1 0.09 0.03 276 2 123 by freq Benign 0.842 49 radical 171860 21q22.3 "phosphofructokinase, liver" 1798 rs1057335 SERPINF2 5345 17 1604403 NM_000934 NP_000925 A/G R434K plus 12395343 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.24 0.2 0.05 260 3 0.16 0.01 1578 3 123 "HapMap,freq,cluster" Borderline 1.132 5 Tolerant 0.38 2.75 32 conservative 262850 17p13 "serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2" 1799 rs1057335 SERPINF2 5345 17 1604403 NM_000934 NP_000925 A/G R434K plus 12395343 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.2 0.05 260 3 0.16 0.01 1578 3 123 "HapMap,freq,cluster" Borderline 1.132 5 Tolerant 0.38 2.75 32 conservative 262850 17p13 "serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2" 1800 rs1057335 SERPINF2 5345 17 1604403 NM_000934 NP_000925 A/G R434K plus 23790978 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.2 0.05 260 3 0.16 0.01 1578 3 123 "HapMap,freq,cluster" Borderline 1.132 5 Tolerant 0.38 2.75 32 conservative 262850 17p13 "serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2" 1801 rs1057868 POR 5447 7 75259657 NM_000941 NP_000932 C/T A503V plus 3172746 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 48 0.25 0.39 0.15 140 2 0.4 0 1492 1 123 "by cluster,freq" Benign 0.71 19 moderately conservative 124015 7q11.2 P450 (cytochrome) oxidoreductase 1802 rs1057868 POR 5447 7 75259657 NM_000941 NP_000932 C/T A503V plus 3172746 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.39 0.15 140 2 0.4 0 1492 1 123 "by cluster,freq" Benign 0.71 19 moderately conservative 124015 7q11.2 P450 (cytochrome) oxidoreductase 1803 rs1057910 CYP2C9 1559 10 96731043 NM_000771 NP_000762 A/C I359L plus 5586419 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.1 0.06 0.04 236 2 0.03 0.01 756 4 123 "by cluster,freq" Possibly damaging 1.759 152 Potentially intolerant 0.09 2.79 165 conservative 601130 10q24 "cytochrome P450, family 2, subfamily C, polypeptide 9" 1804 rs1057910 CYP2C9 1559 10 96731043 NM_000771 NP_000762 A/C I359L plus 12588583 693 EGP_SNPS PDR90 NIHPDR 176 0.04 0.06 0.04 236 2 0.03 0.01 756 4 123 "by cluster,freq" Possibly damaging 1.759 152 Potentially intolerant 0.09 2.79 165 conservative 601130 10q24 "cytochrome P450, family 2, subfamily C, polypeptide 9" 1805 rs1057954 RANBP2 5903 2 108826855 NM_006267 NP_006258 G/T V548L plus 24819280 1303 SEQUENOM CEPH CEPH (92) 184 0.18 0.18 0 184 1 123 by freq conservative 601181 2q12.3 RAN binding protein 2 1806 rs1057957 RANBP2 5903 2 108826955 NM_006267 NP_006258 A/G C581Y plus 24819282 1303 SEQUENOM CEPH CEPH (92) 184 0.28 0.28 0 184 1 123 by freq radical 601181 2q12.3 RAN binding protein 2 1807 rs1058402 PVR 5817 19 49842454 NM_006505 NP_006496 A/G A67T plus 3206987 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.05 0.05 0 120 1 0.18 0 1478 1 106 "HapMap,submitter,freq,cluster" Benign 0.203 11 Tolerant 0.67 2.76 37 moderately conservative 173850 19q13.2 poliovirus receptor 1808 rs1058587 GDF15 9518 19 18360422 NM_004864 NP_004855 C/G H202D minus 1540261 1303 SEQUENOM CEPH CEPH (92) 92 0.31 0.28 0.05 140 2 0.26 0.18 94 2 123 "by doubleHit,freq" moderately conservative 605312 19p13.1-13.2 growth differentiation factor 15 1809 rs1058587 GDF15 9518 19 18360422 NM_004864 NP_004855 C/G H202D minus 24196841 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.28 0.05 140 2 0.26 0.18 94 2 123 "by doubleHit,freq" moderately conservative 605312 19p13.1-13.2 growth differentiation factor 15 1810 rs1058768 TINAG 27283 6 54294106 NM_014464 NP_055279 C/T S158P plus 10272044 1303 SEQUENOM CEPH CEPH (92) 92 0.33 0.33 0 140 2 0.15 0.02 1574 3 123 "by doubleHit,freq,cluster" Probably damaging 2.1 5 Tolerant 0.76 2.75 78 moderately conservative 606749 6p11.2-p12 tubulointerstitial nephritis antigen 1811 rs1058768 TINAG 27283 6 54294106 NM_014464 NP_055279 C/T S158P plus 24372618 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.33 0 140 2 0.15 0.02 1574 3 123 "by doubleHit,freq,cluster" Probably damaging 2.1 5 Tolerant 0.76 2.75 78 moderately conservative 606749 6p11.2-p12 tubulointerstitial nephritis antigen 1812 rs1058793 ATP10D 57205 4 47424974 NM_020453 NP_065186 A/G V1240I plus 24174249 1371 PERLEGEN AFD_EUR_PANEL European American (24) 38 0.05 0.21 0.1 222 2 0.43 0.01 1554 3 123 "by doubleHit,freq,cluster" Tolerant 0.97 2.86 15 conservative 4p12 "ATPase, Class V, type 10D" 1813 rs1058793 ATP10D 57205 4 47424974 NM_020453 NP_065186 A/G V1240I plus 24796213 1303 SEQUENOM CEPH CEPH (92) 184 0.24 0.21 0.1 222 2 0.43 0.01 1554 3 123 "by doubleHit,freq,cluster" Tolerant 0.97 2.86 15 conservative 4p12 "ATPase, Class V, type 10D" 1814 rs1058808 ERBB2 2064 17 35137563 NM_004448 NP_004439 C/G P1170A plus 3177859 619 WICVAR MITOGPOP6 CORIELL Mixed 54 0.41 0.4 0.08 484 5 0.48 0.05 1588 3 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.645 10 conservative 164870 17q21.1 "v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)" 1815 rs1058808 ERBB2 2064 17 35137563 NM_004448 NP_004439 C/G P1170A plus 5608583 693 EGP_SNPS PDR90 NIHPDR 170 0.48 0.4 0.08 484 5 0.48 0.05 1588 3 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.645 10 conservative 164870 17q21.1 "v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)" 1816 rs1058808 ERBB2 2064 17 35137563 NM_004448 NP_004439 C/G P1170A plus 5608583 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.29 0.4 0.08 484 5 0.48 0.05 1588 3 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.645 10 conservative 164870 17q21.1 "v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)" 1817 rs1058808 ERBB2 2064 17 35137563 NM_004448 NP_004439 C/G P1170A plus 5608583 1303 SEQUENOM CEPH CEPH (92) 92 0.4 0.4 0.08 484 5 0.48 0.05 1588 3 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.645 10 conservative 164870 17q21.1 "v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)" 1818 rs1058808 ERBB2 2064 17 35137563 NM_004448 NP_004439 C/G P1170A plus 24110922 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.4 0.08 484 5 0.48 0.05 1588 3 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.645 10 conservative 164870 17q21.1 "v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)" 1819 rs1059060 PMS2 5395 7 5790581 NM_000535 NP_000526 A/G N775S minus 2667728 506 NCBI NIHPDR NIHPDR 74 0.41 0.32 0.17 122 2 106 "by cluster,freq" Potentially intolerant 0.08 2.83 11 conservative 600259 7p22.2 PMS2 postmeiotic segregation increased 2 (S. cerevisiae) 1820 rs1059060 PMS2 5395 7 5790581 NM_000535 NP_000526 A/G N775S minus 3172639 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 48 0.17 0.32 0.17 122 2 106 "by cluster,freq" Potentially intolerant 0.08 2.83 11 conservative 600259 7p22.2 PMS2 postmeiotic segregation increased 2 (S. cerevisiae) 1821 rs1059199 ZNF562 54811 19 9625128 NM_017656 NP_060126 A/G E188K minus 1541440 1303 SEQUENOM CEPH CEPH (92) 92 0.24 0.24 0 92 1 86 by freq Intolerant 0 2.77 301 moderately conservative 19p13.2 zinc finger protein 562 1822 rs1059240 HOMER3 9454 19 18901312 NM_004838 NP_004829 C/G S342R minus 16794995 1303 SEQUENOM CEPH CEPH (92) 92 0.1 0.1 0 92 1 121 "by cluster,freq" Potentially damaging 1.36 15 moderately radical 604800 19p13.11 homer homolog 3 (Drosophila) 1823 rs1059369 GDF15 9518 19 18358141 NM_004864 NP_004855 A/T S48T minus 8819829 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.29 0.32 0.03 154 2 0.32 0.03 1850 5 120 "by doubleHit,freq,cluster" Tolerant 0.38 2.92 65 moderately conservative 605312 19p13.1-13.2 growth differentiation factor 15 1824 rs1059369 GDF15 9518 19 18358141 NM_004864 NP_004855 A/T S48T minus 8819829 1303 SEQUENOM CEPH CEPH (92) 92 0.34 0.32 0.03 154 2 0.32 0.03 1850 5 120 "by doubleHit,freq,cluster" Tolerant 0.38 2.92 65 moderately conservative 605312 19p13.1-13.2 growth differentiation factor 15 1825 rs1059463 HLA-A 3105 6 30018721 NM_002116 NP_002107 C/G Q94H plus 20421629 1303 SEQUENOM CEPH CEPH (92) 92 0.21 0.21 0 92 1 121 "by cluster,freq" Benign 0.211 442 conservative 142800 6p21.3 "major histocompatibility complex, class I, A" 1826 rs1059509 HLA-A 3105 6 30019133 NM_002116 NP_002107 A/C N151K plus 20421684 1303 SEQUENOM CEPH CEPH (92) 92 0.25 0.25 0 92 1 121 by freq moderately conservative 142800 6p21.3 "major histocompatibility complex, class I, A" 1827 rs1059516 HLA-A 3105 6 30019177 NM_002116 NP_002107 C/T I166T plus 20421695 1303 SEQUENOM CEPH CEPH (92) 92 0.37 0.37 0 92 1 121 by freq moderately conservative 142800 6p21.3 "major histocompatibility complex, class I, A" 1828 rs1059519 GDF15 9518 19 18358024 NM_004864 NP_004855 C/G V9L minus 6903896 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.21 0.34 0.1 220 3 0.41 0.06 1934 7 123 "HapMap,doubleHit,freq,cluster" conservative 605312 19p13.1-13.2 growth differentiation factor 15 1829 rs1059519 GDF15 9518 19 18358024 NM_004864 NP_004855 C/G V9L minus 6903896 885 TSC-CSHL HapMap-CEPH-30-trios 110 0.4 0.34 0.1 220 3 0.41 0.06 1934 7 123 "HapMap,doubleHit,freq,cluster" conservative 605312 19p13.1-13.2 growth differentiation factor 15 1830 rs1059519 GDF15 9518 19 18358024 NM_004864 NP_004855 C/G V9L minus 24684769 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.34 0.1 220 3 0.41 0.06 1934 7 123 "HapMap,doubleHit,freq,cluster" conservative 605312 19p13.1-13.2 growth differentiation factor 15 1831 rs1059539 HLA-A 3105 6 30019225 NM_002116 NP_002107 C/T A182V plus 24797204 1303 SEQUENOM CEPH CEPH (92) 184 0.14 0.14 0 184 1 123 by freq Benign 0.39 442 moderately conservative 142800 6p21.3 "major histocompatibility complex, class I, A" 1832 rs1059576 HLA-DRB1 3123 6 32660050 NM_002124 NP_002115 A/C H62N minus 24796309 1303 SEQUENOM CEPH CEPH (92) 184 0.45 0.45 0 184 1 123 by freq Benign 0.837 452 moderately conservative 142857 6p21.3 "major histocompatibility complex, class II, DR beta 1" 1833 rs1059779 WBSCR21 83451 7 72595162 NM_148914 NP_683712 A/G E125G minus 1542691 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.23 0.22 0.02 212 2 120 "HapMap,submitter,freq,cluster" Tolerant 0.87 2.84 45 moderately conservative 7q11.23 Williams Beuren syndrome chromosome region 21 1834 rs1059779 WBSCR21 83451 7 72595162 NM_148914 NP_683712 A/G E125G minus 17153080 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.22 0.02 212 2 120 "HapMap,submitter,freq,cluster" Tolerant 0.87 2.84 45 moderately conservative 7q11.23 Williams Beuren syndrome chromosome region 21 1835 rs1059913 KLF4 9314 9 107329286 NM_004235 NP_004226 C/G T306S minus 1542982 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.02 0 92 1 86 by freq Benign 0.9 6 Tolerant 0.49 2.85 41 moderately conservative 602253 9q31 Kruppel-like factor 4 (gut) 1836 rs1060105 SBNO1 55206 12 122331099 NM_018183 NP_060653 A/G S728N minus 20952993 1303 SEQUENOM CEPH CEPH (92) 92 0.28 0.26 0.03 140 2 0.04 0 46 1 123 "by doubleHit,freq" Borderline 1.148 7 conservative 12q24.31 "sno, strawberry notch homolog 1 (Drosophila)" 1837 rs1060105 SBNO1 55206 12 122331099 NM_018183 NP_060653 A/G S728N minus 24362690 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.26 0.03 140 2 0.04 0 46 1 123 "by doubleHit,freq" Borderline 1.148 7 conservative 12q24.31 "sno, strawberry notch homolog 1 (Drosophila)" 1838 rs1060242 ADHFE1 137872 8 67543082 NM_144650 NP_653251 C/T C401R plus 24538000 1371 PERLEGEN AFD_EUR_PANEL European American (24) 24 0.5 0.5 0 24 1 0.41 0.05 1568 3 123 "by doubleHit,freq,cluster" Probably damaging 2.112 15 radical 8q12.3 "alcohol dehydrogenase, iron containing, 1" 1839 rs1060463 CYP4F11 57834 19 15886176 NM_021187 NP_067010 A/G D446N minus 1544179 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.39 0.26 0.21 212 2 123 "HapMap,submitter,freq" Benign 0.733 40 conservative 19p13.1 "cytochrome P450, family 4, subfamily F, polypeptide 11" 1840 rs1060463 CYP4F11 57834 19 15886176 NM_021187 NP_067010 A/G D446N minus 21506661 1303 SEQUENOM CEPH CEPH (92) 92 0.09 0.26 0.21 212 2 123 "HapMap,submitter,freq" Benign 0.733 40 conservative 19p13.1 "cytochrome P450, family 4, subfamily F, polypeptide 11" 1841 rs1060900 TRIM16 10626 17 15472727 NM_006470 NP_006461 A/G N541S minus 24797218 1303 SEQUENOM CEPH CEPH (92) 184 0.1 0.1 0 184 1 123 by freq Potentially damaging 1.279 7 Tolerant 0.87 2.78 7 conservative 17p11.2 tripartite motif-containing 16 1842 rs1061347 SENP6 26054 6 76445079 NM_015571 NP_056386 A/G E637K plus 1546156 1303 SEQUENOM CEPH CEPH (92) 92 0.32 0.32 0 92 1 106 by freq Potentially damaging 1.409 7 moderately conservative 605003 6q13-q14.3 SUMO1/sentrin specific protease 6 1843 rs1061472 ATP7B 540 13 51422489 NM_000053 NP_000044 A/G K832R minus 16621895 1303 SEQUENOM CEPH CEPH (92) 92 0.34 0.38 0.08 140 2 0.4 0.11 94 2 123 "by doubleHit,freq,cluster" Potentially damaging 1.252 20 Tolerant 0.28 2.74 31 conservative 606882 13q14.2-q21 "ATPase, Cu++ transporting, beta polypeptide (Wilson disease)" 1844 rs1061472 ATP7B 540 13 51422489 NM_000053 NP_000044 A/G K832R minus 23438167 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.38 0.08 140 2 0.4 0.11 94 2 123 "by doubleHit,freq,cluster" Potentially damaging 1.252 20 Tolerant 0.28 2.74 31 conservative 606882 13q14.2-q21 "ATPase, Cu++ transporting, beta polypeptide (Wilson disease)" 1845 rs1061494 TNC 3371 9 114926134 NM_002160 NP_002151 C/T Q680R plus 2609198 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.46 0.41 0.07 254 3 0.33 0.2 86 2 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 1 2.92 20 conservative 187380 9q33 tenascin C (hexabrachion) 1846 rs1061494 TNC 3371 9 114926134 NM_002160 NP_002151 C/T Q680R plus 2609198 1303 SEQUENOM CEPH CEPH (92) 92 0.34 0.41 0.07 254 3 0.33 0.2 86 2 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 1 2.92 20 conservative 187380 9q33 tenascin C (hexabrachion) 1847 rs1061494 TNC 3371 9 114926134 NM_002160 NP_002151 C/T Q680R plus 23531666 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.45 0.41 0.07 254 3 0.33 0.2 86 2 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 1 2.92 20 conservative 187380 9q33 tenascin C (hexabrachion) 1848 rs1061622 TNFRSF1B 7133 1 12187221 NM_001066 NP_001057 G/T M196R plus 3173181 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 48 0.13 0.19 0.03 2201 5 0.23 0.01 94 2 123 "by submitter,freq,cluster" Benign 0.473 10 Intolerant 0.03 2.78 49 moderately conservative 191191 1p36.3-p36.2 "tumor necrosis factor receptor superfamily, member 1B" 1849 rs1061622 TNFRSF1B 7133 1 12187221 NM_001066 NP_001057 G/T M196R plus 7990727 693 EGP_SNPS PDR90 NIHPDR 172 0.13 0.19 0.03 2201 5 0.23 0.01 94 2 123 "by submitter,freq,cluster" Benign 0.473 10 Intolerant 0.03 2.78 49 moderately conservative 191191 1p36.3-p36.2 "tumor necrosis factor receptor superfamily, member 1B" 1850 rs1061622 TNFRSF1B 7133 1 12187221 NM_001066 NP_001057 G/T M196R plus 7990727 1303 SEQUENOM CEPH CEPH (92) 92 0.12 0.19 0.03 2201 5 0.23 0.01 94 2 123 "by submitter,freq,cluster" Benign 0.473 10 Intolerant 0.03 2.78 49 moderately conservative 191191 1p36.3-p36.2 "tumor necrosis factor receptor superfamily, member 1B" 1851 rs1061622 TNFRSF1B 7133 1 12187221 NM_001066 NP_001057 G/T M196R plus 12568611 887 CUORCGL AMERICAN CAUCASIANS American Caucasians 1841 0.2 0.19 0.03 2201 5 0.23 0.01 94 2 123 "by submitter,freq,cluster" Benign 0.473 10 Intolerant 0.03 2.78 49 moderately conservative 191191 1p36.3-p36.2 "tumor necrosis factor receptor superfamily, member 1B" 1852 rs1061622 TNFRSF1B 7133 1 12187221 NM_001066 NP_001057 G/T M196R plus 23845243 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.19 0.03 2201 5 0.23 0.01 94 2 123 "by submitter,freq,cluster" Benign 0.473 10 Intolerant 0.03 2.78 49 moderately conservative 191191 1p36.3-p36.2 "tumor necrosis factor receptor superfamily, member 1B" 1853 rs1061679 LILRB1 10859 19 59834895 NM_006669 NP_006660 C/T L68P plus 5363752 1303 SEQUENOM CEPH CEPH (92) 92 0.28 0.28 0 92 1 120 "by doubleHit,freq,cluster" Benign 0.8 53 moderately conservative 604811 19q13.4 "leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1" 1854 rs1061680 LILRB1 10859 19 59835264 NM_006669 NP_006660 C/T I142T plus 5363753 1303 SEQUENOM CEPH CEPH (92) 92 0.23 0.23 0 92 1 119 "by doubleHit,freq,cluster" Benign 0.547 53 moderately conservative 604811 19q13.4 "leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1" 1855 rs1061681 LILRB1 10859 19 59835303 NM_006669 NP_006660 G/T S155I plus 3035032 1303 SEQUENOM CEPH CEPH (92) 92 0.35 0.35 0 92 1 119 "by doubleHit,freq,cluster" Benign 0.478 53 moderately radical 604811 19q13.4 "leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1" 1856 rs1061768 ZNF283 284349 19 49044479 XM_371174 XP_371174 A/G R802H plus 1547014 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.24 0.19 0.06 260 3 0.13 0 94 2 123 "HapMap,submitter,freq,cluster" conservative 19q13.32 zinc finger protein 283 1857 rs1061768 ZNF283 284349 19 49044479 XM_371174 XP_371174 A/G R802H plus 1547014 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.19 0.06 260 3 0.13 0 94 2 123 "HapMap,submitter,freq,cluster" conservative 19q13.32 zinc finger protein 283 1858 rs1061768 ZNF283 284349 19 49044479 XM_371174 XP_371174 A/G R802H plus 23765062 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.19 0.06 260 3 0.13 0 94 2 123 "HapMap,submitter,freq,cluster" conservative 19q13.32 zinc finger protein 283 1859 rs1061769 ZNF283 284349 19 49044506 XM_371174 XP_371174 A/G C811Y plus 24820782 1303 SEQUENOM CEPH CEPH (92) 184 0.3 0.3 0 184 1 123 "by doubleHit,freq,cluster" radical 19q13.32 zinc finger protein 283 1860 rs1062505 GPLD1 2822 6 24558061 NM_001503 NP_001494 A/G V461M minus 1548594 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.44 0 92 1 86 by freq Benign 0.846 10 Tolerant 0.21 2.82 42 conservative 602515 6p22.3-p22.2 glycosylphosphatidylinositol specific phospholipase D1 1861 rs1062553 EHHADH 1962 3 186435907 NM_001966 NP_001957 C/T T75I minus 1548675 1303 SEQUENOM CEPH CEPH (92) 92 0.13 0.13 0 92 1 86 by freq Potentially damaging 1.422 6 moderately conservative 607037 3q26.3-q28 "enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase" 1862 rs1062557 GRP 2922 18 55038487 NM_002091 NP_002082 A/C R4S plus 10910226 1303 SEQUENOM CEPH CEPH (92) 93 0.01 0.08 0.13 141 2 0.19 0.03 1582 3 123 "by doubleHit,freq,cluster" moderately radical 137260 18q21.1-q21.32 gastrin-releasing peptide 1863 rs1062557 GRP 2922 18 55038487 NM_002091 NP_002082 A/C R4S plus 24203977 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.08 0.13 141 2 0.19 0.03 1582 3 123 "by doubleHit,freq,cluster" moderately radical 137260 18q21.1-q21.32 gastrin-releasing peptide 1864 rs1062633 MST1R 4486 3 49899944 NM_002447 NP_002438 A/G R1335G minus 10069016 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.45 0.45 0.02 260 3 0.25 0.14 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially intolerant 0.1 2.76 20 moderately radical 600168 3p21.3 macrophage stimulating 1 receptor (c-met-related tyrosine kinase) 1865 rs1062633 MST1R 4486 3 49899944 NM_002447 NP_002438 A/G R1335G minus 10069016 1303 SEQUENOM CEPH CEPH (92) 92 0.46 0.45 0.02 260 3 0.25 0.14 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially intolerant 0.1 2.76 20 moderately radical 600168 3p21.3 macrophage stimulating 1 receptor (c-met-related tyrosine kinase) 1866 rs1062633 MST1R 4486 3 49899944 NM_002447 NP_002438 A/G R1335G minus 24276084 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.45 0.02 260 3 0.25 0.14 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially intolerant 0.1 2.76 20 moderately radical 600168 3p21.3 macrophage stimulating 1 receptor (c-met-related tyrosine kinase) 1867 rs1062786 MKRN1 23608 7 139607634 NM_013446 NP_038474 C/T V439A minus 1549160 1303 SEQUENOM CEPH CEPH (92) 92 0.14 0.14 0 92 1 86 by freq Benign 0.204 8 Tolerant 0.54 2.95 19 moderately conservative 607754 7q34 "makorin, ring finger protein, 1" 1868 rs1063156 ZNF85 7639 19 20923956 NM_003429 NP_003420 A/G T266A plus 1550003 1303 SEQUENOM CEPH CEPH (92) 92 0.13 0.13 0 92 1 86 by freq Benign 0.524 137 moderately conservative 603899 19p13.1-p12 "zinc finger protein 85 (HPF4, HTF1)" 1869 rs1063273 PRSS3 5646 9 33788529 NM_002771 NP_002762 C/G T167S plus 1550260 1303 SEQUENOM CEPH CEPH (92) 92 0.17 0.17 0 92 1 86 by freq Benign 0.811 141 Tolerant 1 2.77 113 moderately conservative 9p11.2 "protease, serine, 3 (mesotrypsin)" 1870 rs1063478 HLA-DMA 3108 6 33025522 NM_006120 NP_006111 C/T V166I plus 2240338 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 20 0.15 0.11 0.04 366 5 0.14 0.09 118 3 123 "HapMap,doubleHit,freq" Benign 0.84 19 Tolerant 0.27 2.84 266 conservative 142855 6p21.3 "major histocompatibility complex, class II, DM alpha" 1871 rs1063478 HLA-DMA 3108 6 33025522 NM_006120 NP_006111 C/T V166I plus 2240338 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 86 0.12 0.11 0.04 366 5 0.14 0.09 118 3 123 "HapMap,doubleHit,freq" Benign 0.84 19 Tolerant 0.27 2.84 266 conservative 142855 6p21.3 "major histocompatibility complex, class II, DM alpha" 1872 rs1063478 HLA-DMA 3108 6 33025522 NM_006120 NP_006111 C/T V166I plus 2240338 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.08 0.11 0.04 366 5 0.14 0.09 118 3 123 "HapMap,doubleHit,freq" Benign 0.84 19 Tolerant 0.27 2.84 266 conservative 142855 6p21.3 "major histocompatibility complex, class II, DM alpha" 1873 rs1063478 HLA-DMA 3108 6 33025522 NM_006120 NP_006111 C/T V166I plus 2240338 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.11 0.04 366 5 0.14 0.09 118 3 123 "HapMap,doubleHit,freq" Benign 0.84 19 Tolerant 0.27 2.84 266 conservative 142855 6p21.3 "major histocompatibility complex, class II, DM alpha" 1874 rs1063478 HLA-DMA 3108 6 33025522 NM_006120 NP_006111 C/T V166I plus 24169460 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.11 0.04 366 5 0.14 0.09 118 3 123 "HapMap,doubleHit,freq" Benign 0.84 19 Tolerant 0.27 2.84 266 conservative 142855 6p21.3 "major histocompatibility complex, class II, DM alpha" 1875 rs1063535 MKI67 4288 10 129792271 NM_002417 NP_002408 C/T P2608L minus 12078765 1303 SEQUENOM CEPH CEPH (92) 92 0.38 0.38 0 140 2 0.38 0.11 94 2 123 "by doubleHit,freq,cluster" Tolerant 0.28 2.89 9 moderately conservative 176741 10q25-qter antigen identified by monoclonal antibody Ki-67 1876 rs1063535 MKI67 4288 10 129792271 NM_002417 NP_002408 C/T P2608L minus 23644000 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.38 0 140 2 0.38 0.11 94 2 123 "by doubleHit,freq,cluster" Tolerant 0.28 2.89 9 moderately conservative 176741 10q25-qter antigen identified by monoclonal antibody Ki-67 1877 rs1063582 LOXL2 4017 8 23223298 NM_002318 NP_002309 A/C M570L minus 19764713 1303 SEQUENOM CEPH CEPH (92) 92 0.29 0.29 0 140 2 0.29 0.06 92 2 123 "by doubleHit,freq,cluster" Borderline 1.092 19 Tolerant 1 3.05 22 conservative 606663 8p21.3-p21.2 lysyl oxidase-like 2 1878 rs1063582 LOXL2 4017 8 23223298 NM_002318 NP_002309 A/C M570L minus 23498008 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.29 0 140 2 0.29 0.06 92 2 123 "by doubleHit,freq,cluster" Borderline 1.092 19 Tolerant 1 3.05 22 conservative 606663 8p21.3-p21.2 lysyl oxidase-like 2 1879 rs1063739 GPT 2875 8 145700535 NM_005309 NP_005300 A/C H14N plus 2747868 1303 SEQUENOM CEPH CEPH (92) 92 0.34 0.34 0 92 1 120 "by doubleHit,freq,cluster" Tolerant 1 2.99 15 moderately conservative 138200 8q24.3 glutamic-pyruvate transaminase (alanine aminotransferase) 1880 rs1063743 TACC3 10460 4 1697219 NM_006342 NP_006333 A/G G287S plus 1551392 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.2 0 92 1 106 by freq Tolerant 0.49 2.92 6 moderately conservative 605303 4p16.3 "transforming, acidic coiled-coil containing protein 3" 1881 rs1063856 VWF 7450 12 6023795 NM_000552 NP_000543 A/G T789A minus 2401695 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.34 0.28 0.14 294 4 0.28 0.21 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.039 10 Tolerant 1 3.17 24 moderately conservative 193400 12p13.3 von Willebrand factor 1882 rs1063856 VWF 7450 12 6023795 NM_000552 NP_000543 A/G T789A minus 2401695 1303 SEQUENOM CEPH CEPH (92) 92 0.1 0.28 0.14 294 4 0.28 0.21 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.039 10 Tolerant 1 3.17 24 moderately conservative 193400 12p13.3 von Willebrand factor 1883 rs1063856 VWF 7450 12 6023795 NM_000552 NP_000543 A/G T789A minus 3172987 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 36 0.42 0.28 0.14 294 4 0.28 0.21 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.039 10 Tolerant 1 3.17 24 moderately conservative 193400 12p13.3 von Willebrand factor 1884 rs1063856 VWF 7450 12 6023795 NM_000552 NP_000543 A/G T789A minus 23713949 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.28 0.14 294 4 0.28 0.21 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.039 10 Tolerant 1 3.17 24 moderately conservative 193400 12p13.3 von Willebrand factor 1885 rs1063900 SBF1 6305 22 49191231 NM_002972 NP_002963 A/G W676X minus 1551666 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.04 0 92 1 86 by freq Probably damaging Intolerant radical 603560 22q13.33 SET binding factor 1 1886 rs1064074 USH1C 10083 11 17476318 NM_153676 NP_710142 C/G E819D minus 10665480 1303 SEQUENOM CEPH CEPH (92) 92 0.46 0.45 0.03 140 2 0.36 0.1 94 2 123 "by doubleHit,freq,cluster" conservative 605242 11p15.1-p14 "Usher syndrome 1C (autosomal recessive, severe)" 1887 rs1064074 USH1C 10083 11 17476318 NM_153676 NP_710142 C/G E819D minus 23639433 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.45 0.03 140 2 0.36 0.1 94 2 123 "by doubleHit,freq,cluster" conservative 605242 11p15.1-p14 "Usher syndrome 1C (autosomal recessive, severe)" 1888 rs1064210 MLL2 8085 12 47732307 NM_003482 NP_003473 A/G A476T minus 1552377 1303 SEQUENOM CEPH CEPH (92) 92 0.09 0.09 0 92 1 86 by freq moderately conservative 602113 12q12-q14 myeloid/lymphoid or mixed-lineage leukemia 2 1889 rs1064524 ITGAL 3683 16 30400324 NM_002209 NP_002200 C/T R214W plus 16360704 649 FHCRC POPU1 USA (20) 3 0.03 0.08 0.02 134 3 120 by freq Possibly damaging 1.828 8 moderately radical 153370 16p11.2 "integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)" 1890 rs1064524 ITGAL 3683 16 30400324 NM_002209 NP_002200 C/T R214W plus 16360704 649 FHCRC POPU1 USA (20) 39 0.05 0.08 0.02 134 3 120 by freq Possibly damaging 1.828 8 moderately radical 153370 16p11.2 "integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)" 1891 rs1064524 ITGAL 3683 16 30400324 NM_002209 NP_002200 C/T R214W plus 16360704 1303 SEQUENOM CEPH CEPH (92) 92 0.09 0.08 0.02 134 3 120 by freq Possibly damaging 1.828 8 moderately radical 153370 16p11.2 "integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)" 1892 rs1065674 NUP133 55746 1 225930073 NM_018230 NP_060700 A/G Q406R minus 6809927 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.19 0.06 140 2 0.27 0.2 94 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.189 8 Tolerant 1 2.8 12 conservative 607613 1q42.13 nucleoporin 133kDa 1893 rs1065674 NUP133 55746 1 225930073 NM_018230 NP_060700 A/G Q406R minus 23228588 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.19 0.06 140 2 0.27 0.2 94 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.189 8 Tolerant 1 2.8 12 conservative 607613 1q42.13 nucleoporin 133kDa 1894 rs1065761 CHIT1 1118 1 199917750 NM_003465 NP_003456 C/G A442G minus 1556811 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 46 0.1 0.25 0.15 138 2 86 "by doubleHit,freq" Possibly damaging 1.523 16 Tolerant 0.74 3.05 27 moderately conservative 600031 1q31-q32 chitinase 1 (chitotriosidase) 1895 rs1065761 CHIT1 1118 1 199917750 NM_003465 NP_003456 C/G A442G minus 1556811 1303 SEQUENOM CEPH CEPH (92) 92 0.33 0.25 0.15 138 2 86 "by doubleHit,freq" Possibly damaging 1.523 16 Tolerant 0.74 3.05 27 moderately conservative 600031 1q31-q32 chitinase 1 (chitotriosidase) 1896 rs1065782 IGFBP1 3484 7 45704798 NM_000596 NP_000587 A/G V183I plus 13452532 693 EGP_SNPS PDR90 NIHPDR 170 0.01 0.01 0 170 1 120 "HapMap,cluster" Benign 0.86 12 Borderline 0.12 2.79 27 conservative 146730 7p13-p12 insulin-like growth factor binding protein 1 1897 rs1073123 TSC1 7248 9 132816458 NM_000368 NP_000359 A/G M322T plus 7904139 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.11 0.14 0.04 260 3 0.17 0.04 94 2 123 "HapMap,submitter,freq" Borderline 1.037 5 moderately conservative 605284 9q34 tuberous sclerosis 1 1898 rs1073123 TSC1 7248 9 132816458 NM_000368 NP_000359 A/G M322T plus 7904139 1303 SEQUENOM CEPH CEPH (92) 92 0.15 0.14 0.04 260 3 0.17 0.04 94 2 123 "HapMap,submitter,freq" Borderline 1.037 5 moderately conservative 605284 9q34 tuberous sclerosis 1 1899 rs1073123 TSC1 7248 9 132816458 NM_000368 NP_000359 A/G M322T plus 23677213 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.14 0.04 260 3 0.17 0.04 94 2 123 "HapMap,submitter,freq" Borderline 1.037 5 moderately conservative 605284 9q34 tuberous sclerosis 1 1900 rs1076669 ECE1 1889 1 21319161 NM_001397 NP_001388 C/T T341I minus 91101 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.13 0.05 140 2 123 "by doubleHit,freq,cluster" Potentially damaging 1.334 31 Borderline 0.18 2.74 53 moderately conservative 600423 1p36.1 endothelin converting enzyme 1 1901 rs1076669 ECE1 1889 1 21319161 NM_001397 NP_001388 C/T T341I minus 24236499 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.13 0.05 140 2 123 "by doubleHit,freq,cluster" Potentially damaging 1.334 31 Borderline 0.18 2.74 53 moderately conservative 600423 1p36.1 endothelin converting enzyme 1 1902 rs1078543 PINX1 54984 8 10660548 NM_017884 NP_060354 A/T S254C plus 6687319 1303 SEQUENOM CEPH CEPH (92) 92 0.19 0.18 0.03 140 2 0.12 0.07 1360 3 123 by freq moderately radical 606505 8p23 PIN2-interacting protein 1 1903 rs1078543 PINX1 54984 8 10660548 NM_017884 NP_060354 A/T S254C plus 23368365 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.18 0.03 140 2 0.12 0.07 1360 3 123 by freq moderately radical 606505 8p23 PIN2-interacting protein 1 1904 rs1105168 FAT2 2196 5 150867075 NM_001447 NP_001438 A/G P4117L plus 11741234 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.43 0.45 0.03 260 3 0.18 0.04 1576 3 123 "HapMap,freq" moderately conservative 604269 5q32-q33 FAT tumor suppressor homolog 2 (Drosophila) 1905 rs1105168 FAT2 2196 5 150867075 NM_001447 NP_001438 A/G P4117L plus 11741234 1303 SEQUENOM CEPH CEPH (92) 92 0.48 0.45 0.03 260 3 0.18 0.04 1576 3 123 "HapMap,freq" moderately conservative 604269 5q32-q33 FAT tumor suppressor homolog 2 (Drosophila) 1906 rs1105168 FAT2 2196 5 150867075 NM_001447 NP_001438 A/G P4117L plus 24686687 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.45 0.03 260 3 0.18 0.04 1576 3 123 "HapMap,freq" moderately conservative 604269 5q32-q33 FAT tumor suppressor homolog 2 (Drosophila) 1907 rs1105879 UGT1A6 54578 2 234384202 NM_001072 NP_001063 G/T R184S minus 7863109 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.31 0.3 0.02 260 3 0.21 0.09 94 2 123 "HapMap,freq" Potentially damaging 1.29 77 Borderline 0.11 2.78 162 moderately radical 606431 2q37 "UDP glycosyltransferase 1 family, polypeptide A6" 1908 rs1105879 UGT1A6 54578 2 234384202 NM_001072 NP_001063 G/T R184S minus 7863109 1303 SEQUENOM CEPH CEPH (92) 92 0.27 0.3 0.02 260 3 0.21 0.09 94 2 123 "HapMap,freq" Potentially damaging 1.29 77 Borderline 0.11 2.78 162 moderately radical 606431 2q37 "UDP glycosyltransferase 1 family, polypeptide A6" 1909 rs1105879 UGT1A6 54578 2 234384202 NM_001072 NP_001063 G/T R184S minus 24281292 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.3 0.02 260 3 0.21 0.09 94 2 123 "HapMap,freq" Potentially damaging 1.29 77 Borderline 0.11 2.78 162 moderately radical 606431 2q37 "UDP glycosyltransferase 1 family, polypeptide A6" 1910 rs1106042 PIWIL1 9271 12 129366518 NM_004764 NP_004755 A/G R527K plus 1294401 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 80 0.03 0.03 0 80 1 0.15 0 1484 1 123 by freq Benign 0.115 6 conservative 605571 12q24.33 piwi-like 1 (Drosophila) 1911 rs1107413 SRPRB 58477 3 135007415 NM_021203 NP_067026 C/G V9L minus 1300186 1303 SEQUENOM CEPH CEPH (92) 92 0.3 0.3 0 92 1 120 "by doubleHit,freq,cluster" Benign 0.675 5 conservative 3q22.1 "signal recognition particle receptor, B subunit" 1912 rs1109643 GORASP1 64689 3 39114780 NM_031899 NP_114105 C/T T425M minus 1308933 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 80 0.01 0.01 0 80 1 0.09 0.07 160 2 113 by freq moderately conservative 606867 3p22-p21.33 "golgi reassembly stacking protein 1, 65kDa" 1913 rs1110061 NR5A1 2516 9 124342356 NM_004959 NP_004950 C/G G146A plus 7867081 1303 SEQUENOM CEPH CEPH (92) 92 0.03 0.03 0 92 1 123 by freq Benign 0.21 37 Tolerant 0.8 2.92 53 moderately conservative 184757 9q33 "nuclear receptor subfamily 5, group A, member 1" 1914 rs1122206 RDH8 50700 19 9990552 NM_015725 NP_056540 C/G H136Q plus 1457672 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 72 0.07 0.2 0.16 222 3 0.12 0.09 276 4 123 by freq Probably damaging 2.532 7 Tolerant 0.25 2.75 19 conservative 608575 19p13.2-p13.3 retinol dehydrogenase 8 (all-trans) 1915 rs1122206 RDH8 50700 19 9990552 NM_015725 NP_056540 C/G H136Q plus 1457672 760 TSC-CSHL CEL_CAUCASIAN CELERA Caucasians (30) 58 0.12 0.2 0.16 222 3 0.12 0.09 276 4 123 by freq Probably damaging 2.532 7 Tolerant 0.25 2.75 19 conservative 608575 19p13.2-p13.3 retinol dehydrogenase 8 (all-trans) 1916 rs1122206 RDH8 50700 19 9990552 NM_015725 NP_056540 C/G H136Q plus 3181271 1303 SEQUENOM CEPH CEPH (92) 92 0.36 0.2 0.16 222 3 0.12 0.09 276 4 123 by freq Probably damaging 2.532 7 Tolerant 0.25 2.75 19 conservative 608575 19p13.2-p13.3 retinol dehydrogenase 8 (all-trans) 1917 rs1122955 ZNF132 7691 19 63638015 NM_003433 NP_003424 A/G G203D minus 1460347 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.31 0.21 0.08 298 5 0.11 0.06 276 5 123 by freq Tolerant 0.65 2.76 34 moderately conservative 604074 19q13.4 zinc finger protein 132 (clone pHZ-12) 1918 rs1122955 ZNF132 7691 19 63638015 NM_003433 NP_003424 A/G G203D minus 1460347 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 12 0.08 0.21 0.08 298 5 0.11 0.06 276 5 123 by freq Tolerant 0.65 2.76 34 moderately conservative 604074 19q13.4 zinc finger protein 132 (clone pHZ-12) 1919 rs1122955 ZNF132 7691 19 63638015 NM_003433 NP_003424 A/G G203D minus 3176390 619 WICVAR MITOGPOP6 CORIELL Mixed 64 0.14 0.21 0.08 298 5 0.11 0.06 276 5 123 by freq Tolerant 0.65 2.76 34 moderately conservative 604074 19q13.4 zinc finger protein 132 (clone pHZ-12) 1920 rs1122955 ZNF132 7691 19 63638015 NM_003433 NP_003424 A/G G203D minus 16803662 1303 SEQUENOM CEPH CEPH (92) 92 0.21 0.21 0.08 298 5 0.11 0.06 276 5 123 by freq Tolerant 0.65 2.76 34 moderately conservative 604074 19q13.4 zinc finger protein 132 (clone pHZ-12) 1921 rs1122955 ZNF132 7691 19 63638015 NM_003433 NP_003424 A/G G203D minus 24689526 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.17 0.21 0.08 298 5 0.11 0.06 276 5 123 by freq Tolerant 0.65 2.76 34 moderately conservative 604074 19q13.4 zinc finger protein 132 (clone pHZ-12) 1922 rs1125488 IFNT1 338376 9 21471556 NM_176891 NP_795372 A/C Q46H minus 1479442 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.06 0.05 0.01 166 2 123 "HapMap,submitter,freq" Intolerant 0.03 2.76 124 conservative 9p21.3 interferon tau-1 1923 rs1125488 IFNT1 338376 9 21471556 NM_176891 NP_795372 A/C Q46H minus 24296953 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.04 0.05 0.01 166 2 123 "HapMap,submitter,freq" Intolerant 0.03 2.76 124 conservative 9p21.3 interferon tau-1 1924 rs1126483 ENPEP 2028 4 111767309 NM_001977 NP_001968 C/T V218A plus 3206805 902 AFFY Caucasian 22 0.09 0.09 0 22 1 0.33 0.05 1520 3 121 "by doubleHit,submitter,freq,cluster" Borderline 1.227 5 Tolerant 1 2.84 28 moderately conservative 138297 4q25 glutamyl aminopeptidase (aminopeptidase A) 1925 rs1126497 TACSTD1 4072 2 47512757 NM_002354 NP_002345 C/T M115T plus 1508999 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.46 0.45 0.02 212 2 120 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.273 5 moderately conservative 185535 2p21 tumor-associated calcium signal transducer 1 1926 rs1126497 TACSTD1 4072 2 47512757 NM_002354 NP_002345 C/T M115T plus 14496587 1303 SEQUENOM CEPH CEPH (92) 92 0.43 0.45 0.02 212 2 120 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.273 5 moderately conservative 185535 2p21 tumor-associated calcium signal transducer 1 1927 rs1126667 ALOX12 239 17 6843484 NM_000697 NP_000688 A/G Q261R plus 3255012 506 NCBI NIHPDR NIHPDR 80 0.48 0.42 0.07 228 4 0.36 0.07 474 7 123 "by doubleHit,freq,cluster" Benign 0.614 25 conservative 152391 17p13.1 arachidonate 12-lipoxygenase 1928 rs1126667 ALOX12 239 17 6843484 NM_000697 NP_000688 A/G Q261R plus 6903645 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.45 0.42 0.07 228 4 0.36 0.07 474 7 123 "by doubleHit,freq,cluster" Benign 0.614 25 conservative 152391 17p13.1 arachidonate 12-lipoxygenase 1929 rs1126667 ALOX12 239 17 6843484 NM_000697 NP_000688 A/G Q261R plus 16343714 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 44 0.39 0.42 0.07 228 4 0.36 0.07 474 7 123 "by doubleHit,freq,cluster" Benign 0.614 25 conservative 152391 17p13.1 arachidonate 12-lipoxygenase 1930 rs1126667 ALOX12 239 17 6843484 NM_000697 NP_000688 A/G Q261R plus 24209169 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.31 0.42 0.07 228 4 0.36 0.07 474 7 123 "by doubleHit,freq,cluster" Benign 0.614 25 conservative 152391 17p13.1 arachidonate 12-lipoxygenase 1931 rs1126671 ADH4 127 4 100405592 NM_000670 NP_000661 A/G I309V minus 13402833 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.33 0.37 0.07 212 2 119 "HapMap,submitter,freq,cluster" Benign 0.425 153 Borderline 0.14 2.81 399 conservative 103740 4q22 "alcohol dehydrogenase 4 (class II), pi polypeptide" 1932 rs1126671 ADH4 127 4 100405592 NM_000670 NP_000661 A/G I309V minus 13402833 1303 SEQUENOM CEPH CEPH (92) 92 0.43 0.37 0.07 212 2 119 "HapMap,submitter,freq,cluster" Benign 0.425 153 Borderline 0.14 2.81 399 conservative 103740 4q22 "alcohol dehydrogenase 4 (class II), pi polypeptide" 1933 rs1126933 CDH3 1001 16 67279034 NM_001793 NP_001784 C/G Q563H plus 14827740 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.47 0.01 138 2 0.28 0.21 94 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.09 32 Tolerant 0.47 2.78 48 conservative 114021 16q22.1 "cadherin 3, type 1, P-cadherin (placental)" 1934 rs1126933 CDH3 1001 16 67279034 NM_001793 NP_001784 C/G Q563H plus 24681068 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.48 0.47 0.01 138 2 0.28 0.21 94 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.09 32 Tolerant 0.47 2.78 48 conservative 114021 16q22.1 "cadherin 3, type 1, P-cadherin (placental)" 1935 rs1129670 PGAM2 5224 7 43875686 XM_498188 XP_498188 A/C T227P minus 1520222 1303 SEQUENOM CEPH CEPH (92) 92 0.03 0.03 0 92 1 123 by freq Possibly damaging 1.599 101 conservative 261670 7p13-p12 phosphoglycerate mutase 2 (muscle) 1936 rs1129923 DUSP23 54935 1 156565139 NM_017823 NP_060293 A/G G131S plus 1520997 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.11 0.07 0.05 260 3 0.02 0 46 1 123 "HapMap,submitter,freq,cluster" Intolerant 0 2.78 36 moderately conservative 1q23.1 dual specificity phosphatase 23 1937 rs1129923 DUSP23 54935 1 156565139 NM_017823 NP_060293 A/G G131S plus 1520997 1303 SEQUENOM CEPH CEPH (92) 92 0.03 0.07 0.05 260 3 0.02 0 46 1 123 "HapMap,submitter,freq,cluster" Intolerant 0 2.78 36 moderately conservative 1q23.1 dual specificity phosphatase 23 1938 rs1129923 DUSP23 54935 1 156565139 NM_017823 NP_060293 A/G G131S plus 23155328 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.07 0.05 260 3 0.02 0 46 1 123 "HapMap,submitter,freq,cluster" Intolerant 0 2.78 36 moderately conservative 1q23.1 dual specificity phosphatase 23 1939 rs1130643 SPARCL1 8404 4 88769985 NM_004684 NP_004675 A/G T419A minus 11678719 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.11 0.13 0.04 260 3 0.24 0.11 92 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0 5 Tolerant 0.55 3.09 48 moderately conservative 606041 4q22.1 "SPARC-like 1 (mast9, hevin)" 1940 rs1130643 SPARCL1 8404 4 88769985 NM_004684 NP_004675 A/G T419A minus 11678719 1303 SEQUENOM CEPH CEPH (92) 92 0.18 0.13 0.04 260 3 0.24 0.11 92 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0 5 Tolerant 0.55 3.09 48 moderately conservative 606041 4q22.1 "SPARC-like 1 (mast9, hevin)" 1941 rs1130643 SPARCL1 8404 4 88769985 NM_004684 NP_004675 A/G T419A minus 23228089 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.13 0.04 260 3 0.24 0.11 92 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0 5 Tolerant 0.55 3.09 48 moderately conservative 606041 4q22.1 "SPARC-like 1 (mast9, hevin)" 1942 rs1131356 FLNB 2317 3 58084202 NM_001457 NP_001448 A/G D1157N plus 6446979 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.21 0.32 0.14 260 3 0.24 0.16 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.739 25 conservative 603381 3p14.3 "filamin B, beta (actin binding protein 278)" 1943 rs1131356 FLNB 2317 3 58084202 NM_001457 NP_001448 A/G D1157N plus 6446979 1303 SEQUENOM CEPH CEPH (92) 92 0.46 0.32 0.14 260 3 0.24 0.16 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.739 25 conservative 603381 3p14.3 "filamin B, beta (actin binding protein 278)" 1944 rs1131356 FLNB 2317 3 58084202 NM_001457 NP_001448 A/G D1157N plus 23282703 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.32 0.14 260 3 0.24 0.16 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.739 25 conservative 603381 3p14.3 "filamin B, beta (actin binding protein 278)" 1945 rs1131857 CPOX 1371 3 99790386 NM_000097 NP_000088 A/C N272H minus 2503520 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 90 0.11 0.11 0.07 216 3 0.34 0.18 48 2 119 "by doubleHit,freq,cluster" Benign 0.493 8 Borderline 0.12 3.03 79 moderately conservative 121300 3q12 coproporphyrinogen oxidase 1946 rs1131857 CPOX 1371 3 99790386 NM_000097 NP_000088 A/C N272H minus 3176110 619 WICVAR MITOGPOP6 CORIELL Mixed 34 0.24 0.11 0.07 216 3 0.34 0.18 48 2 119 "by doubleHit,freq,cluster" Benign 0.493 8 Borderline 0.12 3.03 79 moderately conservative 121300 3q12 coproporphyrinogen oxidase 1947 rs1131857 CPOX 1371 3 99790386 NM_000097 NP_000088 A/C N272H minus 14226076 1303 SEQUENOM CEPH CEPH (92) 92 0.07 0.11 0.07 216 3 0.34 0.18 48 2 119 "by doubleHit,freq,cluster" Benign 0.493 8 Borderline 0.12 3.03 79 moderately conservative 121300 3q12 coproporphyrinogen oxidase 1948 rs1132528 YTHDC2 64848 5 112956912 NM_022828 NP_073739 A/T L1409Q plus 24437625 1371 PERLEGEN AFD_EUR_PANEL European American (24) 24 0.5 0.5 0 24 1 0.25 0.04 1566 3 123 by freq moderately radical 5q22.3 YTH domain containing 2 1949 rs1132899 APOC4 346 19 50139876 NM_001646 NP_001637 C/T L36P plus 24572109 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.45 0.45 0 44 1 0.39 0.06 362 4 123 "by doubleHit,freq,cluster" moderately conservative 600745 19q13.2 apolipoprotein C-IV 1950 rs1134921 GAK 2580 4 833338 NM_005255 NP_005246 A/G D1297N minus 1536705 1303 SEQUENOM CEPH CEPH (92) 92 0.19 0.19 0 92 1 120 by freq Potentially damaging 1.436 5 conservative 602052 4p16 cyclin G associated kinase 1951 rs1135045 GGA2 23062 16 23397212 NM_015044 NP_055859 C/G A424P minus 12351308 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.13 0.13 0 166 2 0.32 0 1572 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.557 6 Tolerant 0.33 2.88 17 conservative 606005 16p12 "golgi associated, gamma adaptin ear containing, ARF binding protein 2" 1952 rs1135045 GGA2 23062 16 23397212 NM_015044 NP_055859 C/G A424P minus 23965094 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.13 0.13 0 166 2 0.32 0 1572 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.557 6 Tolerant 0.33 2.88 17 conservative 606005 16p12 "golgi associated, gamma adaptin ear containing, ARF binding protein 2" 1953 rs1136287 SERPINF1 5176 17 1620026 NM_002615 NP_002606 C/T T72M plus 16740281 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.35 0.33 0.03 260 3 0.31 0.19 94 2 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.705 12 Potentially intolerant 0.09 2.77 11 moderately conservative 172860 17p13.1 "serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1" 1954 rs1136287 SERPINF1 5176 17 1620026 NM_002615 NP_002606 C/T T72M plus 16740281 1303 SEQUENOM CEPH CEPH (92) 92 0.33 0.33 0.03 260 3 0.31 0.19 94 2 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.705 12 Potentially intolerant 0.09 2.77 11 moderately conservative 172860 17p13.1 "serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1" 1955 rs1136287 SERPINF1 5176 17 1620026 NM_002615 NP_002606 C/T T72M plus 23998451 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.33 0.03 260 3 0.31 0.19 94 2 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.705 12 Potentially intolerant 0.09 2.77 11 moderately conservative 172860 17p13.1 "serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1" 1956 rs1136410 ADPRT 142 1 222862037 NM_001618 NP_001609 C/T V762A minus 2667857 506 NCBI NIHPDR NIHPDR 96 0.22 0.17 0.05 474 5 0.36 0.11 1934 7 123 "by doubleHit,freq,cluster" Potentially damaging 1.295 13 Tolerant 0.44 2.77 24 moderately conservative 173870 1q41-q42 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase) 1957 rs1136410 ADPRT 142 1 222862037 NM_001618 NP_001609 C/T V762A minus 4480525 693 EGP_SNPS PDR90 NIHPDR 176 0.19 0.17 0.05 474 5 0.36 0.11 1934 7 123 "by doubleHit,freq,cluster" Potentially damaging 1.295 13 Tolerant 0.44 2.77 24 moderately conservative 173870 1q41-q42 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase) 1958 rs1136410 ADPRT 142 1 222862037 NM_001618 NP_001609 C/T V762A minus 5586195 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.11 0.17 0.05 474 5 0.36 0.11 1934 7 123 "by doubleHit,freq,cluster" Potentially damaging 1.295 13 Tolerant 0.44 2.77 24 moderately conservative 173870 1q41-q42 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase) 1959 rs1136410 ADPRT 142 1 222862037 NM_001618 NP_001609 C/T V762A minus 16458167 1303 SEQUENOM CEPH CEPH (92) 92 0.12 0.17 0.05 474 5 0.36 0.11 1934 7 123 "by doubleHit,freq,cluster" Potentially damaging 1.295 13 Tolerant 0.44 2.77 24 moderately conservative 173870 1q41-q42 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase) 1960 rs1136410 ADPRT 142 1 222862037 NM_001618 NP_001609 C/T V762A minus 23858521 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.17 0.05 474 5 0.36 0.11 1934 7 123 "by doubleHit,freq,cluster" Potentially damaging 1.295 13 Tolerant 0.44 2.77 24 moderately conservative 173870 1q41-q42 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase) 1961 rs1137100 LEPR 3953 1 65748462 NM_002303 NP_002294 A/G K109R plus 12568615 887 CUORCGL AMERICAN CAUCASIANS American Caucasians 1838 0.29 0.29 0 1886 2 0.14 0.04 94 2 123 "by doubleHit,freq,cluster" Benign 0.141 30 conservative 601007 1p31 leptin receptor 1962 rs1137100 LEPR 3953 1 65748462 NM_002303 NP_002294 A/G K109R plus 24236809 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.29 0 1886 2 0.14 0.04 94 2 123 "by doubleHit,freq,cluster" Benign 0.141 30 conservative 601007 1p31 leptin receptor 1963 rs1137101 LEPR 3953 1 65770534 NM_002303 NP_002294 A/G Q223R plus 1543089 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.48 0.38 0.12 577 6 0.3 0.11 575 8 123 "by cluster,freq" Benign 0.394 30 Tolerant 0.8 3.24 22 conservative 601007 1p31 leptin receptor 1964 rs1137101 LEPR 3953 1 65770534 NM_002303 NP_002294 A/G Q223R plus 3176444 619 WICVAR MITOGPOP6 CORIELL Mixed 46 0.28 0.38 0.12 577 6 0.3 0.11 575 8 123 "by cluster,freq" Benign 0.394 30 Tolerant 0.8 3.24 22 conservative 601007 1p31 leptin receptor 1965 rs1137101 LEPR 3953 1 65770534 NM_002303 NP_002294 A/G Q223R plus 12675515 775 SNP500CANCER CAUC1 Caucasian (31) 31 0.5 0.38 0.12 577 6 0.3 0.11 575 8 123 "by cluster,freq" Benign 0.394 30 Tolerant 0.8 3.24 22 conservative 601007 1p31 leptin receptor 1966 rs1137101 LEPR 3953 1 65770534 NM_002303 NP_002294 A/G Q223R plus 24236819 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.38 0.12 577 6 0.3 0.11 575 8 123 "by cluster,freq" Benign 0.394 30 Tolerant 0.8 3.24 22 conservative 601007 1p31 leptin receptor 1967 rs1137101 LEPR 3953 1 65770534 NM_002303 NP_002294 A/G Q223R plus 24796087 1303 SEQUENOM CEPH CEPH (92) 184 0.24 0.38 0.12 577 6 0.3 0.11 575 8 123 "by cluster,freq" Benign 0.394 30 Tolerant 0.8 3.24 22 conservative 601007 1p31 leptin receptor 1968 rs1137101 LEPR 3953 1 65770534 NM_002303 NP_002294 A/G Q223R plus 24796667 1303 SEQUENOM CEPH CEPH (92) 184 0.46 0.38 0.12 577 6 0.3 0.11 575 8 123 "by cluster,freq" Benign 0.394 30 Tolerant 0.8 3.24 22 conservative 601007 1p31 leptin receptor 1969 rs1138294 MAP3K6 9064 1 27372775 NM_004672 NP_004663 C/T T455I minus 9844384 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.44 0 92 1 116 "by doubleHit,freq,cluster" Tolerant 0.66 2.95 17 moderately conservative 604468 1p35.3 mitogen-activated protein kinase kinase kinase 6 1970 rs1138358 BCL2A1 597 15 78050400 NM_004049 NP_004040 G/T N39K minus 4929433 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.25 0.25 0.06 260 3 0.49 0.01 70 2 123 "HapMap,submitter,freq,cluster" Borderline 1.117 7 Tolerant 0.39 2.8 72 moderately conservative 601056 15q24.3 BCL2-related protein A1 1971 rs1138358 BCL2A1 597 15 78050400 NM_004049 NP_004040 G/T N39K minus 4929433 1303 SEQUENOM CEPH CEPH (92) 92 0.3 0.25 0.06 260 3 0.49 0.01 70 2 123 "HapMap,submitter,freq,cluster" Borderline 1.117 7 Tolerant 0.39 2.8 72 moderately conservative 601056 15q24.3 BCL2-related protein A1 1972 rs1138358 BCL2A1 597 15 78050400 NM_004049 NP_004040 G/T N39K minus 24064940 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.25 0.06 260 3 0.49 0.01 70 2 123 "HapMap,submitter,freq,cluster" Borderline 1.117 7 Tolerant 0.39 2.8 72 moderately conservative 601056 15q24.3 BCL2-related protein A1 1973 rs1139776 KDR 3791 4 55804828 NM_002253 NP_002244 A/T V848E minus 1549277 1303 SEQUENOM CEPH CEPH (92) 92 0.03 0.03 0 92 1 106 by freq Possibly damaging 1.745 8 Intolerant 0 2.93 23 moderately radical 191306 4q11-q12 kinase insert domain receptor (a type III receptor tyrosine kinase) 1974 rs1141223 ENDOGL1 9941 3 38540580 NM_005107 NP_005098 G/T G277V plus 1552276 1303 SEQUENOM CEPH CEPH (92) 92 0.07 0.07 0 92 1 86 by freq moderately radical 604051 3p21.3 endonuclease G-like 1 1975 rs1143650 HSD17B4 3295 5 118860143 NM_000414 NP_000405 C/G T292S plus 1556782 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 56 0.03 0.03 0 56 1 0.09 0 44 1 123 "by doubleHit,freq,cluster" Benign 0.373 18 Tolerant 0.62 2.91 36 moderately conservative 601860 5q21 hydroxysteroid (17-beta) dehydrogenase 4 1976 rs1143678 ITGAM 3684 16 31250506 NM_000632 NP_000623 C/T P1146S plus 1556828 523 WIAF-CSNP WIAF-CSNP-MITOGPOP4 "Europeans (20), Asians (10) and African-Americans (10)" 62 0.33 0.2 0.13 182 2 116 "HapMap,doubleHit,freq,cluster" moderately conservative 120980 16p11.2 "integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide)" 1977 rs1143678 ITGAM 3684 16 31250506 NM_000632 NP_000623 C/T P1146S plus 10844979 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.13 0.2 0.13 182 2 116 "HapMap,doubleHit,freq,cluster" moderately conservative 120980 16p11.2 "integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide)" 1978 rs1144507 ZNF202 7753 11 123105685 NM_003455 NP_003446 A/G V154A plus 4062641 1303 SEQUENOM CEPH CEPH (92) 92 0.41 0.41 0 92 1 123 "by doubleHit,freq" Tolerant 0.7 2.84 19 moderately conservative 603430 11q23.3 zinc finger protein 202 1979 rs1145234 PMS1 5378 2 190558065 NM_000534 NP_000525 C/T Y793H plus 2978052 506 NCBI NIHPDR NIHPDR 82 0.01 0.01 0 254 2 123 "by cluster,freq" moderately conservative 600258 2q31.1 PMS1 postmeiotic segregation increased 1 (S. cerevisiae) 1980 rs1145234 PMS1 5378 2 190558065 NM_000534 NP_000525 C/T Y793H plus 7986979 693 EGP_SNPS PDR90 NIHPDR 172 0.01 0.01 0 254 2 123 "by cluster,freq" moderately conservative 600258 2q31.1 PMS1 postmeiotic segregation increased 1 (S. cerevisiae) 1981 rs1147990 TTC4 7268 1 54894321 NM_004623 NP_004614 A/T S47T minus 2439493 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 12 0.25 0.25 0 12 1 0.41 0 22 1 120 "by doubleHit,freq,cluster" Borderline 1.047 9 moderately conservative 606753 1p31.3 tetratricopeptide repeat domain 4 1982 rs1150258 IL24 11009 1 203463300 NM_006850 NP_006841 A/G Y124H minus 4328649 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 23 0.5 0.35 0.11 115 2 0.21 0 48 1 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.39 2.78 44 moderately conservative 604136 1q32 interleukin 24 1983 rs1150258 IL24 11009 1 203463300 NM_006850 NP_006841 A/G Y124H minus 16404286 1303 SEQUENOM CEPH CEPH (92) 92 0.31 0.35 0.11 115 2 0.21 0 48 1 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.39 2.78 44 moderately conservative 604136 1q32 interleukin 24 1984 rs1152888 IRAK3 11213 12 64891495 NM_007199 NP_009130 A/G I147V plus 1593320 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.09 0.09 0.03 252 3 0.43 0 974 2 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 604459 12q14.2 interleukin-1 receptor-associated kinase 3 1985 rs1152888 IRAK3 11213 12 64891495 NM_007199 NP_009130 A/G I147V plus 1593320 1303 SEQUENOM CEPH CEPH (92) 92 0.07 0.09 0.03 252 3 0.43 0 974 2 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 604459 12q14.2 interleukin-1 receptor-associated kinase 3 1986 rs1152888 IRAK3 11213 12 64891495 NM_007199 NP_009130 A/G I147V plus 15356011 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.15 0.09 0.03 252 3 0.43 0 974 2 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 604459 12q14.2 interleukin-1 receptor-associated kinase 3 1987 rs1153850 SPATA5L1 79029 15 43482275 NM_024063 NP_076968 C/G R119P minus 2234075 1303 SEQUENOM CEPH CEPH (92) 92 0.29 0.29 0 92 1 0.47 0 36 1 123 "by doubleHit,freq,cluster" Tolerant 0.27 2.92 69 moderately radical 15q15.1 spermatogenesis associated 5-like 1 1988 rs1154510 HPD 3242 12 120758055 NM_002150 NP_002141 A/G T33A minus 1593356 1303 SEQUENOM CEPH CEPH (92) 92 0.19 0.16 0.06 140 2 0.15 0.16 92 2 123 "by doubleHit,freq,cluster" Possibly damaging 1.656 19 moderately conservative 276710 12q24-qter 4-hydroxyphenylpyruvate dioxygenase 1989 rs1154510 HPD 3242 12 120758055 NM_002150 NP_002141 A/G T33A minus 23934720 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.16 0.06 140 2 0.15 0.16 92 2 123 "by doubleHit,freq,cluster" Possibly damaging 1.656 19 moderately conservative 276710 12q24-qter 4-hydroxyphenylpyruvate dioxygenase 1990 rs1159148 AIM1 202 6 107073878 XM_166300 XP_166300 G/T Q916P minus 5523567 1303 SEQUENOM CEPH CEPH (92) 92 0.14 0.17 0.06 140 2 0.14 0.11 94 2 123 "by doubleHit,submitter,freq" moderately conservative 601797 6q21 absent in melanoma 1 1991 rs1159148 AIM1 202 6 107073878 XM_166300 XP_166300 G/T Q916P minus 24360619 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.17 0.06 140 2 0.14 0.11 94 2 123 "by doubleHit,submitter,freq" moderately conservative 601797 6q21 absent in melanoma 1 1992 rs1168312 HELB 92797 12 65011469 NM_033647 NP_387467 A/G T980I minus 1592382 1303 SEQUENOM CEPH CEPH (92) 92 0.18 0.17 0.02 140 2 0.2 0.02 1570 3 123 "by cluster,freq" moderately conservative 12q14.2 helicase (DNA) B 1993 rs1168312 HELB 92797 12 65011469 NM_033647 NP_387467 A/G T980I minus 24214106 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.17 0.02 140 2 0.2 0.02 1570 3 123 "by cluster,freq" moderately conservative 12q14.2 helicase (DNA) B 1994 rs1169288 TCF1 6927 12 119879370 NM_000545 NP_000536 G/T I27L minus 1595449 1303 SEQUENOM CEPH CEPH (92) 92 0.29 0.28 0.01 136 2 0.49 0.07 1578 3 123 "by doubleHit,freq,cluster" Benign 0.45 6 Tolerant 0.3 3.12 32 conservative 142410 12q24.2 "transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor" 1995 rs1169288 TCF1 6927 12 119879370 NM_000545 NP_000536 G/T I27L minus 23932948 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.27 0.28 0.01 136 2 0.49 0.07 1578 3 123 "by doubleHit,freq,cluster" Benign 0.45 6 Tolerant 0.3 3.12 32 conservative 142410 12q24.2 "transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor" 1996 rs1177573 PSMD9 5715 12 120800418 NM_002813 NP_002804 A/G R134W minus 1626025 1303 SEQUENOM CEPH CEPH (92) 92 0.23 0.23 0 92 1 116 "by doubleHit,freq,cluster" Possibly damaging 1.737 7 Intolerant 0.02 2.92 12 moderately radical 603146 12q24.31-q24.32 "proteasome (prosome, macropain) 26S subunit, non-ATPase, 9" 1997 rs1183768 KIAA0625 23064 9 132232785 NM_015046 NP_055861 C/T G1252R plus 23435981 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.17 0 48 1 0.27 0.02 1582 3 123 "by doubleHit,submitter,freq,cluster" moderately radical 608465 9q34.3 senataxin 1998 rs1185193 KIAA0625 23064 9 132232963 NM_015046 NP_055861 A/C D1192E plus 1658019 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.09 0.13 0.04 260 3 0.28 0 1582 3 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 608465 9q34.3 senataxin 1999 rs1185193 KIAA0625 23064 9 132232963 NM_015046 NP_055861 A/C D1192E plus 1658019 1303 SEQUENOM CEPH CEPH (92) 92 0.17 0.13 0.04 260 3 0.28 0 1582 3 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 608465 9q34.3 senataxin 2000 rs1185193 KIAA0625 23064 9 132232963 NM_015046 NP_055861 A/C D1192E plus 24002626 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0.04 260 3 0.28 0 1582 3 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 608465 9q34.3 senataxin 2001 rs1185244 HELB 92797 12 65011427 NM_033647 NP_387467 A/G P966L minus 1658154 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.38 0.39 0.03 260 3 0.39 0.01 1566 3 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially intolerant 0.1 3.22 25 moderately conservative 12q14.2 helicase (DNA) B 2002 rs1185244 HELB 92797 12 65011427 NM_033647 NP_387467 A/G P966L minus 1658154 1303 SEQUENOM CEPH CEPH (92) 92 0.37 0.39 0.03 260 3 0.39 0.01 1566 3 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially intolerant 0.1 3.22 25 moderately conservative 12q14.2 helicase (DNA) B 2003 rs1185244 HELB 92797 12 65011427 NM_033647 NP_387467 A/G P966L minus 24705914 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.39 0.03 260 3 0.39 0.01 1566 3 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially intolerant 0.1 3.22 25 moderately conservative 12q14.2 helicase (DNA) B 2004 rs1185845 HCFC2 29915 12 102983163 NM_013320 NP_037452 C/T E379K minus 1659754 1303 SEQUENOM CEPH CEPH (92) 92 0.42 0.42 0 92 1 100 by freq Tolerant 0.25 2.85 20 moderately conservative 607926 12q23.3 host cell factor 2 2005 rs1206038 EGFL4 1954 19 47554875 NM_001410 NP_001401 C/T K1299E minus 1733434 1303 SEQUENOM CEPH CEPH (92) 92 0.06 0.06 0 92 1 89 "by doubleHit,freq" Tolerant 0.65 2.93 29 moderately conservative 604267 19q12 "EGF-like-domain, multiple 4" 2006 rs1211554 HUS1B 135458 6 601143 NM_148959 NP_683762 A/C D268Y plus 1752893 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.1 0.08 0.02 260 3 0.26 0.21 92 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially intolerant 0.06 2.97 12 radical 6p25.3 HUS1 checkpoint homolog b (S. pombe) 2007 rs1211554 HUS1B 135458 6 601143 NM_148959 NP_683762 A/C D268Y plus 1752893 1303 SEQUENOM CEPH CEPH (92) 92 0.06 0.08 0.02 260 3 0.26 0.21 92 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially intolerant 0.06 2.97 12 radical 6p25.3 HUS1 checkpoint homolog b (S. pombe) 2008 rs1211554 HUS1B 135458 6 601143 NM_148959 NP_683762 A/C D268Y plus 23394992 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0.02 260 3 0.26 0.21 92 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially intolerant 0.06 2.97 12 radical 6p25.3 HUS1 checkpoint homolog b (S. pombe) 2009 rs1218825 MTIF3 219402 13 26907920 NM_152912 NP_690876 C/G F243L plus 4084835 902 AFFY Caucasian 24 0.04 0.02 0.02 116 2 0.39 0.04 1562 4 121 "by doubleHit,freq,cluster" conservative 13q12.2 mitochondrial translational initiation factor 3 2010 rs1218825 MTIF3 219402 13 26907920 NM_152912 NP_690876 C/G F243L plus 4084835 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.02 0.02 116 2 0.39 0.04 1562 4 121 "by doubleHit,freq,cluster" conservative 13q12.2 mitochondrial translational initiation factor 3 2011 rs1227051 CDH23 64072 10 73171562 NM_022124 NP_071407 C/T A1575T minus 23626293 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.31 0.08 94 2 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.58 2.83 17 moderately conservative 605516 10q21-q22 cadherin-like 23 2012 rs1227065 CDH23 64072 10 73162085 NM_022124 NP_071407 C/T N1351D minus 24116348 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.19 0.03 94 2 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.93 3.02 11 conservative 605516 10q21-q22 cadherin-like 23 2013 rs1229984 ADH1B 125 4 100596497 NM_000668 NP_000659 A/G H48R minus 1823175 1303 SEQUENOM CEPH CEPH (92) 92 0.12 0.12 0.01 154 2 0.19 0.14 342 4 121 "by doubleHit,freq,cluster" Borderline 1.071 239 Tolerant 0.22 2.79 357 conservative 103720 4q21-q23 "alcohol dehydrogenase IB (class I), beta polypeptide" 2014 rs1229984 ADH1B 125 4 100596497 NM_000668 NP_000659 A/G H48R minus 5586189 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.11 0.12 0.01 154 2 0.19 0.14 342 4 121 "by doubleHit,freq,cluster" Borderline 1.071 239 Tolerant 0.22 2.79 357 conservative 103720 4q21-q23 "alcohol dehydrogenase IB (class I), beta polypeptide" 2015 rs1233428 ZNF233 353355 19 49470245 NM_181756 NP_861421 A/C K531T plus 1842601 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.34 0.35 0.03 259 3 0.2 0.01 86 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.524 6 moderately conservative 19q13.32 zinc finger protein 233 2016 rs1233428 ZNF233 353355 19 49470245 NM_181756 NP_861421 A/C K531T plus 1842601 1303 SEQUENOM CEPH CEPH (92) 91 0.35 0.35 0.03 259 3 0.2 0.01 86 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.524 6 moderately conservative 19q13.32 zinc finger protein 233 2017 rs1233428 ZNF233 353355 19 49470245 NM_181756 NP_861421 A/C K531T plus 24685339 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.35 0.03 259 3 0.2 0.01 86 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.524 6 moderately conservative 19q13.32 zinc finger protein 233 2018 rs1243469 RNASE7 84659 14 20581337 NM_032572 NP_115961 C/T H116Y plus 2599511 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 24 0.08 0.13 0.04 376 5 0.09 0.05 1636 5 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 14q11.2 "ribonuclease, RNase A family, 7" 2019 rs1243469 RNASE7 84659 14 20581337 NM_032572 NP_115961 C/T H116Y plus 2599511 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 94 0.13 0.13 0.04 376 5 0.09 0.05 1636 5 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 14q11.2 "ribonuclease, RNase A family, 7" 2020 rs1243469 RNASE7 84659 14 20581337 NM_032572 NP_115961 C/T H116Y plus 2846941 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.13 0.13 0.04 376 5 0.09 0.05 1636 5 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 14q11.2 "ribonuclease, RNase A family, 7" 2021 rs1243469 RNASE7 84659 14 20581337 NM_032572 NP_115961 C/T H116Y plus 2846941 1303 SEQUENOM CEPH CEPH (92) 92 0.09 0.13 0.04 376 5 0.09 0.05 1636 5 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 14q11.2 "ribonuclease, RNase A family, 7" 2022 rs1243469 RNASE7 84659 14 20581337 NM_032572 NP_115961 C/T H116Y plus 23815036 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.13 0.04 376 5 0.09 0.05 1636 5 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 14q11.2 "ribonuclease, RNase A family, 7" 2023 rs1260326 GCKR 2646 2 27642591 NM_001486 NP_001477 C/T L446P plus 2468242 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.43 0.43 0.01 336 4 0.39 0.04 1632 5 123 "by doubleHit,freq,cluster" Probably damaging 2.55 7 moderately conservative 600842 2p23 glucokinase (hexokinase 4) regulator 2024 rs1260326 GCKR 2646 2 27642591 NM_001486 NP_001477 C/T L446P plus 2468242 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 182 0.42 0.43 0.01 336 4 0.39 0.04 1632 5 123 "by doubleHit,freq,cluster" Probably damaging 2.55 7 moderately conservative 600842 2p23 glucokinase (hexokinase 4) regulator 2025 rs1260326 GCKR 2646 2 27642591 NM_001486 NP_001477 C/T L446P plus 12568673 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.43 0.01 336 4 0.39 0.04 1632 5 123 "by doubleHit,freq,cluster" Probably damaging 2.55 7 moderately conservative 600842 2p23 glucokinase (hexokinase 4) regulator 2026 rs1260326 GCKR 2646 2 27642591 NM_001486 NP_001477 C/T L446P plus 24292559 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.43 0.01 336 4 0.39 0.04 1632 5 123 "by doubleHit,freq,cluster" Probably damaging 2.55 7 moderately conservative 600842 2p23 glucokinase (hexokinase 4) regulator 2027 rs1263872 RNASE7 84659 14 20581298 NM_032572 NP_115961 C/G A103P plus 2853722 1303 SEQUENOM CEPH CEPH (92) 92 0.09 0.09 0 92 1 0.08 0 1468 1 121 "by doubleHit,freq,cluster" conservative 14q11.2 "ribonuclease, RNase A family, 7" 2028 rs1274958 AXUD1 64651 3 39159963 NM_033027 NP_149016 A/G V453I minus 1987567 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 83 0.4 0.31 0.13 175 2 0.25 0.06 1660 3 119 "by doubleHit,freq,cluster" conservative 606458 3p22 AXIN1 up-regulated 1 2029 rs1274958 AXUD1 64651 3 39159963 NM_033027 NP_149016 A/G V453I minus 1987567 1303 SEQUENOM CEPH CEPH (92) 92 0.22 0.31 0.13 175 2 0.25 0.06 1660 3 119 "by doubleHit,freq,cluster" conservative 606458 3p22 AXIN1 up-regulated 1 2030 rs1287637 NPHP4 261734 1 5869428 NM_015102 NP_055917 A/T L939X minus 2821971 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.16 0.16 0 120 1 0.18 0 1490 1 120 "HapMap,freq,cluster" Probably damaging Intolerant radical 607215 1p36.22 nephronophthisis 4 2031 rs1288775 GATM 2628 15 43448970 NM_001482 NP_001473 A/T Q110H plus 2033575 1303 SEQUENOM CEPH CEPH (92) 92 0.4 0.33 0.13 140 2 0.14 0.01 1540 3 123 "by submitter,freq,cluster" Benign 0.56 15 Tolerant 0.59 2.94 28 conservative 602360 15q15.1 glycine amidinotransferase (L-arginine:glycine amidinotransferase) 2032 rs1288775 GATM 2628 15 43448970 NM_001482 NP_001473 A/T Q110H plus 24468497 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.33 0.13 140 2 0.14 0.01 1540 3 123 "by submitter,freq,cluster" Benign 0.56 15 Tolerant 0.59 2.94 28 conservative 602360 15q15.1 glycine amidinotransferase (L-arginine:glycine amidinotransferase) 2033 rs1318196 ZC3HDC3 23144 8 144691485 NM_015117 NP_055932 A/G S399G minus 2085849 1303 SEQUENOM CEPH CEPH (92) 92 0.11 0.11 0 92 1 0.23 0 1480 1 120 "by doubleHit,freq,cluster" moderately conservative 8q24.3 zinc finger CCCH type domain containing 3 2034 rs1318648 ESPL1 9700 12 51956812 NM_012291 NP_036423 G/T S614R minus 2086473 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.36 0.3 0.08 274 4 0.21 0.06 1624 5 123 "HapMap,doubleHit,freq,cluster" moderately radical 604143 8 extra spindle poles like 1 (S. cerevisiae) 2035 rs1318648 ESPL1 9700 12 51956812 NM_012291 NP_036423 G/T S614R minus 2086473 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.34 0.3 0.08 274 4 0.21 0.06 1624 5 123 "HapMap,doubleHit,freq,cluster" moderately radical 604143 8 extra spindle poles like 1 (S. cerevisiae) 2036 rs1318648 ESPL1 9700 12 51956812 NM_012291 NP_036423 G/T S614R minus 2086473 1303 SEQUENOM CEPH CEPH (92) 92 0.21 0.3 0.08 274 4 0.21 0.06 1624 5 123 "HapMap,doubleHit,freq,cluster" moderately radical 604143 8 extra spindle poles like 1 (S. cerevisiae) 2037 rs1318648 ESPL1 9700 12 51956812 NM_012291 NP_036423 G/T S614R minus 23365363 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.3 0.08 274 4 0.21 0.06 1624 5 123 "HapMap,doubleHit,freq,cluster" moderately radical 604143 8 extra spindle poles like 1 (S. cerevisiae) 2038 rs1328361 GUCY1B2 2974 13 50492742 NM_004129 NP_004120 G/T N316H plus 2099509 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.38 0.35 0.05 212 2 0.07 0 1490 1 121 "HapMap,doubleHit,submitter,freq,cluster" Probably damaging 2.059 10 Tolerant 1 2.83 40 moderately conservative 603695 13q14.2-q14.3 "guanylate cyclase 1, soluble, beta 2" 2039 rs1328361 GUCY1B2 2974 13 50492742 NM_004129 NP_004120 G/T N316H plus 2099509 1303 SEQUENOM CEPH CEPH (92) 92 0.31 0.35 0.05 212 2 0.07 0 1490 1 121 "HapMap,doubleHit,submitter,freq,cluster" Probably damaging 2.059 10 Tolerant 1 2.83 40 moderately conservative 603695 13q14.2-q14.3 "guanylate cyclase 1, soluble, beta 2" 2040 rs1334811 TEK 7010 9 27180655 NM_000459 NP_000450 A/G V486I plus 2108192 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 82 0.07 0.05 0.02 294 3 0.13 0.17 164 2 88 "HapMap,submitter,freq" Benign 0.756 11 Potentially intolerant 0.09 2.82 38 conservative 600221 9p21 "TEK tyrosine kinase, endothelial (venous malformations, multiple cutaneous and mucosal)" 2041 rs1334811 TEK 7010 9 27180655 NM_000459 NP_000450 A/G V486I plus 2108192 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.03 0.05 0.02 294 3 0.13 0.17 164 2 88 "HapMap,submitter,freq" Benign 0.756 11 Potentially intolerant 0.09 2.82 38 conservative 600221 9p21 "TEK tyrosine kinase, endothelial (venous malformations, multiple cutaneous and mucosal)" 2042 rs1334811 TEK 7010 9 27180655 NM_000459 NP_000450 A/G V486I plus 2108192 1303 SEQUENOM CEPH CEPH (92) 92 0.05 0.05 0.02 294 3 0.13 0.17 164 2 88 "HapMap,submitter,freq" Benign 0.756 11 Potentially intolerant 0.09 2.82 38 conservative 600221 9p21 "TEK tyrosine kinase, endothelial (venous malformations, multiple cutaneous and mucosal)" 2043 rs1340623 AIM1 202 6 107066692 XM_166300 XP_166300 C/G P551R plus 2116200 1303 SEQUENOM CEPH CEPH (92) 92 0.21 0.19 0.05 132 2 0.28 0.07 78 2 123 "by doubleHit,freq,cluster" moderately radical 601797 6q21 absent in melanoma 1 2044 rs1340623 AIM1 202 6 107066692 XM_166300 XP_166300 C/G P551R plus 23324612 1371 PERLEGEN AFD_EUR_PANEL European American (24) 40 0.13 0.19 0.05 132 2 0.28 0.07 78 2 123 "by doubleHit,freq,cluster" moderately radical 601797 6q21 absent in melanoma 1 2045 rs1341023 BPI 671 20 36366074 NM_001725 NP_001716 C/T A16V plus 7987409 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.43 0.38 0.05 186 4 0.43 0.02 140 3 123 "by doubleHit,freq,cluster" moderately conservative 109195 20q11.23-q12 bactericidal/permeability-increasing protein 2046 rs1341023 BPI 671 20 36366074 NM_001725 NP_001716 C/T A16V plus 7987409 848 IIPGA-WEISS-MARTINEZ E-1 CEPH 6 0.17 0.38 0.05 186 4 0.43 0.02 140 3 123 "by doubleHit,freq,cluster" moderately conservative 109195 20q11.23-q12 bactericidal/permeability-increasing protein 2047 rs1341023 BPI 671 20 36366074 NM_001725 NP_001716 C/T A16V plus 8328180 1303 SEQUENOM CEPH CEPH (92) 92 0.36 0.38 0.05 186 4 0.43 0.02 140 3 123 "by doubleHit,freq,cluster" moderately conservative 109195 20q11.23-q12 bactericidal/permeability-increasing protein 2048 rs1341023 BPI 671 20 36366074 NM_001725 NP_001716 C/T A16V plus 24207643 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.38 0.05 186 4 0.43 0.02 140 3 123 "by doubleHit,freq,cluster" moderately conservative 109195 20q11.23-q12 bactericidal/permeability-increasing protein 2049 rs1342642 IL20RA 53832 6 137364906 NM_014432 NP_055247 C/T L382F minus 2118976 782 TSC-CSHL WICGR6_CAUCASIAN_POOLED WICGR Caucasian (48) 96 0.14 0.27 0.13 265 5 0.11 0.09 250 6 123 "by doubleHit,submitter,freq" Potentially intolerant 0.1 2.95 6 conservative 605620 6q22.33-q23.1 "interleukin 20 receptor, alpha" 2050 rs1342642 IL20RA 53832 6 137364906 NM_014432 NP_055247 C/T L382F minus 2118976 902 AFFY Caucasian 24 0.29 0.27 0.13 265 5 0.11 0.09 250 6 123 "by doubleHit,submitter,freq" Potentially intolerant 0.1 2.95 6 conservative 605620 6q22.33-q23.1 "interleukin 20 receptor, alpha" 2051 rs1342642 IL20RA 53832 6 137364906 NM_014432 NP_055247 C/T L382F minus 2118976 904 AFFY CEPH 5 0.5 0.27 0.13 265 5 0.11 0.09 250 6 123 "by doubleHit,submitter,freq" Potentially intolerant 0.1 2.95 6 conservative 605620 6q22.33-q23.1 "interleukin 20 receptor, alpha" 2052 rs1342642 IL20RA 53832 6 137364906 NM_014432 NP_055247 C/T L382F minus 2118976 1303 SEQUENOM CEPH CEPH (92) 92 0.41 0.27 0.13 265 5 0.11 0.09 250 6 123 "by doubleHit,submitter,freq" Potentially intolerant 0.1 2.95 6 conservative 605620 6q22.33-q23.1 "interleukin 20 receptor, alpha" 2053 rs1342642 IL20RA 53832 6 137364906 NM_014432 NP_055247 C/T L382F minus 24426907 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.27 0.13 265 5 0.11 0.09 250 6 123 "by doubleHit,submitter,freq" Potentially intolerant 0.1 2.95 6 conservative 605620 6q22.33-q23.1 "interleukin 20 receptor, alpha" 2054 rs1344642 STK36 27148 2 219380767 NM_015690 NP_056505 A/G R583Q plus 2121686 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.33 0.36 0.06 168 2 0.14 0.06 1590 3 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.334 5 conservative 607652 2q35 "serine/threonine kinase 36 (fused homolog, Drosophila)" 2055 rs1344642 STK36 27148 2 219380767 NM_015690 NP_056505 A/G R583Q plus 24658679 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.36 0.06 168 2 0.14 0.06 1590 3 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.334 5 conservative 607652 2q35 "serine/threonine kinase 36 (fused homolog, Drosophila)" 2056 rs1345658 ZNF30 90075 19 40126846 NM_194325 NP_919306 C/T R298K minus 2122958 902 AFFY Caucasian 20 0.5 0.43 0.05 154 3 0.41 0.04 1622 4 120 "by doubleHit,freq,cluster" Possibly damaging 1.57 242 conservative 19q13.13 zinc finger protein 30 (KOX 28) 2057 rs1345658 ZNF30 90075 19 40126846 NM_194325 NP_919306 C/T R298K minus 2122958 904 AFFY CEPH 42 0.48 0.43 0.05 154 3 0.41 0.04 1622 4 120 "by doubleHit,freq,cluster" Possibly damaging 1.57 242 conservative 19q13.13 zinc finger protein 30 (KOX 28) 2058 rs1345658 ZNF30 90075 19 40126846 NM_194325 NP_919306 C/T R298K minus 2122958 1303 SEQUENOM CEPH CEPH (92) 92 0.4 0.43 0.05 154 3 0.41 0.04 1622 4 120 "by doubleHit,freq,cluster" Possibly damaging 1.57 242 conservative 19q13.13 zinc finger protein 30 (KOX 28) 2059 rs1346044 WRN 7486 8 31144196 NM_000553 NP_000544 C/T C1367R plus 2123516 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.36 0.22 0.05 806 9 0.18 0.05 464 7 123 "HapMap,submitter,freq,cluster" Probably damaging 2.631 6 radical 604611 8p12-p11.2 Werner syndrome 2060 rs1346044 WRN 7486 8 31144196 NM_000553 NP_000544 C/T C1367R plus 2123516 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 92 0.22 0.22 0.05 806 9 0.18 0.05 464 7 123 "HapMap,submitter,freq,cluster" Probably damaging 2.631 6 radical 604611 8p12-p11.2 Werner syndrome 2061 rs1346044 WRN 7486 8 31144196 NM_000553 NP_000544 C/T C1367R plus 2123516 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.23 0.22 0.05 806 9 0.18 0.05 464 7 123 "HapMap,submitter,freq,cluster" Probably damaging 2.631 6 radical 604611 8p12-p11.2 Werner syndrome 2062 rs1346044 WRN 7486 8 31144196 NM_000553 NP_000544 C/T C1367R plus 2123516 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.22 0.05 806 9 0.18 0.05 464 7 123 "HapMap,submitter,freq,cluster" Probably damaging 2.631 6 radical 604611 8p12-p11.2 Werner syndrome 2063 rs1346044 WRN 7486 8 31144196 NM_000553 NP_000544 C/T C1367R plus 3177102 619 WICVAR MITOGPOP6 CORIELL Mixed 30 0.17 0.22 0.05 806 9 0.18 0.05 464 7 123 "HapMap,submitter,freq,cluster" Probably damaging 2.631 6 radical 604611 8p12-p11.2 Werner syndrome 2064 rs1346044 WRN 7486 8 31144196 NM_000553 NP_000544 C/T C1367R plus 4318955 506 NCBI NIHPDR NIHPDR 168 0.19 0.22 0.05 806 9 0.18 0.05 464 7 123 "HapMap,submitter,freq,cluster" Probably damaging 2.631 6 radical 604611 8p12-p11.2 Werner syndrome 2065 rs1346044 WRN 7486 8 31144196 NM_000553 NP_000544 C/T C1367R plus 5586956 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.29 0.22 0.05 806 9 0.18 0.05 464 7 123 "HapMap,submitter,freq,cluster" Probably damaging 2.631 6 radical 604611 8p12-p11.2 Werner syndrome 2066 rs1346044 WRN 7486 8 31144196 NM_000553 NP_000544 C/T C1367R plus 16359638 693 EGP_SNPS PDR90 NIHPDR 180 0.19 0.22 0.05 806 9 0.18 0.05 464 7 123 "HapMap,submitter,freq,cluster" Probably damaging 2.631 6 radical 604611 8p12-p11.2 Werner syndrome 2067 rs1346044 WRN 7486 8 31144196 NM_000553 NP_000544 C/T C1367R plus 24474353 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.22 0.05 806 9 0.18 0.05 464 7 123 "HapMap,submitter,freq,cluster" Probably damaging 2.631 6 radical 604611 8p12-p11.2 Werner syndrome 2068 rs1359590 FRMPD1 22844 9 37719786 NM_014907 NP_055722 A/G A225V minus 2142109 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 16 0.13 0.25 0.08 318 4 0.08 0.02 1544 3 111 "HapMap,submitter,freq,cluster" moderately conservative 9p13.1 FERM and PDZ domain containing 1 2069 rs1359590 FRMPD1 22844 9 37719786 NM_014907 NP_055722 A/G A225V minus 2142109 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 90 0.2 0.25 0.08 318 4 0.08 0.02 1544 3 111 "HapMap,submitter,freq,cluster" moderately conservative 9p13.1 FERM and PDZ domain containing 1 2070 rs1359590 FRMPD1 22844 9 37719786 NM_014907 NP_055722 A/G A225V minus 2142109 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.23 0.25 0.08 318 4 0.08 0.02 1544 3 111 "HapMap,submitter,freq,cluster" moderately conservative 9p13.1 FERM and PDZ domain containing 1 2071 rs1359590 FRMPD1 22844 9 37719786 NM_014907 NP_055722 A/G A225V minus 2142109 1303 SEQUENOM CEPH CEPH (92) 92 0.35 0.25 0.08 318 4 0.08 0.02 1544 3 111 "HapMap,submitter,freq,cluster" moderately conservative 9p13.1 FERM and PDZ domain containing 1 2072 rs1366257 ZNF534 147658 19 57633352 XM_496320 XP_496320 A/G G289E plus 2151289 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 82 0.05 0.05 0 82 1 0.22 0.03 159 2 121 "by cluster,freq" Intolerant 0.01 2.77 37 moderately conservative 19q13.41 zinc finger protein 534 2073 rs1367117 APOB 338 2 21175552 NM_000384 NP_000375 A/G T98I plus 2152528 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.27 0.34 0.12 274 3 0.19 0.05 440 5 121 "HapMap,doubleHit,freq,cluster" moderately conservative 107730 2p24-p23 apolipoprotein B (including Ag(x) antigen) 2074 rs1367117 APOB 338 2 21175552 NM_000384 NP_000375 A/G T98I plus 2152528 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.34 0.12 274 3 0.19 0.05 440 5 121 "HapMap,doubleHit,freq,cluster" moderately conservative 107730 2p24-p23 apolipoprotein B (including Ag(x) antigen) 2075 rs1367117 APOB 338 2 21175552 NM_000384 NP_000375 A/G T98I plus 12675269 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.27 0.34 0.12 274 3 0.19 0.05 440 5 121 "HapMap,doubleHit,freq,cluster" moderately conservative 107730 2p24-p23 apolipoprotein B (including Ag(x) antigen) 2076 rs1372085 ADPRTL1 143 13 23906588 NM_006437 NP_006428 C/T I1564T minus 2159221 1303 SEQUENOM CEPH CEPH (92) 92 0.15 0.15 0 92 1 121 "by doubleHit,freq,cluster" moderately conservative 607519 13q11 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1 2077 rs1377210 AGXT2L1 64850 4 110031720 NM_031279 NP_112569 C/T S185P minus 2166131 1303 SEQUENOM CEPH CEPH (92) 92 0.15 0.15 0 92 1 0.47 0 1490 1 108 "by doubleHit,freq,cluster" Probably damaging 2.131 13 Tolerant 0.22 2.77 36 moderately conservative 4q25 alanine-glyoxylate aminotransferase 2-like 1 2078 rs1395388 TGM4 7047 3 44923678 NM_003241 NP_003232 C/G E437Q minus 2190904 1303 SEQUENOM CEPH CEPH (92) 92 0.06 0.06 0 92 1 111 by freq Tolerant 0.64 2.78 17 conservative 600585 3p22-p21.33 transglutaminase 4 (prostate) 2079 rs1397706 LY75 4065 2 160554512 NM_002349 NP_002340 A/G D692N minus 2194121 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.07 0.08 0.01 284 4 0.23 0.11 98 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.031 5 Borderline 0.11 2.79 22 conservative 604524 2q24 lymphocyte antigen 75 2080 rs1397706 LY75 4065 2 160554512 NM_002349 NP_002340 A/G D692N minus 2194121 902 AFFY Caucasian 24 0.08 0.08 0.01 284 4 0.23 0.11 98 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.031 5 Borderline 0.11 2.79 22 conservative 604524 2q24 lymphocyte antigen 75 2081 rs1397706 LY75 4065 2 160554512 NM_002349 NP_002340 A/G D692N minus 2194121 1303 SEQUENOM CEPH CEPH (92) 92 0.09 0.08 0.01 284 4 0.23 0.11 98 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.031 5 Borderline 0.11 2.79 22 conservative 604524 2q24 lymphocyte antigen 75 2082 rs1397706 LY75 4065 2 160554512 NM_002349 NP_002340 A/G D692N minus 23898403 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0.01 284 4 0.23 0.11 98 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.031 5 Borderline 0.11 2.79 22 conservative 604524 2q24 lymphocyte antigen 75 2083 rs1402467 SULT1C2 27233 2 108453326 NM_006588 NP_006579 C/G D5E plus 2200602 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.19 0.19 0 212 2 0.5 0 120 1 120 "HapMap,doubleHit,submitter,freq,cluster" conservative 608357 2q11.1-q11.2 "sulfotransferase family, cytosolic, 1C, member 2" 2084 rs1402467 SULT1C2 27233 2 108453326 NM_006588 NP_006579 C/G D5E plus 2200602 1303 SEQUENOM CEPH CEPH (92) 92 0.19 0.19 0 212 2 0.5 0 120 1 120 "HapMap,doubleHit,submitter,freq,cluster" conservative 608357 2q11.1-q11.2 "sulfotransferase family, cytosolic, 1C, member 2" 2085 rs1409986 PTGER3 5733 1 71043519 NM_000957 NP_000948 C/T S375P minus 2210718 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.1 0.12 0.02 176 2 121 by freq moderately conservative 176806 1p31.2 prostaglandin E receptor 3 (subtype EP3) 2086 rs1409986 PTGER3 5733 1 71043519 NM_000957 NP_000948 C/T S375P minus 2210718 1303 SEQUENOM CEPH CEPH (92) 92 0.13 0.12 0.02 176 2 121 by freq moderately conservative 176806 1p31.2 prostaglandin E receptor 3 (subtype EP3) 2087 rs1422795 ADAM19 8728 5 156868942 NM_033274 NP_150377 A/G S284G minus 2228226 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 83 0.35 0.27 0.07 263 4 0.17 0.08 1790 6 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.38 2.8 21 moderately conservative 603640 5q32-q33 a disintegrin and metalloproteinase domain 19 (meltrin beta) 2088 rs1422795 ADAM19 8728 5 156868942 NM_033274 NP_150377 A/G S284G minus 2228226 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.27 0.07 263 4 0.17 0.08 1790 6 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.38 2.8 21 moderately conservative 603640 5q32-q33 a disintegrin and metalloproteinase domain 19 (meltrin beta) 2089 rs1422795 ADAM19 8728 5 156868942 NM_033274 NP_150377 A/G S284G minus 15357301 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.3 0.27 0.07 263 4 0.17 0.08 1790 6 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.38 2.8 21 moderately conservative 603640 5q32-q33 a disintegrin and metalloproteinase domain 19 (meltrin beta) 2090 rs1422795 ADAM19 8728 5 156868942 NM_033274 NP_150377 A/G S284G minus 23475698 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.27 0.07 263 4 0.17 0.08 1790 6 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.38 2.8 21 moderately conservative 603640 5q32-q33 a disintegrin and metalloproteinase domain 19 (meltrin beta) 2091 rs1426310 DSG1 1828 18 27152292 NM_001942 NP_001933 A/G M11V plus 2233235 1303 SEQUENOM CEPH CEPH (92) 92 0.35 0.35 0 92 1 88 "by doubleHit,freq" Benign 0.717 8 conservative 125670 18q12.1 desmoglein 1 2092 rs1428180 ZNF534 147658 19 57632983 XM_496320 XP_496320 C/T F166S plus 24204270 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.24 0.05 94 2 123 "by submitter,freq,cluster" Tolerant 0.46 2.76 34 radical 19q13.41 zinc finger protein 534 2093 rs1429077 ZC3HDC7 29066 16 11783704 NM_014153 NP_054872 A/G N3S minus 2237299 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.03 0.03 0.01 168 2 0.2 0 46 1 123 "HapMap,freq,cluster" conservative 16p13-p12 zinc finger CCCH type domain containing 7 2094 rs1429077 ZC3HDC7 29066 16 11783704 NM_014153 NP_054872 A/G N3S minus 23528438 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.03 0.01 168 2 0.2 0 46 1 123 "HapMap,freq,cluster" conservative 16p13-p12 zinc finger CCCH type domain containing 7 2095 rs1429148 PECR 55825 2 216749185 NM_018441 NP_060911 C/T E149K plus 2237380 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.08 0.07 0.01 168 2 0.32 0.02 1560 3 123 "HapMap,submitter,freq,cluster" Potentially damaging 1.409 8 Tolerant 0.45 2.8 24 moderately conservative 605843 2q35 peroxisomal trans-2-enoyl-CoA reductase 2096 rs1429148 PECR 55825 2 216749185 NM_018441 NP_060911 C/T E149K plus 23292110 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.07 0.01 168 2 0.32 0.02 1560 3 123 "HapMap,submitter,freq,cluster" Potentially damaging 1.409 8 Tolerant 0.45 2.8 24 moderately conservative 605843 2q35 peroxisomal trans-2-enoyl-CoA reductase 2097 rs1432862 FAT2 2196 5 150926966 NM_001447 NP_001438 A/G R574C plus 2242324 1303 SEQUENOM CEPH CEPH (92) 92 0.33 0.33 0 92 1 119 "by doubleHit,submitter,freq,cluster" Intolerant 0.04 2.88 15 radical 604269 5q32-q33 FAT tumor suppressor homolog 2 (Drosophila) 2098 rs1455555 SERPINB5 5268 18 59321762 NM_002639 NP_002630 C/T I319V minus 2272884 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.47 0.48 0.02 130 2 0.46 0 1562 2 111 "by submitter,freq,cluster" Tolerant 0.99 2.76 55 conservative 154790 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 5" 2099 rs1455555 SERPINB5 5268 18 59321762 NM_002639 NP_002630 C/T I319V minus 2272884 1303 SEQUENOM CEPH CEPH (92) 46 0.5 0.48 0.02 130 2 0.46 0 1562 2 111 "by submitter,freq,cluster" Tolerant 0.99 2.76 55 conservative 154790 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 5" 2100 rs1465789 ZNF132 7691 19 63637868 NM_003433 NP_003424 C/T P252L minus 2286110 760 TSC-CSHL CEL_CAUCASIAN CELERA Caucasians (30) 60 0.4 0.42 0.02 674 6 0.26 0.03 1708 5 123 "HapMap,doubleHit,freq,cluster" Tolerant 0.71 2.76 34 moderately conservative 604074 19q13.4 zinc finger protein 132 (clone pHZ-12) 2101 rs1465789 ZNF132 7691 19 63637868 NM_003433 NP_003424 C/T P252L minus 2286110 761 TSC-CSHL CEL_CAUCASIAN_CEPH CELERA CEPH Caucasians (661) 322 0.44 0.42 0.02 674 6 0.26 0.03 1708 5 123 "HapMap,doubleHit,freq,cluster" Tolerant 0.71 2.76 34 moderately conservative 604074 19q13.4 zinc finger protein 132 (clone pHZ-12) 2102 rs1465789 ZNF132 7691 19 63637868 NM_003433 NP_003424 C/T P252L minus 2286110 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.43 0.42 0.02 674 6 0.26 0.03 1708 5 123 "HapMap,doubleHit,freq,cluster" Tolerant 0.71 2.76 34 moderately conservative 604074 19q13.4 zinc finger protein 132 (clone pHZ-12) 2103 rs1465789 ZNF132 7691 19 63637868 NM_003433 NP_003424 C/T P252L minus 2286110 1303 SEQUENOM CEPH CEPH (92) 92 0.39 0.42 0.02 674 6 0.26 0.03 1708 5 123 "HapMap,doubleHit,freq,cluster" Tolerant 0.71 2.76 34 moderately conservative 604074 19q13.4 zinc finger protein 132 (clone pHZ-12) 2104 rs1465789 ZNF132 7691 19 63637868 NM_003433 NP_003424 C/T P252L minus 3176391 619 WICVAR MITOGPOP6 CORIELL Mixed 32 0.41 0.42 0.02 674 6 0.26 0.03 1708 5 123 "HapMap,doubleHit,freq,cluster" Tolerant 0.71 2.76 34 moderately conservative 604074 19q13.4 zinc finger protein 132 (clone pHZ-12) 2105 rs1465789 ZNF132 7691 19 63637868 NM_003433 NP_003424 C/T P252L minus 24689523 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.42 0.02 674 6 0.26 0.03 1708 5 123 "HapMap,doubleHit,freq,cluster" Tolerant 0.71 2.76 34 moderately conservative 604074 19q13.4 zinc finger protein 132 (clone pHZ-12) 2106 rs1467558 CD44 960 11 35186249 NM_000610 NP_000601 A/G I479T minus 2288053 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.18 0.21 0.08 284 4 0.08 0 48 1 123 "HapMap,submitter,freq,cluster" Benign 0.332 6 moderately conservative 107269 11p13 CD44 antigen (homing function and Indian blood group system) 2107 rs1467558 CD44 960 11 35186249 NM_000610 NP_000601 A/G I479T minus 2288053 902 AFFY Caucasian 24 0.13 0.21 0.08 284 4 0.08 0 48 1 123 "HapMap,submitter,freq,cluster" Benign 0.332 6 moderately conservative 107269 11p13 CD44 antigen (homing function and Indian blood group system) 2108 rs1467558 CD44 960 11 35186249 NM_000610 NP_000601 A/G I479T minus 2288053 1303 SEQUENOM CEPH CEPH (92) 92 0.3 0.21 0.08 284 4 0.08 0 48 1 123 "HapMap,submitter,freq,cluster" Benign 0.332 6 moderately conservative 107269 11p13 CD44 antigen (homing function and Indian blood group system) 2109 rs1467558 CD44 960 11 35186249 NM_000610 NP_000601 A/G I479T minus 24544256 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.21 0.08 284 4 0.08 0 48 1 123 "HapMap,submitter,freq,cluster" Benign 0.332 6 moderately conservative 107269 11p13 CD44 antigen (homing function and Indian blood group system) 2110 rs1469087 ZNF135 7694 19 63264791 NM_003436 NP_003427 C/T G22D minus 2289734 782 TSC-CSHL WICGR6_CAUCASIAN_POOLED WICGR Caucasian (48) 96 0.18 0.16 0.02 236 3 0.35 0.25 154 3 123 "by doubleHit,freq,cluster" Probably damaging 2.012 9 moderately conservative 604077 19q13.4 zinc finger protein 135 (clone pHZ-17) 2111 rs1469087 ZNF135 7694 19 63264791 NM_003436 NP_003427 C/T G22D minus 2289734 1303 SEQUENOM CEPH CEPH (92) 92 0.14 0.16 0.02 236 3 0.35 0.25 154 3 123 "by doubleHit,freq,cluster" Probably damaging 2.012 9 moderately conservative 604077 19q13.4 zinc finger protein 135 (clone pHZ-17) 2112 rs1469087 ZNF135 7694 19 63264791 NM_003436 NP_003427 C/T G22D minus 24076476 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.16 0.02 236 3 0.35 0.25 154 3 123 "by doubleHit,freq,cluster" Probably damaging 2.012 9 moderately conservative 604077 19q13.4 zinc finger protein 135 (clone pHZ-17) 2113 rs1470414 PASK 23178 2 241797486 NM_015148 NP_055963 A/G V250I minus 2291210 782 TSC-CSHL WICGR6_CAUCASIAN_POOLED WICGR Caucasian (48) 96 0.44 0.4 0.06 236 3 0.17 0.14 178 3 123 "by doubleHit,submitter,freq,cluster" conservative 607505 2q37.3 PAS domain containing serine/threonine kinase 2114 rs1470414 PASK 23178 2 241797486 NM_015148 NP_055963 A/G V250I minus 2291210 1303 SEQUENOM CEPH CEPH (92) 92 0.34 0.4 0.06 236 3 0.17 0.14 178 3 123 "by doubleHit,submitter,freq,cluster" conservative 607505 2q37.3 PAS domain containing serine/threonine kinase 2115 rs1470414 PASK 23178 2 241797486 NM_015148 NP_055963 A/G V250I minus 24345045 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.4 0.06 236 3 0.17 0.14 178 3 123 "by doubleHit,submitter,freq,cluster" conservative 607505 2q37.3 PAS domain containing serine/threonine kinase 2116 rs1476387 SMPD2 6610 6 109871228 NM_003080 NP_003071 G/T R265S plus 2297824 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.43 0.35 0.09 196 3 0.23 0.27 40 2 121 "by doubleHit,freq,cluster" moderately radical 603498 6q21 "sphingomyelin phosphodiesterase 2, neutral membrane (neutral sphingomyelinase)" 2117 rs1476387 SMPD2 6610 6 109871228 NM_003080 NP_003071 G/T R265S plus 2297824 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 90 0.42 0.35 0.09 196 3 0.23 0.27 40 2 121 "by doubleHit,freq,cluster" moderately radical 603498 6q21 "sphingomyelin phosphodiesterase 2, neutral membrane (neutral sphingomyelinase)" 2118 rs1476387 SMPD2 6610 6 109871228 NM_003080 NP_003071 G/T R265S plus 2297824 1303 SEQUENOM CEPH CEPH (92) 92 0.27 0.35 0.09 196 3 0.23 0.27 40 2 121 "by doubleHit,freq,cluster" moderately radical 603498 6q21 "sphingomyelin phosphodiesterase 2, neutral membrane (neutral sphingomyelinase)" 2119 rs1476703 ASK 10926 7 87159059 NM_006716 NP_006707 A/T Y112N minus 2298167 1303 SEQUENOM CEPH CEPH (92) 92 0.4 0.4 0 92 1 88 by freq moderately radical 604281 7q21.3 activator of S phase kinase 2120 rs1494555 IL7R 3575 5 35906947 NM_002185 NP_002176 C/T V138I minus 2322286 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 7 0.5 0.26 0.09 543 8 0.42 0.11 1814 10 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.089 6 Tolerant 0.47 2.79 56 conservative 146661 5p13 interleukin 7 receptor 2121 rs1494555 IL7R 3575 5 35906947 NM_002185 NP_002176 C/T V138I minus 2322286 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.26 0.26 0.09 543 8 0.42 0.11 1814 10 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.089 6 Tolerant 0.47 2.79 56 conservative 146661 5p13 interleukin 7 receptor 2122 rs1494555 IL7R 3575 5 35906947 NM_002185 NP_002176 C/T V138I minus 3172789 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 54 0.44 0.26 0.09 543 8 0.42 0.11 1814 10 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.089 6 Tolerant 0.47 2.79 56 conservative 146661 5p13 interleukin 7 receptor 2123 rs1494555 IL7R 3575 5 35906947 NM_002185 NP_002176 C/T V138I minus 12675491 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.32 0.26 0.09 543 8 0.42 0.11 1814 10 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.089 6 Tolerant 0.47 2.79 56 conservative 146661 5p13 interleukin 7 receptor 2124 rs1494555 IL7R 3575 5 35906947 NM_002185 NP_002176 C/T V138I minus 16336709 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 44 0.25 0.26 0.09 543 8 0.42 0.11 1814 10 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.089 6 Tolerant 0.47 2.79 56 conservative 146661 5p13 interleukin 7 receptor 2125 rs1494555 IL7R 3575 5 35906947 NM_002185 NP_002176 C/T V138I minus 22366715 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.25 0.26 0.09 543 8 0.42 0.11 1814 10 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.089 6 Tolerant 0.47 2.79 56 conservative 146661 5p13 interleukin 7 receptor 2126 rs1494555 IL7R 3575 5 35906947 NM_002185 NP_002176 C/T V138I minus 22366715 1303 SEQUENOM CEPH CEPH (92) 92 0.13 0.26 0.09 543 8 0.42 0.11 1814 10 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.089 6 Tolerant 0.47 2.79 56 conservative 146661 5p13 interleukin 7 receptor 2127 rs1494555 IL7R 3575 5 35906947 NM_002185 NP_002176 C/T V138I minus 24186977 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.26 0.09 543 8 0.42 0.11 1814 10 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.089 6 Tolerant 0.47 2.79 56 conservative 146661 5p13 interleukin 7 receptor 2128 rs1494558 IL7R 3575 5 35896825 NM_002185 NP_002176 A/G I66T minus 2322289 1303 SEQUENOM CEPH CEPH (92) 92 0.36 0.32 0.09 140 2 0.24 0.06 142 3 123 "by doubleHit,freq,cluster" Possibly damaging 1.711 6 moderately conservative 146661 5p13 interleukin 7 receptor 2129 rs1494558 IL7R 3575 5 35896825 NM_002185 NP_002176 A/G I66T minus 24186943 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.32 0.09 140 2 0.24 0.06 142 3 123 "by doubleHit,freq,cluster" Possibly damaging 1.711 6 moderately conservative 146661 5p13 interleukin 7 receptor 2130 rs1494961 HEL308 113510 4 84731659 NM_133636 NP_598375 C/T V306I plus 2322942 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.48 0.46 0.03 260 3 0.39 0.03 1580 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.711 5 conservative 606769 4q21.3 DNA helicase HEL308 2131 rs1494961 HEL308 113510 4 84731659 NM_133636 NP_598375 C/T V306I plus 2322942 1303 SEQUENOM CEPH CEPH (92) 92 0.43 0.46 0.03 260 3 0.39 0.03 1580 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.711 5 conservative 606769 4q21.3 DNA helicase HEL308 2132 rs1494961 HEL308 113510 4 84731659 NM_133636 NP_598375 C/T V306I plus 24236342 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.46 0.03 260 3 0.39 0.03 1580 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.711 5 conservative 606769 4q21.3 DNA helicase HEL308 2133 rs1503185 PTPRJ 5795 11 48103198 NM_002843 NP_002834 C/T R326Q minus 2334363 1303 SEQUENOM CEPH CEPH (92) 92 0.28 0.24 0.06 190 3 0.36 0.1 94 2 123 "by doubleHit,freq,cluster" Tolerant 0.5 2.79 21 conservative 600925 11p11.2 "protein tyrosine phosphatase, receptor type, J" 2134 rs1503185 PTPRJ 5795 11 48103198 NM_002843 NP_002834 C/T R326Q minus 3176749 619 WICVAR MITOGPOP6 CORIELL Mixed 50 0.22 0.24 0.06 190 3 0.36 0.1 94 2 123 "by doubleHit,freq,cluster" Tolerant 0.5 2.79 21 conservative 600925 11p11.2 "protein tyrosine phosphatase, receptor type, J" 2135 rs1503185 PTPRJ 5795 11 48103198 NM_002843 NP_002834 C/T R326Q minus 23783912 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.24 0.06 190 3 0.36 0.1 94 2 123 "by doubleHit,freq,cluster" Tolerant 0.5 2.79 21 conservative 600925 11p11.2 "protein tyrosine phosphatase, receptor type, J" 2136 rs1521808 ABCB11 8647 2 169609235 NM_003742 NP_003733 A/G E1186K minus 2359844 782 TSC-CSHL WICGR6_CAUCASIAN_POOLED WICGR Caucasian (48) 96 0.01 0.01 0 96 1 0.01 0 494 1 120 "by cluster,freq" Potentially damaging 1.473 10 Intolerant 0.05 2.86 31 moderately conservative 603201 2q24 "ATP-binding cassette, sub-family B (MDR/TAP), member 11" 2137 rs1527482 SEMA3C 10512 7 80072181 NM_006379 NP_006370 A/G V337M minus 2367564 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.02 0 92 1 0.1 0.03 994 3 123 "by cluster,freq" Potentially damaging 1.285 13 Intolerant 0 2.75 48 conservative 602645 7q21-q31 "sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C" 2138 rs1532918 TMF1 7110 3 69165398 NM_007114 NP_009045 C/G D798H minus 2373936 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.13 0.17 0.04 260 3 0.05 0 40 1 123 "HapMap,submitter,freq" Probably damaging 2.064 6 Potentially intolerant 0.06 2.76 10 moderately conservative 601126 3p21-p12 TATA element modulatory factor 1 2139 rs1532918 TMF1 7110 3 69165398 NM_007114 NP_009045 C/G D798H minus 2373936 1303 SEQUENOM CEPH CEPH (92) 92 0.19 0.17 0.04 260 3 0.05 0 40 1 123 "HapMap,submitter,freq" Probably damaging 2.064 6 Potentially intolerant 0.06 2.76 10 moderately conservative 601126 3p21-p12 TATA element modulatory factor 1 2140 rs1532918 TMF1 7110 3 69165398 NM_007114 NP_009045 C/G D798H minus 24329072 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.17 0.04 260 3 0.05 0 40 1 123 "HapMap,submitter,freq" Probably damaging 2.064 6 Potentially intolerant 0.06 2.76 10 moderately conservative 601126 3p21-p12 TATA element modulatory factor 1 2141 rs1536690 ZNF169 169841 9 94134865 NM_194320 NP_919301 A/G P59L minus 2378115 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.14 0.14 0.01 168 2 0.18 0.14 94 2 123 "HapMap,doubleHit,freq,cluster" Probably damaging 2.19 7 Borderline 0.11 2.79 28 moderately conservative 603404 9q22.32 zinc finger protein 169 2142 rs1536690 ZNF169 169841 9 94134865 NM_194320 NP_919301 A/G P59L minus 23726710 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.14 0.01 168 2 0.18 0.14 94 2 123 "HapMap,doubleHit,freq,cluster" Probably damaging 2.19 7 Borderline 0.11 2.79 28 moderately conservative 603404 9q22.32 zinc finger protein 169 2143 rs1537232 DNAH8 1769 6 39059976 NM_001371 NP_001362 C/T T4106M plus 2378696 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.15 0.17 0.04 132 2 0.36 0.06 1658 4 123 "by doubleHit,submitter,freq,cluster" Probably damaging 2.05 8 Potentially intolerant 0.09 2.75 17 moderately conservative 603337 6p21.31-p21.1 "dynein, axonemal, heavy polypeptide 8" 2144 rs1537232 DNAH8 1769 6 39059976 NM_001371 NP_001362 C/T T4106M plus 23996349 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.17 0.04 132 2 0.36 0.06 1658 4 123 "by doubleHit,submitter,freq,cluster" Probably damaging 2.05 8 Potentially intolerant 0.09 2.75 17 moderately conservative 603337 6p21.31-p21.1 "dynein, axonemal, heavy polypeptide 8" 2145 rs1538660 IKBKAP 8518 9 108721380 NM_003640 NP_003631 C/T P1158L minus 2380235 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.13 0.17 0.08 314 4 0.32 0.1 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.879 7 Tolerant 0.23 2.93 14 moderately conservative 603722 9q31 "inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein" 2146 rs1538660 IKBKAP 8518 9 108721380 NM_003640 NP_003631 C/T P1158L minus 2380235 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.17 0.08 314 4 0.32 0.1 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.879 7 Tolerant 0.23 2.93 14 moderately conservative 603722 9q31 "inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein" 2147 rs1538660 IKBKAP 8518 9 108721380 NM_003640 NP_003631 C/T P1158L minus 3177973 619 WICVAR MITOGPOP6 CORIELL Mixed 54 0.31 0.17 0.08 314 4 0.32 0.1 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.879 7 Tolerant 0.23 2.93 14 moderately conservative 603722 9q31 "inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein" 2148 rs1538660 IKBKAP 8518 9 108721380 NM_003640 NP_003631 C/T P1158L minus 23784406 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.17 0.08 314 4 0.32 0.1 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.879 7 Tolerant 0.23 2.93 14 moderately conservative 603722 9q31 "inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein" 2149 rs1541314 MUC5B 4587 11 1220099 XM_039877 XP_039877 A/G G1705S plus 2383163 1303 SEQUENOM CEPH CEPH (92) 92 0.06 0.06 0 92 1 101 by freq moderately conservative 600770 11p15 "mucin 5, subtype B, tracheobronchial" 2150 rs1545133 POLR1B 84172 2 113025704 NM_019014 NP_061887 C/T S295L plus 2387383 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.4 0.4 0.04 296 3 0.33 0.17 126 2 88 "HapMap,doubleHit,submitter,freq" Borderline 1.084 5 Tolerant 0.57 2.84 23 moderately radical 2q13 "polymerase (RNA) I polypeptide B, 128kDa" 2151 rs1545133 POLR1B 84172 2 113025704 NM_019014 NP_061887 C/T S295L plus 2387383 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.37 0.4 0.04 296 3 0.33 0.17 126 2 88 "HapMap,doubleHit,submitter,freq" Borderline 1.084 5 Tolerant 0.57 2.84 23 moderately radical 2q13 "polymerase (RNA) I polypeptide B, 128kDa" 2152 rs1545133 POLR1B 84172 2 113025704 NM_019014 NP_061887 C/T S295L plus 2387383 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.4 0.04 296 3 0.33 0.17 126 2 88 "HapMap,doubleHit,submitter,freq" Borderline 1.084 5 Tolerant 0.57 2.84 23 moderately radical 2q13 "polymerase (RNA) I polypeptide B, 128kDa" 2153 rs1547742 SIPA1L2 57568 1 228874776 NM_020808 NP_065859 C/T S1179L minus 2390318 1303 SEQUENOM CEPH CEPH (92) 92 0.13 0.13 0 92 1 111 by freq Possibly damaging 1.56 15 moderately radical 1q42.2 signal-induced proliferation-associated 1 like 2 2154 rs1551886 ALDH3B2 222 11 67187338 NM_000695 NP_000686 C/T H361R plus 2394818 1303 SEQUENOM CEPH CEPH (92) 92 0.12 0.1 0.04 142 2 0.05 0 1488 1 121 "by cluster,freq" Possibly damaging 1.979 21 conservative 601917 11q13 "aldehyde dehydrogenase 3 family, member B2" 2155 rs1551886 ALDH3B2 222 11 67187338 NM_000695 NP_000686 C/T H361R plus 3172760 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 50 0.06 0.1 0.04 142 2 0.05 0 1488 1 121 "by cluster,freq" Possibly damaging 1.979 21 conservative 601917 11q13 "aldehyde dehydrogenase 3 family, member B2" 2156 rs1551888 ALDH3B2 222 11 67190445 NM_000695 NP_000686 C/T S52N plus 2394820 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.15 0.02 144 2 121 "by cluster,freq" Possibly damaging 1.838 21 conservative 601917 11q13 "aldehyde dehydrogenase 3 family, member B2" 2157 rs1551888 ALDH3B2 222 11 67190445 NM_000695 NP_000686 C/T S52N plus 3172759 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 52 0.13 0.15 0.02 144 2 121 "by cluster,freq" Possibly damaging 1.838 21 conservative 601917 11q13 "aldehyde dehydrogenase 3 family, member B2" 2158 rs1554005 ACOXL 55289 2 111315189 NM_018308 NP_060778 C/T T78M plus 24357304 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.21 0 48 1 0.15 0.03 94 2 123 "by doubleHit,submitter,freq,cluster" Borderline 0.15 2.8 13 moderately conservative 2q13 acyl-Coenzyme A oxidase-like 2159 rs1555498 IL20RA 53832 6 137367540 NM_014432 NP_055247 C/T V259I plus 2398734 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.02 0.02 0 120 1 0.41 0 46 1 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.88 2.81 13 conservative 605620 6q22.33-q23.1 "interleukin 20 receptor, alpha" 2160 rs1558876 KIAA1001 22901 17 63876286 NM_014960 NP_055775 C/G T236S plus 2402353 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.41 0.42 0.02 168 2 0.16 0.01 1574 3 123 "HapMap,doubleHit,freq,cluster" Tolerant 0.61 2.76 26 moderately conservative 17q24.3 Arylsulfatase G 2161 rs1558876 KIAA1001 22901 17 63876286 NM_014960 NP_055775 C/G T236S plus 24588040 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.42 0.02 168 2 0.16 0.01 1574 3 123 "HapMap,doubleHit,freq,cluster" Tolerant 0.61 2.76 26 moderately conservative 17q24.3 Arylsulfatase G 2162 rs1558878 KIAA1001 22901 17 63876399 NM_014960 NP_055775 C/T W274R plus 2402355 1303 SEQUENOM CEPH CEPH (92) 92 0.32 0.32 0 92 1 0.24 0 1498 1 120 "by doubleHit,freq,cluster" Tolerant 0.76 2.76 26 moderately radical 17q24.3 Arylsulfatase G 2163 rs1566734 PTPRJ 5795 11 48101951 NM_002843 NP_002834 G/T Q276P minus 2410866 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.14 0.11 0.07 260 3 0.19 0.03 1586 3 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.33 2.82 19 moderately conservative 600925 11p11.2 "protein tyrosine phosphatase, receptor type, J" 2164 rs1566734 PTPRJ 5795 11 48101951 NM_002843 NP_002834 G/T Q276P minus 2410866 1303 SEQUENOM CEPH CEPH (92) 92 0.03 0.11 0.07 260 3 0.19 0.03 1586 3 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.33 2.82 19 moderately conservative 600925 11p11.2 "protein tyrosine phosphatase, receptor type, J" 2165 rs1566734 PTPRJ 5795 11 48101951 NM_002843 NP_002834 G/T Q276P minus 24208003 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.11 0.07 260 3 0.19 0.03 1586 3 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.33 2.82 19 moderately conservative 600925 11p11.2 "protein tyrosine phosphatase, receptor type, J" 2166 rs1572983 BAAT 570 9 101213183 NM_001701 NP_001692 C/T R20Q plus 2417719 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.35 0.29 0.08 260 3 0.4 0.01 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.107 8 Tolerant 0.55 2.84 32 conservative 602938 9q22.3 bile acid Coenzyme A: amino acid N-acyltransferase (glycine N-choloyltransferase) 2167 rs1572983 BAAT 570 9 101213183 NM_001701 NP_001692 C/T R20Q plus 2417719 1303 SEQUENOM CEPH CEPH (92) 92 0.21 0.29 0.08 260 3 0.4 0.01 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.107 8 Tolerant 0.55 2.84 32 conservative 602938 9q22.3 bile acid Coenzyme A: amino acid N-acyltransferase (glycine N-choloyltransferase) 2168 rs1572983 BAAT 570 9 101213183 NM_001701 NP_001692 C/T R20Q plus 23517997 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.29 0.08 260 3 0.4 0.01 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.107 8 Tolerant 0.55 2.84 32 conservative 602938 9q22.3 bile acid Coenzyme A: amino acid N-acyltransferase (glycine N-choloyltransferase) 2169 rs1573496 ADH7 131 4 100706847 NM_000673 NP_000664 C/G G80A plus 2418264 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.21 0.15 0.03 106 2 88 by freq Probably damaging 2.008 152 Intolerant 0 2.81 399 moderately conservative 600086 4q23-q24 "alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide" 2170 rs1573496 ADH7 131 4 100706847 NM_000673 NP_000664 C/G G80A plus 2418264 1303 SEQUENOM CEPH CEPH (92) 92 0.14 0.15 0.03 106 2 88 by freq Probably damaging 2.008 152 Intolerant 0 2.81 399 moderately conservative 600086 4q23-q24 "alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide" 2171 rs1599882 GZMM 3004 19 500678 NM_005317 NP_005308 C/T R221G minus 2290434 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.01 0.01 0 212 2 121 HapMap moderately radical 600311 19p13.3 granzyme M (lymphocyte met-ase 1) 2172 rs1599882 GZMM 3004 19 500678 NM_005317 NP_005308 C/T R221G minus 2290434 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.01 0 212 2 121 HapMap moderately radical 600311 19p13.3 granzyme M (lymphocyte met-ase 1) 2173 rs1611775 KCNA7 3743 19 54265937 NM_031886 NP_114092 C/G P189R minus 16790996 1303 SEQUENOM CEPH CEPH (92) 92 0.15 0.15 0 92 1 121 "by doubleHit,freq,cluster" Benign 0.012 87 Tolerant 0.41 3.16 95 moderately radical 176268 19q13.3 "potassium voltage-gated channel, shaker-related subfamily, member 7" 2174 rs1613662 GP6 51206 19 60228407 NM_016363 NP_057447 A/G P219S plus 12471451 1303 SEQUENOM CEPH CEPH (92) 92 0.25 0.22 0.05 140 2 0.15 0 46 1 123 "by doubleHit,freq,cluster" moderately conservative 605546 19q13.4 glycoprotein VI (platelet) 2175 rs1613662 GP6 51206 19 60228407 NM_016363 NP_057447 A/G P219S plus 24694158 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.22 0.05 140 2 0.15 0 46 1 123 "by doubleHit,freq,cluster" moderately conservative 605546 19q13.4 glycoprotein VI (platelet) 2176 rs1619896 ATAD3A 55210 1 1537833 NM_018188 NP_060658 C/T S101N minus 2435682 1303 SEQUENOM CEPH CEPH (92) 92 0.3 0.3 0 92 1 89 by freq Potentially damaging 1.266 6 conservative 1p36.33 "ATPase family, AAA domain containing 3A" 2177 rs1644731 RDH8 50700 19 9992999 NM_015725 NP_056540 A/G M202T minus 3289013 1303 SEQUENOM CEPH CEPH (92) 92 0.3 0.3 0 92 1 121 "by doubleHit,freq,cluster" Benign 0.628 7 Tolerant 0.56 2.89 17 moderately conservative 608575 19p13.2-p13.3 retinol dehydrogenase 8 (all-trans) 2178 rs1648348 SLC27A2 11001 15 48262058 NM_003645 NP_003636 A/C K48Q plus 2469591 1303 SEQUENOM CEPH CEPH (92) 92 0.49 0.49 0 92 1 121 "by doubleHit,freq,cluster" Benign 0.046 16 moderately conservative 603247 15q21.2 "solute carrier family 27 (fatty acid transporter), member 2" 2179 rs1654413 GP6 51206 19 60218171 NM_016363 NP_057447 A/T L317Q plus 2477198 1303 SEQUENOM CEPH CEPH (92) 92 0.27 0.23 0.09 136 2 0.26 0.08 92 2 123 "by doubleHit,freq,cluster" moderately radical 605546 19q13.4 glycoprotein VI (platelet) 2180 rs1654413 GP6 51206 19 60218171 NM_016363 NP_057447 A/T L317Q plus 23778688 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.14 0.23 0.09 136 2 0.26 0.08 92 2 123 "by doubleHit,freq,cluster" moderately radical 605546 19q13.4 glycoprotein VI (platelet) 2181 rs1654416 GP6 51206 19 60221847 NM_016363 NP_057447 C/T E237K plus 2477201 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.19 0.17 0.02 258 3 0.21 0.03 1554 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 605546 19q13.4 glycoprotein VI (platelet) 2182 rs1654416 GP6 51206 19 60221847 NM_016363 NP_057447 C/T E237K plus 2477201 1303 SEQUENOM CEPH CEPH (92) 92 0.15 0.17 0.02 258 3 0.21 0.03 1554 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 605546 19q13.4 glycoprotein VI (platelet) 2183 rs1654416 GP6 51206 19 60221847 NM_016363 NP_057447 C/T E237K plus 23778720 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.17 0.02 258 3 0.21 0.03 1554 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 605546 19q13.4 glycoprotein VI (platelet) 2184 rs1656922 KNG1 3827 3 187925720 NM_000893 NP_000884 C/T M178T plus 7985061 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 42 0.38 0.41 0.03 134 2 0.45 0.01 142 2 121 "by doubleHit,freq,cluster" Potentially damaging 1.361 23 Tolerant 0.59 2.84 31 moderately conservative 228960 3q27 kininogen 1 2185 rs1656922 KNG1 3827 3 187925720 NM_000893 NP_000884 C/T M178T plus 7985061 1303 SEQUENOM CEPH CEPH (92) 92 0.43 0.41 0.03 134 2 0.45 0.01 142 2 121 "by doubleHit,freq,cluster" Potentially damaging 1.361 23 Tolerant 0.59 2.84 31 moderately conservative 228960 3q27 kininogen 1 2186 rs1671152 GP6 51206 19 60218157 NM_016363 NP_057447 G/T N322H plus 2497940 1303 SEQUENOM CEPH CEPH (92) 92 0.39 0.3 0.17 140 2 0.24 0 46 1 123 "by doubleHit,freq,cluster" moderately conservative 605546 19q13.4 glycoprotein VI (platelet) 2187 rs1671152 GP6 51206 19 60218157 NM_016363 NP_057447 G/T N322H plus 23778686 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.3 0.17 140 2 0.24 0 46 1 123 "by doubleHit,freq,cluster" moderately conservative 605546 19q13.4 glycoprotein VI (platelet) 2188 rs1673407 PKHD1L1 93035 8 110529664 NM_177531 NP_803875 A/C V1965L minus 3102431 885 TSC-CSHL HapMap-CEPH-30-trios 60 0.5 0.42 0.12 108 2 0.32 0.23 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 607843 8q23.2 polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1 2189 rs1673407 PKHD1L1 93035 8 110529664 NM_177531 NP_803875 A/C V1965L minus 24083720 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.42 0.12 108 2 0.32 0.23 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 607843 8q23.2 polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1 2190 rs1673408 PKHD1L1 93035 8 110524497 NM_177531 NP_803875 G/T R1514S minus 19764146 885 TSC-CSHL HapMap-CEPH-30-trios 60 0.5 0.42 0.12 108 2 0.48 0 92 2 123 "HapMap,submitter,freq,cluster" moderately radical 607843 8q23.2 polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1 2191 rs1673408 PKHD1L1 93035 8 110524497 NM_177531 NP_803875 G/T R1514S minus 23573564 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.42 0.12 108 2 0.48 0 92 2 123 "HapMap,submitter,freq,cluster" moderately radical 607843 8q23.2 polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1 2192 rs1675404 BLVRB 645 19 45656164 NM_000713 NP_000704 C/T A70T plus 2503396 1303 SEQUENOM CEPH CEPH (92) 92 0.05 0.05 0 92 1 89 by freq Potentially damaging 1.413 9 Intolerant 0.03 2.84 14 moderately conservative 600941 19q13.1-q13.2 biliverdin reductase B (flavin reductase (NADPH)) 2193 rs1678160 SP100 6672 2 231159268 NM_003113 NP_003104 A/G M433V plus 9960068 1303 SEQUENOM CEPH CEPH (92) 92 0.24 0.27 0.06 140 2 0.09 0.03 1382 3 123 "by doubleHit,submitter,freq,cluster" conservative 604585 2q37.1 nuclear antigen Sp100 2194 rs1678160 SP100 6672 2 231159268 NM_003113 NP_003104 A/G M433V plus 24330020 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.27 0.06 140 2 0.09 0.03 1382 3 123 "by doubleHit,submitter,freq,cluster" conservative 604585 2q37.1 nuclear antigen Sp100 2195 rs1693482 ADH1C 126 4 100621143 NM_000669 NP_000660 C/T R272Q plus 8819648 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.48 0.48 0 62 1 0.28 0.11 342 4 121 "by cluster,freq" Benign 0.477 162 Intolerant 0.02 2.79 398 conservative 103730 4q21-q23 "alcohol dehydrogenase 1C (class I), gamma polypeptide" 2196 rs1709189 SLC5A8 160728 12 100089986 NM_145913 NP_666018 C/T V193I plus 2544667 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.18 0.19 0.03 168 2 0.39 0.08 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.739 11 conservative 608044 12q23.3 "solute carrier family 5 (iodide transporter), member 8" 2197 rs1709189 SLC5A8 160728 12 100089986 NM_145913 NP_666018 C/T V193I plus 24006574 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.19 0.03 168 2 0.39 0.08 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.739 11 conservative 608044 12q23.3 "solute carrier family 5 (iodide transporter), member 8" 2198 rs1713449 TEP1 7011 14 19911547 NM_007110 NP_009041 C/T V2214I plus 2549690 1303 SEQUENOM CEPH CEPH (92) 92 0.4 0.31 0.09 238 4 0.23 0.05 1936 7 123 "by submitter,freq,cluster" conservative 601686 14q11.2 telomerase-associated protein 1 2199 rs1713449 TEP1 7011 14 19911547 NM_007110 NP_009041 C/T V2214I plus 3172658 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 36 0.31 0.31 0.09 238 4 0.23 0.05 1936 7 123 "by submitter,freq,cluster" conservative 601686 14q11.2 telomerase-associated protein 1 2200 rs1713449 TEP1 7011 14 19911547 NM_007110 NP_009041 C/T V2214I plus 6903954 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.23 0.31 0.09 238 4 0.23 0.05 1936 7 123 "by submitter,freq,cluster" conservative 601686 14q11.2 telomerase-associated protein 1 2201 rs1713449 TEP1 7011 14 19911547 NM_007110 NP_009041 C/T V2214I plus 23814907 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.31 0.09 238 4 0.23 0.05 1936 7 123 "by submitter,freq,cluster" conservative 601686 14q11.2 telomerase-associated protein 1 2202 rs1713456 TEP1 7011 14 19919933 NM_007110 NP_009041 C/T C1468Y plus 2549698 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 24 0.17 0.17 0.03 378 5 0.23 0.14 48 2 120 "HapMap,doubleHit,freq,cluster" radical 601686 14q11.2 telomerase-associated protein 1 2203 rs1713456 TEP1 7011 14 19919933 NM_007110 NP_009041 C/T C1468Y plus 2549698 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 94 0.2 0.17 0.03 378 5 0.23 0.14 48 2 120 "HapMap,doubleHit,freq,cluster" radical 601686 14q11.2 telomerase-associated protein 1 2204 rs1713456 TEP1 7011 14 19919933 NM_007110 NP_009041 C/T C1468Y plus 2549698 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.14 0.17 0.03 378 5 0.23 0.14 48 2 120 "HapMap,doubleHit,freq,cluster" radical 601686 14q11.2 telomerase-associated protein 1 2205 rs1713456 TEP1 7011 14 19919933 NM_007110 NP_009041 C/T C1468Y plus 2549698 1303 SEQUENOM CEPH CEPH (92) 92 0.18 0.17 0.03 378 5 0.23 0.14 48 2 120 "HapMap,doubleHit,freq,cluster" radical 601686 14q11.2 telomerase-associated protein 1 2206 rs1713456 TEP1 7011 14 19919933 NM_007110 NP_009041 C/T C1468Y plus 3172663 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 48 0.15 0.17 0.03 378 5 0.23 0.14 48 2 120 "HapMap,doubleHit,freq,cluster" radical 601686 14q11.2 telomerase-associated protein 1 2207 rs1713457 TEP1 7011 14 19919996 NM_007110 NP_009041 C/G S1447T plus 2549699 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.07 0.03 0.01 258 4 0.14 0 22 1 102 by freq moderately conservative 601686 14q11.2 telomerase-associated protein 1 2208 rs1713457 TEP1 7011 14 19919996 NM_007110 NP_009041 C/G S1447T plus 2549699 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 94 0.03 0.03 0.01 258 4 0.14 0 22 1 102 by freq moderately conservative 601686 14q11.2 telomerase-associated protein 1 2209 rs1713457 TEP1 7011 14 19919996 NM_007110 NP_009041 C/G S1447T plus 2549699 1303 SEQUENOM CEPH CEPH (92) 92 0.03 0.03 0.01 258 4 0.14 0 22 1 102 by freq moderately conservative 601686 14q11.2 telomerase-associated protein 1 2210 rs1713457 TEP1 7011 14 19919996 NM_007110 NP_009041 C/G S1447T plus 3172665 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 58 0.02 0.03 0.01 258 4 0.14 0 22 1 102 by freq moderately conservative 601686 14q11.2 telomerase-associated protein 1 2211 rs1718119 P2RX7 5027 12 120077823 NM_002562 NP_002553 C/T A348T minus 2903833 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.42 0.04 140 2 0.24 0.16 94 2 123 "by doubleHit,freq" Benign 0.227 5 Tolerant 1 2.92 80 moderately conservative 602566 12q24 "purinergic receptor P2X, ligand-gated ion channel, 7" 2212 rs1718119 P2RX7 5027 12 120077823 NM_002562 NP_002553 C/T A348T minus 24357565 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.42 0.04 140 2 0.24 0.16 94 2 123 "by doubleHit,freq" Benign 0.227 5 Tolerant 1 2.92 80 moderately conservative 602566 12q24 "purinergic receptor P2X, ligand-gated ion channel, 7" 2213 rs1726803 POLD1 5424 19 55597122 NM_002691 NP_002682 A/G S173N plus 3177356 619 WICVAR MITOGPOP6 CORIELL Mixed 56 0.04 0.04 0.02 484 4 123 "by cluster,freq" Benign 0.081 25 Tolerant 0.51 2.86 27 conservative 174761 19q13.3 "polymerase (DNA directed), delta 1, catalytic subunit 125kDa" 2214 rs1726803 POLD1 5424 19 55597122 NM_002691 NP_002682 A/G S173N plus 4480013 506 NCBI NIHPDR NIHPDR 160 0.05 0.04 0.02 484 4 123 "by cluster,freq" Benign 0.081 25 Tolerant 0.51 2.86 27 conservative 174761 19q13.3 "polymerase (DNA directed), delta 1, catalytic subunit 125kDa" 2215 rs1726803 POLD1 5424 19 55597122 NM_002691 NP_002682 A/G S173N plus 4480823 693 EGP_SNPS PDR90 NIHPDR 176 0.06 0.04 0.02 484 4 123 "by cluster,freq" Benign 0.081 25 Tolerant 0.51 2.86 27 conservative 174761 19q13.3 "polymerase (DNA directed), delta 1, catalytic subunit 125kDa" 2216 rs1726803 POLD1 5424 19 55597122 NM_002691 NP_002682 A/G S173N plus 4480823 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.04 0.02 484 4 123 "by cluster,freq" Benign 0.081 25 Tolerant 0.51 2.86 27 conservative 174761 19q13.3 "polymerase (DNA directed), delta 1, catalytic subunit 125kDa" 2217 rs1738023 AKR7A3 22977 1 19356547 NM_012067 NP_036199 A/G N215D minus 2871801 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.16 0.16 0 120 1 121 "HapMap,submitter,freq,cluster" Possibly damaging 1.593 26 Tolerant 1 2.92 15 conservative 608477 1p35.1-p36.23 "aldo-keto reductase family 7, member A3 (aflatoxin aldehyde reductase)" 2218 rs1738254 DNAH8 1769 6 38855748 NM_001371 NP_001362 C/T G473R minus 23942748 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.33 0.18 94 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.952 11 Tolerant 1 2.87 15 moderately radical 603337 6p21.31-p21.1 "dynein, axonemal, heavy polypeptide 8" 2219 rs1748020 PADI4 23569 1 17413915 NM_012387 NP_036519 A/G S275F minus 2595326 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.05 0.05 0 120 1 120 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.748 22 Potentially intolerant 0.07 3.07 22 radical 605347 1p36.13 "peptidyl arginine deiminase, type IV" 2220 rs1752428 GPR135 64582 14 59001684 NM_022571 NP_072093 G/T Q5P plus 10735027 1303 SEQUENOM CEPH CEPH (92) 92 0.48 0.48 0 92 1 0.22 0 1104 1 116 "by cluster,freq" moderately conservative 607970 14q23.1 G protein-coupled receptor 135 2221 rs1757095 TNC 3371 9 114927948 NM_002160 NP_002151 C/T Q539R plus 2609181 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.07 0.06 140 2 0.13 0 46 1 123 "by cluster,freq" Tolerant 1 3.05 16 conservative 187380 9q33 tenascin C (hexabrachion) 2222 rs1757095 TNC 3371 9 114927948 NM_002160 NP_002151 C/T Q539R plus 23531725 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.07 0.06 140 2 0.13 0 46 1 123 "by cluster,freq" Tolerant 1 3.05 16 conservative 187380 9q33 tenascin C (hexabrachion) 2223 rs1758272 CNTNAP3 79937 9 39123127 NM_033655 NP_387504 A/C A628S plus 24796367 1303 SEQUENOM CEPH CEPH (92) 184 0.26 0.26 0 184 1 123 by freq Benign 0.645 12 Tolerant 0.7 2.86 32 moderately conservative 9p12 contactin associated protein-like 3 2224 rs1758286 CNTNAP3 79937 9 39166043 NM_033655 NP_387504 C/G R325T minus 24796369 1303 SEQUENOM CEPH CEPH (92) 184 0.36 0.43 0.09 368 2 123 by freq Potentially damaging 1.326 10 Tolerant 0.47 2.92 32 moderately conservative 9p12 contactin associated protein-like 3 2225 rs1758286 CNTNAP3 79937 9 39166043 NM_033655 NP_387504 C/G R325T minus 24803124 1303 SEQUENOM CEPH CEPH (92) 184 0.49 0.43 0.09 368 2 123 by freq Potentially damaging 1.326 10 Tolerant 0.47 2.92 32 moderately conservative 9p12 contactin associated protein-like 3 2226 rs1758567 IFNA1 3439 9 21430535 NM_024013 NP_076918 C/T V10A plus 2611175 1303 SEQUENOM CEPH CEPH (92) 92 0.11 0.22 0.2 150 2 103 by freq Benign 0.173 6 Tolerant 1 2.82 133 moderately conservative 147660 9p22 "interferon, alpha 1" 2227 rs1758567 IFNA1 3439 9 21430535 NM_024013 NP_076918 C/T V10A plus 3173356 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 58 0.4 0.22 0.2 150 2 103 by freq Benign 0.173 6 Tolerant 1 2.82 133 moderately conservative 147660 9p22 "interferon, alpha 1" 2228 rs1760897 TEP1 7011 14 19946093 NM_007110 NP_009041 C/T S116P minus 6903958 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.32 0.26 0.05 274 3 0.24 0.08 1840 5 121 "HapMap,doubleHit,freq,cluster" moderately conservative 601686 14q11.2 telomerase-associated protein 1 2229 rs1760897 TEP1 7011 14 19946093 NM_007110 NP_009041 C/T S116P minus 6903958 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.27 0.26 0.05 274 3 0.24 0.08 1840 5 121 "HapMap,doubleHit,freq,cluster" moderately conservative 601686 14q11.2 telomerase-associated protein 1 2230 rs1760897 TEP1 7011 14 19946093 NM_007110 NP_009041 C/T S116P minus 6903958 1303 SEQUENOM CEPH CEPH (92) 92 0.21 0.26 0.05 274 3 0.24 0.08 1840 5 121 "HapMap,doubleHit,freq,cluster" moderately conservative 601686 14q11.2 telomerase-associated protein 1 2231 rs1760898 TEP1 7011 14 19942721 NM_007110 NP_009041 A/C N307K minus 2614887 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 12 0.25 0.26 0.05 376 5 0.35 0.03 1860 7 113 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 601686 14q11.2 telomerase-associated protein 1 2232 rs1760898 TEP1 7011 14 19942721 NM_007110 NP_009041 A/C N307K minus 2614887 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 90 0.22 0.26 0.05 376 5 0.35 0.03 1860 7 113 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 601686 14q11.2 telomerase-associated protein 1 2233 rs1760898 TEP1 7011 14 19942721 NM_007110 NP_009041 A/C N307K minus 6903952 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.24 0.26 0.05 376 5 0.35 0.03 1860 7 113 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 601686 14q11.2 telomerase-associated protein 1 2234 rs1760898 TEP1 7011 14 19942721 NM_007110 NP_009041 A/C N307K minus 6903952 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.24 0.26 0.05 376 5 0.35 0.03 1860 7 113 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 601686 14q11.2 telomerase-associated protein 1 2235 rs1760898 TEP1 7011 14 19942721 NM_007110 NP_009041 A/C N307K minus 6903952 1303 SEQUENOM CEPH CEPH (92) 92 0.34 0.26 0.05 376 5 0.35 0.03 1860 7 113 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 601686 14q11.2 telomerase-associated protein 1 2236 rs1760903 TEP1 7011 14 19922657 NM_007110 NP_009041 C/T R1055C minus 2614892 1303 SEQUENOM CEPH CEPH (92) 92 0.35 0.29 0.11 142 2 0.43 0 1492 1 116 "by doubleHit,freq,cluster" radical 601686 14q11.2 telomerase-associated protein 1 2237 rs1760903 TEP1 7011 14 19922657 NM_007110 NP_009041 C/T R1055C minus 3172662 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 50 0.18 0.29 0.11 142 2 0.43 0 1492 1 116 "by doubleHit,freq,cluster" radical 601686 14q11.2 telomerase-associated protein 1 2238 rs1760904 TEP1 7011 14 19921869 NM_007110 NP_009041 C/T S1195P minus 2614893 1303 SEQUENOM CEPH CEPH (92) 92 0.34 0.35 0.16 262 4 0.39 0.09 1942 7 123 "by doubleHit,freq,cluster" moderately conservative 601686 14q11.2 telomerase-associated protein 1 2239 rs1760904 TEP1 7011 14 19921869 NM_007110 NP_009041 C/T S1195P minus 3172672 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 60 0.12 0.35 0.16 262 4 0.39 0.09 1942 7 123 "by doubleHit,freq,cluster" moderately conservative 601686 14q11.2 telomerase-associated protein 1 2240 rs1760904 TEP1 7011 14 19921869 NM_007110 NP_009041 C/T S1195P minus 6903953 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.47 0.35 0.16 262 4 0.39 0.09 1942 7 123 "by doubleHit,freq,cluster" moderately conservative 601686 14q11.2 telomerase-associated protein 1 2241 rs1760904 TEP1 7011 14 19921869 NM_007110 NP_009041 C/T S1195P minus 24720766 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.35 0.16 262 4 0.39 0.09 1942 7 123 "by doubleHit,freq,cluster" moderately conservative 601686 14q11.2 telomerase-associated protein 1 2242 rs1766848 HUS1B 135458 6 601555 NM_148959 NP_683762 G/T H130Q plus 24415050 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 0.06 0 48 1 123 "by submitter,freq" Borderline 0.13 2.8 14 conservative 6p25.3 HUS1 checkpoint homolog b (S. pombe) 2243 rs1769259 FBP1 2203 9 94448704 NM_000507 NP_000498 A/G R218K minus 2627448 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.05 0.08 0.06 212 2 121 "HapMap,submitter,freq,cluster" Potentially damaging 1.426 57 Tolerant 0.59 2.83 77 conservative 229700 9q22.3 "fructose-1,6-bisphosphatase 1" 2244 rs1769259 FBP1 2203 9 94448704 NM_000507 NP_000498 A/G R218K minus 2627448 1303 SEQUENOM CEPH CEPH (92) 92 0.13 0.08 0.06 212 2 121 "HapMap,submitter,freq,cluster" Potentially damaging 1.426 57 Tolerant 0.59 2.83 77 conservative 229700 9q22.3 "fructose-1,6-bisphosphatase 1" 2245 rs1778540 VN1R5 317705 1 243745550 NM_173858 NP_776257 C/T STOP46Q plus 23206668 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 0.23 0.14 94 2 123 "by doubleHit,freq,cluster" Probably damaging Intolerant radical 1q44 vomeronasal 1 receptor 5 2246 rs1783147 PKHD1L1 93035 8 110561016 NM_177531 NP_803875 C/G H3050Q minus 3047932 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.42 0.44 0.04 164 2 0.37 0.01 88 2 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 607843 8q23.2 polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1 2247 rs1783147 PKHD1L1 93035 8 110561016 NM_177531 NP_803875 C/G H3050Q minus 24544228 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.48 0.44 0.04 164 2 0.37 0.01 88 2 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 607843 8q23.2 polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1 2248 rs1783174 PKHD1L1 93035 8 110608362 NM_177531 NP_803875 A/G V4220I plus 2647398 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.14 0.18 0.07 260 3 0.32 0.02 1536 3 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 607843 8q23.2 polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1 2249 rs1783174 PKHD1L1 93035 8 110608362 NM_177531 NP_803875 A/G V4220I plus 17969032 1303 SEQUENOM CEPH CEPH (92) 92 0.25 0.18 0.07 260 3 0.32 0.02 1536 3 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 607843 8q23.2 polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1 2250 rs1783174 PKHD1L1 93035 8 110608362 NM_177531 NP_803875 A/G V4220I plus 24084416 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.18 0.07 260 3 0.32 0.02 1536 3 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 607843 8q23.2 polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1 2251 rs1784423 MMP20 9313 11 101982605 NM_004771 NP_004762 C/T V275A minus 24072033 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.33 0.02 214 2 0.36 0.17 94 2 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.78 2.99 31 moderately conservative 604629 11q22.3 matrix metalloproteinase 20 (enamelysin) 2252 rs1784423 MMP20 9313 11 101982605 NM_004771 NP_004762 C/T V275A minus 28446851 693 EGP_SNPS PDR90 NIHPDR 166 0.34 0.33 0.02 214 2 0.36 0.17 94 2 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.78 2.99 31 moderately conservative 604629 11q22.3 matrix metalloproteinase 20 (enamelysin) 2253 rs1784424 MMP20 9313 11 101982587 NM_004771 NP_004762 A/C T281N minus 28446852 693 EGP_SNPS PDR90 NIHPDR 162 0.34 0.34 0 162 1 123 "by doubleHit,freq,cluster" Tolerant 0.48 2.8 43 moderately conservative 604629 11q22.3 matrix metalloproteinase 20 (enamelysin) 2254 rs1799725 SOD2 6648 6 160084283 NM_000636 NP_000627 C/T V16A minus 5586927 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.47 0.48 0.01 220 2 0.33 0.13 340 4 123 "by cluster,freq" Benign 0.019 34 Tolerant 1 2.96 67 moderately conservative 147460 6q25.3 "superoxide dismutase 2, mitochondrial" 2255 rs1799725 SOD2 6648 6 160084283 NM_000636 NP_000627 C/T V16A minus 7990815 693 EGP_SNPS PDR90 NIHPDR 160 0.48 0.48 0.01 220 2 0.33 0.13 340 4 123 "by cluster,freq" Benign 0.019 34 Tolerant 1 2.96 67 moderately conservative 147460 6q25.3 "superoxide dismutase 2, mitochondrial" 2256 rs1799782 XRCC1 7515 19 48749414 NM_006297 NP_006288 C/T R194W minus 3176720 619 WICVAR MITOGPOP6 CORIELL Mixed 50 0.1 0.12 0.03 1194 5 0.16 0.09 510 6 113 "by cluster,freq" Probably damaging 2.495 8 Potentially intolerant 0.09 3.15 16 moderately radical 194360 19q13.2 X-ray repair complementing defective repair in Chinese hamster cells 1 2257 rs1799782 XRCC1 7515 19 48749414 NM_006297 NP_006288 C/T R194W minus 3254964 506 NCBI NIHPDR NIHPDR 814 0.13 0.12 0.03 1194 5 0.16 0.09 510 6 113 "by cluster,freq" Probably damaging 2.495 8 Potentially intolerant 0.09 3.15 16 moderately radical 194360 19q13.2 X-ray repair complementing defective repair in Chinese hamster cells 1 2258 rs1799782 XRCC1 7515 19 48749414 NM_006297 NP_006288 C/T R194W minus 4473975 693 EGP_SNPS PDR90 NIHPDR 176 0.12 0.12 0.03 1194 5 0.16 0.09 510 6 113 "by cluster,freq" Probably damaging 2.495 8 Potentially intolerant 0.09 3.15 16 moderately radical 194360 19q13.2 X-ray repair complementing defective repair in Chinese hamster cells 1 2259 rs1799782 XRCC1 7515 19 48749414 NM_006297 NP_006288 C/T R194W minus 4473975 1303 SEQUENOM CEPH CEPH (92) 92 0.05 0.12 0.03 1194 5 0.16 0.09 510 6 113 "by cluster,freq" Probably damaging 2.495 8 Potentially intolerant 0.09 3.15 16 moderately radical 194360 19q13.2 X-ray repair complementing defective repair in Chinese hamster cells 1 2260 rs1799782 XRCC1 7515 19 48749414 NM_006297 NP_006288 C/T R194W minus 5586972 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.05 0.12 0.03 1194 5 0.16 0.09 510 6 113 "by cluster,freq" Probably damaging 2.495 8 Potentially intolerant 0.09 3.15 16 moderately radical 194360 19q13.2 X-ray repair complementing defective repair in Chinese hamster cells 1 2261 rs1799793 ERCC2 2068 19 50559099 NM_000400 NP_000391 A/G D312N minus 4385668 693 EGP_SNPS PDR90 NIHPDR 164 0.24 0.28 0.11 222 2 0.21 0.11 330 4 121 "by doubleHit,freq,cluster" Benign 0.052 39 Tolerant 0.51 2.88 36 conservative 126340 19q13.3 "excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D)" 2262 rs1799793 ERCC2 2068 19 50559099 NM_000400 NP_000391 A/G D312N minus 6903793 775 SNP500CANCER CAUC1 Caucasian (31) 58 0.41 0.28 0.11 222 2 0.21 0.11 330 4 121 "by doubleHit,freq,cluster" Benign 0.052 39 Tolerant 0.51 2.88 36 conservative 126340 19q13.3 "excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D)" 2263 rs1799802 ERCC4 2072 16 13935582 NM_005236 NP_005227 C/T P379S plus 3172642 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 66 0.02 0.01 0.01 302 3 0.01 0 204 1 113 "by cluster,freq" Probably damaging 2.274 11 Intolerant 0 2.81 14 moderately conservative 133520 16p13.3-p13.11 "excision repair cross-complementing rodent repair deficiency, complementation group 4" 2264 rs1799802 ERCC4 2072 16 13935582 NM_005236 NP_005227 C/T P379S plus 4384382 693 EGP_SNPS PDR90 NIHPDR 174 0.01 0.01 0.01 302 3 0.01 0 204 1 113 "by cluster,freq" Probably damaging 2.274 11 Intolerant 0 2.81 14 moderately conservative 133520 16p13.3-p13.11 "excision repair cross-complementing rodent repair deficiency, complementation group 4" 2265 rs1799802 ERCC4 2072 16 13935582 NM_005236 NP_005227 C/T P379S plus 5586511 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.02 0.01 0.01 302 3 0.01 0 204 1 113 "by cluster,freq" Probably damaging 2.274 11 Intolerant 0 2.81 14 moderately conservative 133520 16p13.3-p13.11 "excision repair cross-complementing rodent repair deficiency, complementation group 4" 2266 rs1799806 ACHE 43 7 100133309 NM_015831 NP_056646 C/G P592R minus 24332885 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.42 0 48 1 0.1 0.04 94 2 123 by freq Potentially intolerant 0.07 3 16 moderately radical 100740 7q22 acetylcholinesterase (YT blood group) 2267 rs1799807 BCHE 590 3 167031231 NM_000055 NP_000046 A/G D98G minus 23355976 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.02 0 46 1 123 "by submitter,freq,cluster" Probably damaging 2.189 20 Intolerant 0.01 2.85 55 moderately conservative 177400 3q26.1-q26.2 butyrylcholinesterase 2268 rs1799811 GSTP1 2950 11 67110155 NM_000852 NP_000843 C/T A114V plus 5586574 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.1 0.04 0.05 238 2 0.04 0.01 244 2 117 "by cluster,freq" Borderline 1.081 26 Potentially intolerant 0.06 2.8 37 moderately conservative 134660 11q13 glutathione S-transferase pi 2269 rs1799811 GSTP1 2950 11 67110155 NM_000852 NP_000843 C/T A114V plus 12585359 693 EGP_SNPS PDR90 NIHPDR 176 0.02 0.04 0.05 238 2 0.04 0.01 244 2 117 "by cluster,freq" Borderline 1.081 26 Potentially intolerant 0.06 2.8 37 moderately conservative 134660 11q13 glutathione S-transferase pi 2270 rs1799814 CYP1A1 1543 15 72800040 NM_000499 NP_000490 A/C T461N minus 5586387 775 SNP500CANCER CAUC1 Caucasian (31) 58 0.07 0.07 0 242 2 0.03 0.01 244 2 123 "by cluster,freq" Benign 0.379 90 Tolerant 0.49 2.81 88 moderately conservative 108330 15q22-q24 "cytochrome P450, family 1, subfamily A, polypeptide 1" 2271 rs1799814 CYP1A1 1543 15 72800040 NM_000499 NP_000490 A/C T461N minus 24796499 1303 SEQUENOM CEPH CEPH (92) 184 0.07 0.07 0 242 2 0.03 0.01 244 2 123 "by cluster,freq" Benign 0.379 90 Tolerant 0.49 2.81 88 moderately conservative 108330 15q22-q24 "cytochrome P450, family 1, subfamily A, polypeptide 1" 2272 rs1799821 CPT2 1376 1 53388469 NM_000098 NP_000089 A/G V368I plus 3172858 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 48 0.27 0.38 0.09 283 4 0.3 0.02 1562 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.287 9 Tolerant 1 2.81 20 conservative 600650 1p32 carnitine palmitoyltransferase II 2273 rs1799821 CPT2 1376 1 53388469 NM_000098 NP_000089 A/G V368I plus 3172858 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.44 0.38 0.09 283 4 0.3 0.02 1562 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.287 9 Tolerant 1 2.81 20 conservative 600650 1p32 carnitine palmitoyltransferase II 2274 rs1799821 CPT2 1376 1 53388469 NM_000098 NP_000089 A/G V368I plus 16403714 1303 SEQUENOM CEPH CEPH (92) 92 0.33 0.38 0.09 283 4 0.3 0.02 1562 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.287 9 Tolerant 1 2.81 20 conservative 600650 1p32 carnitine palmitoyltransferase II 2275 rs1799821 CPT2 1376 1 53388469 NM_000098 NP_000089 A/G V368I plus 24239280 1371 PERLEGEN AFD_EUR_PANEL European American (24) 23 0.5 0.38 0.09 283 4 0.3 0.02 1562 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.287 9 Tolerant 1 2.81 20 conservative 600650 1p32 carnitine palmitoyltransferase II 2276 rs1799822 CPT2 1376 1 53391250 NM_000098 NP_000089 A/G M647V plus 24239285 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.21 0 48 1 0.09 0.06 94 2 123 "by submitter,freq" Borderline 1.16 9 Intolerant 0.05 2.95 18 conservative 600650 1p32 carnitine palmitoyltransferase II 2277 rs1799853 CYP2C9 1559 10 96692037 NM_000771 NP_000762 C/T R144C plus 5586420 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.13 0.08 0.04 242 2 0.06 0.02 298 3 119 "by cluster,freq" Benign 0.861 152 Intolerant 0.02 2.79 164 radical 601130 10q24 "cytochrome P450, family 2, subfamily C, polypeptide 9" 2278 rs1799853 CYP2C9 1559 10 96692037 NM_000771 NP_000762 C/T R144C plus 12588496 693 EGP_SNPS PDR90 NIHPDR 180 0.06 0.08 0.04 242 2 0.06 0.02 298 3 119 "by cluster,freq" Benign 0.861 152 Intolerant 0.02 2.79 164 radical 601130 10q24 "cytochrome P450, family 2, subfamily C, polypeptide 9" 2279 rs1799891 DNASE1 1773 16 3647024 NM_005223 NP_005214 C/G P154A plus 8819951 506 NCBI NIHPDR NIHPDR 168 0.02 0.02 0 168 1 0.01 0 164 1 119 "by cluster,freq" Potentially damaging 1.429 28 Borderline 0.13 2.81 44 conservative 125505 16p13.3 deoxyribonuclease I 2280 rs1799899 TF 7018 3 134958510 NM_001063 NP_001054 A/G G277S plus 8820467 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.04 0.04 0 230 2 123 "by cluster,freq" Benign 0.833 84 Tolerant 0.3 2.81 94 moderately conservative 190000 3q22.1 transferrin 2281 rs1799899 TF 7018 3 134958510 NM_001063 NP_001054 A/G G277S plus 24796201 1303 SEQUENOM CEPH CEPH (92) 184 0.04 0.04 0 230 2 123 "by cluster,freq" Benign 0.833 84 Tolerant 0.3 2.81 94 moderately conservative 190000 3q22.1 transferrin 2282 rs1799930 NAT2 10 8 18302383 NM_000015 NP_000006 A/G R197Q plus 5586800 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.34 0.37 0.02 386 4 0.28 0.04 436 6 123 "by submitter,freq,cluster" Possibly damaging 1.754 34 Borderline 0.14 2.84 41 conservative 243400 8p22 N-acetyltransferase 2 (arylamine N-acetyltransferase) 2283 rs1799930 NAT2 10 8 18302383 NM_000015 NP_000006 A/G R197Q plus 17965718 1303 SEQUENOM CEPH CEPH (92) 92 0.38 0.37 0.02 386 4 0.28 0.04 436 6 123 "by submitter,freq,cluster" Possibly damaging 1.754 34 Borderline 0.14 2.84 41 conservative 243400 8p22 N-acetyltransferase 2 (arylamine N-acetyltransferase) 2284 rs1799930 NAT2 10 8 18302383 NM_000015 NP_000006 A/G R197Q plus 24664953 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.37 0.02 386 4 0.28 0.04 436 6 123 "by submitter,freq,cluster" Possibly damaging 1.754 34 Borderline 0.14 2.84 41 conservative 243400 8p22 N-acetyltransferase 2 (arylamine N-acetyltransferase) 2285 rs1799930 NAT2 10 8 18302383 NM_000015 NP_000006 A/G R197Q plus 24796684 1303 SEQUENOM CEPH CEPH (92) 184 0.38 0.37 0.02 386 4 0.28 0.04 436 6 123 "by submitter,freq,cluster" Possibly damaging 1.754 34 Borderline 0.14 2.84 41 conservative 243400 8p22 N-acetyltransferase 2 (arylamine N-acetyltransferase) 2286 rs1799931 NAT2 10 8 18302650 NM_000015 NP_000006 A/G G286E plus 5586794 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.03 0.03 0.01 110 2 0.08 0.06 342 4 123 "by cluster,freq" Potentially damaging 1.263 30 moderately conservative 243400 8p22 N-acetyltransferase 2 (arylamine N-acetyltransferase) 2287 rs1799931 NAT2 10 8 18302650 NM_000015 NP_000006 A/G G286E plus 24180357 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.03 0.01 110 2 0.08 0.06 342 4 123 "by cluster,freq" Potentially damaging 1.263 30 moderately conservative 243400 8p22 N-acetyltransferase 2 (arylamine N-acetyltransferase) 2288 rs1799944 BRCA2 675 13 31809463 NM_000059 NP_000050 A/G N991D plus 5586315 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.03 0.04 0.01 376 4 0.04 0.02 438 6 123 "by submitter,freq,cluster" Benign 0.203 9 conservative 600185 13q12.3 "breast cancer 2, early onset" 2289 rs1799944 BRCA2 675 13 31809463 NM_000059 NP_000050 A/G N991D plus 16355805 693 EGP_SNPS PDR90 NIHPDR 174 0.05 0.04 0.01 376 4 0.04 0.02 438 6 123 "by submitter,freq,cluster" Benign 0.203 9 conservative 600185 13q12.3 "breast cancer 2, early onset" 2290 rs1799944 BRCA2 675 13 31809463 NM_000059 NP_000050 A/G N991D plus 16355805 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.04 0.01 376 4 0.04 0.02 438 6 123 "by submitter,freq,cluster" Benign 0.203 9 conservative 600185 13q12.3 "breast cancer 2, early onset" 2291 rs1799944 BRCA2 675 13 31809463 NM_000059 NP_000050 A/G N991D plus 24179877 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.04 0.01 376 4 0.04 0.02 438 6 123 "by submitter,freq,cluster" Benign 0.203 9 conservative 600185 13q12.3 "breast cancer 2, early onset" 2292 rs1799954 BRCA2 675 13 31812592 NM_000059 NP_000050 C/T R2034C plus 5586316 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.02 0.05 0.04 202 3 0.01 0 204 1 123 "by cluster,freq" Possibly damaging 1.757 9 radical 600185 13q12.3 "breast cancer 2, early onset" 2293 rs1799954 BRCA2 675 13 31812592 NM_000059 NP_000050 C/T R2034C plus 5586316 1303 SEQUENOM CEPH CEPH (92) 92 0.09 0.05 0.04 202 3 0.01 0 204 1 123 "by cluster,freq" Possibly damaging 1.757 9 radical 600185 13q12.3 "breast cancer 2, early onset" 2294 rs1799954 BRCA2 675 13 31812592 NM_000059 NP_000050 C/T R2034C plus 24406574 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.05 0.04 202 3 0.01 0 204 1 123 "by cluster,freq" Possibly damaging 1.757 9 radical 600185 13q12.3 "breast cancer 2, early onset" 2295 rs1799969 ICAM1 3383 19 10255792 NM_000201 NP_000192 A/G G241R plus 3176192 619 WICVAR MITOGPOP6 CORIELL Mixed 58 0.03 0.08 0.04 468 6 0.02 0 138 3 123 "by cluster,freq" Probably damaging 2.065 13 Tolerant 0.23 2.81 24 moderately radical 147840 19p13.3-p13.2 "intercellular adhesion molecule 1 (CD54), human rhinovirus receptor" 2296 rs1799969 ICAM1 3383 19 10255792 NM_000201 NP_000192 A/G G241R plus 7985467 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.02 0.08 0.04 468 6 0.02 0 138 3 123 "by cluster,freq" Probably damaging 2.065 13 Tolerant 0.23 2.81 24 moderately radical 147840 19p13.3-p13.2 "intercellular adhesion molecule 1 (CD54), human rhinovirus receptor" 2297 rs1799969 ICAM1 3383 19 10255792 NM_000201 NP_000192 A/G G241R plus 7985467 1303 SEQUENOM CEPH CEPH (92) 92 0.13 0.08 0.04 468 6 0.02 0 138 3 123 "by cluster,freq" Probably damaging 2.065 13 Tolerant 0.23 2.81 24 moderately radical 147840 19p13.3-p13.2 "intercellular adhesion molecule 1 (CD54), human rhinovirus receptor" 2298 rs1799969 ICAM1 3383 19 10255792 NM_000201 NP_000192 A/G G241R plus 16360961 649 FHCRC POPU1 USA (20) 40 0.05 0.08 0.04 468 6 0.02 0 138 3 123 "by cluster,freq" Probably damaging 2.065 13 Tolerant 0.23 2.81 24 moderately radical 147840 19p13.3-p13.2 "intercellular adhesion molecule 1 (CD54), human rhinovirus receptor" 2299 rs1799969 ICAM1 3383 19 10255792 NM_000201 NP_000192 A/G G241R plus 24597778 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.08 0.04 468 6 0.02 0 138 3 123 "by cluster,freq" Probably damaging 2.065 13 Tolerant 0.23 2.81 24 moderately radical 147840 19p13.3-p13.2 "intercellular adhesion molecule 1 (CD54), human rhinovirus receptor" 2300 rs1799969 ICAM1 3383 19 10255792 NM_000201 NP_000192 A/G G241R plus 24796639 1303 SEQUENOM CEPH CEPH (92) 184 0.1 0.08 0.04 468 6 0.02 0 138 3 123 "by cluster,freq" Probably damaging 2.065 13 Tolerant 0.23 2.81 24 moderately radical 147840 19p13.3-p13.2 "intercellular adhesion molecule 1 (CD54), human rhinovirus receptor" 2301 rs1799971 OPRM1 4988 6 154452911 NM_000914 NP_000905 A/G N40D plus 12675567 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.15 0.13 0.01 286 3 0.37 0.12 1938 7 123 "by doubleHit,submitter,freq,cluster" Possibly damaging 1.721 39 conservative 600018 6q24-q25 "opioid receptor, mu 1" 2302 rs1799971 OPRM1 4988 6 154452911 NM_000914 NP_000905 A/G N40D plus 23981705 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0.01 286 3 0.37 0.12 1938 7 123 "by doubleHit,submitter,freq,cluster" Possibly damaging 1.721 39 conservative 600018 6q24-q25 "opioid receptor, mu 1" 2303 rs1799971 OPRM1 4988 6 154452911 NM_000914 NP_000905 A/G N40D plus 28447285 914 HG_BONN_CNS_SNPS EURO96 European 176 0.12 0.13 0.01 286 3 0.37 0.12 1938 7 123 "by doubleHit,submitter,freq,cluster" Possibly damaging 1.721 39 conservative 600018 6q24-q25 "opioid receptor, mu 1" 2304 rs1799972 OPRM1 4988 6 154452810 NM_000914 NP_000905 C/T A6V plus 12675575 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.02 0.01 0.01 236 2 0.08 0.06 346 4 123 "by cluster,freq" Benign 0.675 18 moderately conservative 600018 6q24-q25 "opioid receptor, mu 1" 2305 rs1799972 OPRM1 4988 6 154452810 NM_000914 NP_000905 C/T A6V plus 28447284 914 HG_BONN_CNS_SNPS EURO96 European 174 0.01 0.01 0.01 236 2 0.08 0.06 346 4 123 "by cluster,freq" Benign 0.675 18 moderately conservative 600018 6q24-q25 "opioid receptor, mu 1" 2306 rs1799977 MLH1 4292 3 37028572 NM_000249 NP_000240 A/G I219V plus 3256179 506 NCBI NIHPDR NIHPDR 76 0.14 0.23 0.08 472 5 0.11 0.09 436 6 123 "HapMap,submitter,freq,cluster" Benign 0.3 8 Tolerant 0.76 2.83 15 conservative 120436 3p21.3 "mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)" 2307 rs1799977 MLH1 4292 3 37028572 NM_000249 NP_000240 A/G I219V plus 5586769 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.23 0.23 0.08 472 5 0.11 0.09 436 6 123 "HapMap,submitter,freq,cluster" Benign 0.3 8 Tolerant 0.76 2.83 15 conservative 120436 3p21.3 "mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)" 2308 rs1799977 MLH1 4292 3 37028572 NM_000249 NP_000240 A/G I219V plus 5586769 885 TSC-CSHL HapMap-CEPH-30-trios 110 0.33 0.23 0.08 472 5 0.11 0.09 436 6 123 "HapMap,submitter,freq,cluster" Benign 0.3 8 Tolerant 0.76 2.83 15 conservative 120436 3p21.3 "mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)" 2309 rs1799977 MLH1 4292 3 37028572 NM_000249 NP_000240 A/G I219V plus 6312969 693 EGP_SNPS PDR90 NIHPDR 176 0.18 0.23 0.08 472 5 0.11 0.09 436 6 123 "HapMap,submitter,freq,cluster" Benign 0.3 8 Tolerant 0.76 2.83 15 conservative 120436 3p21.3 "mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)" 2310 rs1799977 MLH1 4292 3 37028572 NM_000249 NP_000240 A/G I219V plus 24310960 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.23 0.08 472 5 0.11 0.09 436 6 123 "HapMap,submitter,freq,cluster" Benign 0.3 8 Tolerant 0.76 2.83 15 conservative 120436 3p21.3 "mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)" 2311 rs1799983 NOS3 4846 7 150133759 NM_000603 NP_000594 G/T D298E plus 3332937 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.34 0.37 0.04 478 5 0.21 0.05 998 8 123 "HapMap,doubleHit,freq,cluster" Benign 0.812 24 Tolerant 1 2.86 63 conservative 163729 7q36 nitric oxide synthase 3 (endothelial cell) 2312 rs1799983 NOS3 4846 7 150133759 NM_000603 NP_000594 G/T D298E plus 3332937 1303 SEQUENOM CEPH CEPH (92) 92 0.4 0.37 0.04 478 5 0.21 0.05 998 8 123 "HapMap,doubleHit,freq,cluster" Benign 0.812 24 Tolerant 1 2.86 63 conservative 163729 7q36 nitric oxide synthase 3 (endothelial cell) 2313 rs1799983 NOS3 4846 7 150133759 NM_000603 NP_000594 G/T D298E plus 5112360 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 22 0.5 0.37 0.04 478 5 0.21 0.05 998 8 123 "HapMap,doubleHit,freq,cluster" Benign 0.812 24 Tolerant 1 2.86 63 conservative 163729 7q36 nitric oxide synthase 3 (endothelial cell) 2314 rs1799983 NOS3 4846 7 150133759 NM_000603 NP_000594 G/T D298E plus 12675558 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.33 0.37 0.04 478 5 0.21 0.05 998 8 123 "HapMap,doubleHit,freq,cluster" Benign 0.812 24 Tolerant 1 2.86 63 conservative 163729 7q36 nitric oxide synthase 3 (endothelial cell) 2315 rs1799983 NOS3 4846 7 150133759 NM_000603 NP_000594 G/T D298E plus 24796688 1303 SEQUENOM CEPH CEPH (92) 184 0.37 0.37 0.04 478 5 0.21 0.05 998 8 123 "HapMap,doubleHit,freq,cluster" Benign 0.812 24 Tolerant 1 2.86 63 conservative 163729 7q36 nitric oxide synthase 3 (endothelial cell) 2316 rs1800056 ATM 472 11 107643213 NM_000051 NP_000042 C/T F858L plus 4479867 506 NCBI NIHPDR NIHPDR 176 0.01 0.02 0.01 578 5 0.02 0.01 444 3 123 "HapMap,freq,cluster" Possibly damaging 1.846 5 conservative 607585 11q22-q23 "ataxia telangiectasia mutated (includes complementation groups A, C and D)" 2317 rs1800056 ATM 472 11 107643213 NM_000051 NP_000042 C/T F858L plus 6903668 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.02 0.02 0.01 578 5 0.02 0.01 444 3 123 "HapMap,freq,cluster" Possibly damaging 1.846 5 conservative 607585 11q22-q23 "ataxia telangiectasia mutated (includes complementation groups A, C and D)" 2318 rs1800056 ATM 472 11 107643213 NM_000051 NP_000042 C/T F858L plus 6904892 693 EGP_SNPS PDR90 NIHPDR 174 0.01 0.02 0.01 578 5 0.02 0.01 444 3 123 "HapMap,freq,cluster" Possibly damaging 1.846 5 conservative 607585 11q22-q23 "ataxia telangiectasia mutated (includes complementation groups A, C and D)" 2319 rs1800056 ATM 472 11 107643213 NM_000051 NP_000042 C/T F858L plus 6904892 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.03 0.02 0.01 578 5 0.02 0.01 444 3 123 "HapMap,freq,cluster" Possibly damaging 1.846 5 conservative 607585 11q22-q23 "ataxia telangiectasia mutated (includes complementation groups A, C and D)" 2320 rs1800056 ATM 472 11 107643213 NM_000051 NP_000042 C/T F858L plus 24550884 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.02 0.01 578 5 0.02 0.01 444 3 123 "HapMap,freq,cluster" Possibly damaging 1.846 5 conservative 607585 11q22-q23 "ataxia telangiectasia mutated (includes complementation groups A, C and D)" 2321 rs1800057 ATM 472 11 107648666 NM_000051 NP_000042 C/G P1054R plus 2978404 506 NCBI NIHPDR NIHPDR 94 0.01 0.01 0.01 562 5 0.02 0.01 436 3 123 "by cluster,freq" Probably damaging 2.325 5 moderately radical 607585 11q22-q23 "ataxia telangiectasia mutated (includes complementation groups A, C and D)" 2322 rs1800057 ATM 472 11 107648666 NM_000051 NP_000042 C/G P1054R plus 4479855 506 NCBI NIHPDR NIHPDR 178 0.01 0.01 0.01 562 5 0.02 0.01 436 3 123 "by cluster,freq" Probably damaging 2.325 5 moderately radical 607585 11q22-q23 "ataxia telangiectasia mutated (includes complementation groups A, C and D)" 2323 rs1800057 ATM 472 11 107648666 NM_000051 NP_000042 C/G P1054R plus 5586265 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.02 0.01 0.01 562 5 0.02 0.01 436 3 123 "by cluster,freq" Probably damaging 2.325 5 moderately radical 607585 11q22-q23 "ataxia telangiectasia mutated (includes complementation groups A, C and D)" 2324 rs1800057 ATM 472 11 107648666 NM_000051 NP_000042 C/G P1054R plus 6904922 693 EGP_SNPS PDR90 NIHPDR 180 0.01 0.01 0.01 562 5 0.02 0.01 436 3 123 "by cluster,freq" Probably damaging 2.325 5 moderately radical 607585 11q22-q23 "ataxia telangiectasia mutated (includes complementation groups A, C and D)" 2325 rs1800057 ATM 472 11 107648666 NM_000051 NP_000042 C/G P1054R plus 24550926 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.01 0.01 562 5 0.02 0.01 436 3 123 "by cluster,freq" Probably damaging 2.325 5 moderately radical 607585 11q22-q23 "ataxia telangiectasia mutated (includes complementation groups A, C and D)" 2326 rs1800067 ERCC4 2072 16 13936534 NM_005236 NP_005227 A/G R415Q plus 2924072 506 NCBI NIHPDR NIHPDR 84 0.06 0.06 0.02 556 6 0.04 0.03 294 3 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.595 11 Intolerant 0.04 2.81 14 conservative 133520 16p13.3-p13.11 "excision repair cross-complementing rodent repair deficiency, complementation group 4" 2327 rs1800067 ERCC4 2072 16 13936534 NM_005236 NP_005227 A/G R415Q plus 4384388 693 EGP_SNPS PDR90 NIHPDR 150 0.05 0.06 0.02 556 6 0.04 0.03 294 3 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.595 11 Intolerant 0.04 2.81 14 conservative 133520 16p13.3-p13.11 "excision repair cross-complementing rodent repair deficiency, complementation group 4" 2328 rs1800067 ERCC4 2072 16 13936534 NM_005236 NP_005227 A/G R415Q plus 4384388 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.05 0.06 0.02 556 6 0.04 0.03 294 3 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.595 11 Intolerant 0.04 2.81 14 conservative 133520 16p13.3-p13.11 "excision repair cross-complementing rodent repair deficiency, complementation group 4" 2329 rs1800067 ERCC4 2072 16 13936534 NM_005236 NP_005227 A/G R415Q plus 4384388 1303 SEQUENOM CEPH CEPH (92) 92 0.1 0.06 0.02 556 6 0.04 0.03 294 3 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.595 11 Intolerant 0.04 2.81 14 conservative 133520 16p13.3-p13.11 "excision repair cross-complementing rodent repair deficiency, complementation group 4" 2330 rs1800067 ERCC4 2072 16 13936534 NM_005236 NP_005227 A/G R415Q plus 5586510 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.03 0.06 0.02 556 6 0.04 0.03 294 3 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.595 11 Intolerant 0.04 2.81 14 conservative 133520 16p13.3-p13.11 "excision repair cross-complementing rodent repair deficiency, complementation group 4" 2331 rs1800067 ERCC4 2072 16 13936534 NM_005236 NP_005227 A/G R415Q plus 24519993 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.06 0.02 556 6 0.04 0.03 294 3 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.595 11 Intolerant 0.04 2.81 14 conservative 133520 16p13.3-p13.11 "excision repair cross-complementing rodent repair deficiency, complementation group 4" 2332 rs1800069 ERCC4 2072 16 13949071 NM_005236 NP_005227 C/T I706T plus 2924076 506 NCBI NIHPDR NIHPDR 82 0.01 0.01 0 248 2 103 "by cluster,freq" Possibly damaging 1.86 10 Intolerant 0.01 2.81 14 moderately conservative 133520 16p13.3-p13.11 "excision repair cross-complementing rodent repair deficiency, complementation group 4" 2333 rs1800069 ERCC4 2072 16 13949071 NM_005236 NP_005227 C/T I706T plus 4384469 693 EGP_SNPS PDR90 NIHPDR 166 0.01 0.01 0 248 2 103 "by cluster,freq" Possibly damaging 1.86 10 Intolerant 0.01 2.81 14 moderately conservative 133520 16p13.3-p13.11 "excision repair cross-complementing rodent repair deficiency, complementation group 4" 2334 rs1800076 CFTR 1080 7 116743098 NM_000492 NP_000483 A/G R75Q plus 24796347 1303 SEQUENOM CEPH CEPH (92) 184 0.11 0.11 0 184 1 123 by freq Possibly damaging 1.754 28 Intolerant 0.03 2.94 34 conservative 602421 7q31.2 "cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)" 2335 rs1800098 CFTR 1080 7 116824405 NM_000492 NP_000483 C/G G576A plus 24458873 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.27 0.17 232 2 123 "by submitter,freq" Borderline 1.078 28 Tolerant 0.4 2.92 35 moderately conservative 602421 7q31.2 "cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)" 2336 rs1800098 CFTR 1080 7 116824405 NM_000492 NP_000483 C/G G576A plus 24796349 1303 SEQUENOM CEPH CEPH (92) 184 0.33 0.27 0.17 232 2 123 "by submitter,freq" Borderline 1.078 28 Tolerant 0.4 2.92 35 moderately conservative 602421 7q31.2 "cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)" 2337 rs1800100 CFTR 1080 7 116826174 NM_000492 NP_000483 C/T R668C plus 24458917 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.02 0.01 232 2 123 "by submitter,freq" Probably damaging 2.654 29 Intolerant 0 3.03 33 radical 602421 7q31.2 "cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)" 2338 rs1800100 CFTR 1080 7 116826174 NM_000492 NP_000483 C/T R668C plus 24796350 1303 SEQUENOM CEPH CEPH (92) 184 0.02 0.02 0.01 232 2 123 "by submitter,freq" Probably damaging 2.654 29 Intolerant 0 3.03 33 radical 602421 7q31.2 "cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)" 2339 rs1800107 CFTR 1080 7 116837605 NM_000492 NP_000483 G/T S909I plus 24796351 1303 SEQUENOM CEPH CEPH (92) 184 0.05 0.05 0 184 1 123 by freq Possibly damaging 1.682 29 Borderline 0.16 3.11 34 moderately radical 602421 7q31.2 "cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)" 2340 rs1800124 ERCC4 2072 16 13949578 NM_005236 NP_005227 A/G E875G plus 2924084 506 NCBI NIHPDR NIHPDR 88 0.01 0.01 0.01 314 3 0.01 0.01 250 2 113 "by cluster,freq" Possibly damaging 1.832 10 Intolerant 0.01 2.81 14 moderately conservative 133520 16p13.3-p13.11 "excision repair cross-complementing rodent repair deficiency, complementation group 4" 2341 rs1800124 ERCC4 2072 16 13949578 NM_005236 NP_005227 A/G E875G plus 4384475 693 EGP_SNPS PDR90 NIHPDR 164 0.01 0.01 0.01 314 3 0.01 0.01 250 2 113 "by cluster,freq" Possibly damaging 1.832 10 Intolerant 0.01 2.81 14 moderately conservative 133520 16p13.3-p13.11 "excision repair cross-complementing rodent repair deficiency, complementation group 4" 2342 rs1800124 ERCC4 2072 16 13949578 NM_005236 NP_005227 A/G E875G plus 5586516 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.03 0.01 0.01 314 3 0.01 0.01 250 2 113 "by cluster,freq" Possibly damaging 1.832 10 Intolerant 0.01 2.81 14 moderately conservative 133520 16p13.3-p13.11 "excision repair cross-complementing rodent repair deficiency, complementation group 4" 2343 rs1800127 LRP1 4035 12 55825349 NM_002332 NP_002323 C/T A217V plus 24796453 1303 SEQUENOM CEPH CEPH (92) 184 0.19 0.19 0 184 1 123 by freq Tolerant 0.33 2.87 22 moderately conservative 107770 12q13-q14 low density lipoprotein-related protein 1 (alpha-2-macroglobulin receptor) 2344 rs1800197 PROP1 5626 5 177352573 NM_006261 NP_006252 A/G A142T minus 24314333 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.27 0.27 0 44 1 0.11 0 92 2 123 "by doubleHit,freq,cluster" Potentially damaging 1.486 9 Tolerant 1 2.92 24 moderately conservative 601538 5q35.3 "prophet of Pit1, paired-like homeodomain transcription factor" 2345 rs1800215 COL1A1 1277 17 45620494 NM_000088 NP_000079 A/G T1075A minus 12568584 887 CUORCGL AMERICAN CAUCASIANS American Caucasians 1860 0.02 0.02 0 1860 1 121 "by cluster,freq" moderately conservative 120150 17q21.3-q22.1 "collagen, type I, alpha 1" 2346 rs1800282 FANCA 2175 16 88410508 NM_000135 NP_000126 A/T V6D minus 24803515 1303 SEQUENOM CEPH CEPH (92) 184 0.16 0.16 0 184 1 123 by freq radical 607139 16q24.3 "Fanconi anemia, complementation group A" 2347 rs1800378 VWF 7450 12 6042463 NM_000552 NP_000543 A/G H484R minus 11037304 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.38 0.35 0.06 166 2 0.26 0.14 86 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.962 9 Tolerant 1 3.02 27 conservative 193400 12p13.3 von Willebrand factor 2348 rs1800378 VWF 7450 12 6042463 NM_000552 NP_000543 A/G H484R minus 24166845 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.28 0.35 0.06 166 2 0.26 0.14 86 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.962 9 Tolerant 1 3.02 27 conservative 193400 12p13.3 von Willebrand factor 2349 rs1800385 VWF 7450 12 5998152 NM_000552 NP_000543 G/T V1565L minus 3172990 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 50 0.2 0.2 0 50 1 120 "by doubleHit,submitter,freq" Borderline 1.07 9 conservative 193400 12p13.3 von Willebrand factor 2350 rs1800391 WRN 7486 8 31058246 NM_000553 NP_000544 A/G M387I plus 6903977 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.1 0.06 0.03 374 4 0.05 0.02 328 4 123 "by cluster,freq" Possibly damaging 1.792 6 conservative 604611 8p12-p11.2 Werner syndrome 2351 rs1800391 WRN 7486 8 31058246 NM_000553 NP_000544 A/G M387I plus 6903977 1303 SEQUENOM CEPH CEPH (92) 92 0.03 0.06 0.03 374 4 0.05 0.02 328 4 123 "by cluster,freq" Possibly damaging 1.792 6 conservative 604611 8p12-p11.2 Werner syndrome 2352 rs1800391 WRN 7486 8 31058246 NM_000553 NP_000544 A/G M387I plus 16359390 693 EGP_SNPS PDR90 NIHPDR 180 0.06 0.06 0.03 374 4 0.05 0.02 328 4 123 "by cluster,freq" Possibly damaging 1.792 6 conservative 604611 8p12-p11.2 Werner syndrome 2353 rs1800391 WRN 7486 8 31058246 NM_000553 NP_000544 A/G M387I plus 24473548 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.05 0.06 0.03 374 4 0.05 0.02 328 4 123 "by cluster,freq" Possibly damaging 1.792 6 conservative 604611 8p12-p11.2 Werner syndrome 2354 rs1800435 ALAD 210 9 113233445 NM_000031 NP_000022 C/G K68N minus 2667718 506 NCBI NIHPDR NIHPDR 86 0.05 0.07 0.06 362 4 0.06 0.02 298 3 123 "by cluster,freq" Borderline 1.049 28 Tolerant 1 2.8 59 moderately conservative 125270 9q34 "aminolevulinate, delta-, dehydratase" 2355 rs1800435 ALAD 210 9 113233445 NM_000031 NP_000022 C/G K68N minus 5586228 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.18 0.07 0.06 362 4 0.06 0.02 298 3 123 "by cluster,freq" Borderline 1.049 28 Tolerant 1 2.8 59 moderately conservative 125270 9q34 "aminolevulinate, delta-, dehydratase" 2356 rs1800435 ALAD 210 9 113233445 NM_000031 NP_000022 C/G K68N minus 9805739 693 EGP_SNPS PDR90 NIHPDR 168 0.05 0.07 0.06 362 4 0.06 0.02 298 3 123 "by cluster,freq" Borderline 1.049 28 Tolerant 1 2.8 59 moderately conservative 125270 9q34 "aminolevulinate, delta-, dehydratase" 2357 rs1800435 ALAD 210 9 113233445 NM_000031 NP_000022 C/G K68N minus 24505610 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.07 0.06 362 4 0.06 0.02 298 3 123 "by cluster,freq" Borderline 1.049 28 Tolerant 1 2.8 59 moderately conservative 125270 9q34 "aminolevulinate, delta-, dehydratase" 2358 rs1800440 CYP1B1 1545 2 38209790 NM_000104 NP_000095 A/G N453S minus 5586407 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.19 0.13 0.06 280 3 0.12 0.06 344 4 123 "by cluster,freq" Possibly damaging 1.676 11 Potentially intolerant 0.06 2.79 90 conservative 601771 2p21 "cytochrome P450, family 1, subfamily B, polypeptide 1" 2359 rs1800440 CYP1B1 1545 2 38209790 NM_000104 NP_000095 A/G N453S minus 12724399 693 EGP_SNPS PDR90 NIHPDR 170 0.09 0.13 0.06 280 3 0.12 0.06 344 4 123 "by cluster,freq" Possibly damaging 1.676 11 Potentially intolerant 0.06 2.79 90 conservative 601771 2p21 "cytochrome P450, family 1, subfamily B, polypeptide 1" 2360 rs1800440 CYP1B1 1545 2 38209790 NM_000104 NP_000095 A/G N453S minus 24639447 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.13 0.06 280 3 0.12 0.06 344 4 123 "by cluster,freq" Possibly damaging 1.676 11 Potentially intolerant 0.06 2.79 90 conservative 601771 2p21 "cytochrome P450, family 1, subfamily B, polypeptide 1" 2361 rs1800450 MBL2 4153 10 54201241 NM_000242 NP_000233 A/G G54D minus 3344470 1303 SEQUENOM CEPH CEPH (92) 92 0.34 0.27 0.13 140 2 0.13 0.15 92 2 123 "by doubleHit,freq,cluster" Probably damaging 2.049 19 Intolerant 0 2.83 42 moderately conservative 154545 10q11.2-q21 "mannose-binding lectin (protein C) 2, soluble (opsonic defect)" 2362 rs1800450 MBL2 4153 10 54201241 NM_000242 NP_000233 A/G G54D minus 24109423 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.27 0.13 140 2 0.13 0.15 92 2 123 "by doubleHit,freq,cluster" Probably damaging 2.049 19 Intolerant 0 2.83 42 moderately conservative 154545 10q11.2-q21 "mannose-binding lectin (protein C) 2, soluble (opsonic defect)" 2363 rs1800451 MBL2 4153 10 54201232 NM_000242 NP_000233 A/G G57E minus 24796407 1303 SEQUENOM CEPH CEPH (92) 184 0.05 0.05 0 184 1 123 by freq Probably damaging 2.274 18 Intolerant 0 2.83 42 moderately conservative 154545 10q11.2-q21 "mannose-binding lectin (protein C) 2, soluble (opsonic defect)" 2364 rs1800453 TAP1 6890 6 32922953 NM_000593 NP_000584 A/G D697G minus 23718241 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 0.18 0.02 94 2 123 "by cluster,freq" Benign 0.193 25 Tolerant 1 2.8 75 moderately conservative 170260 6p21.3 "transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)" 2365 rs1800457 DIA1 1727 22 41348769 NM_007326 NP_015565 C/G T94S minus 12584079 693 EGP_SNPS PDR90 NIHPDR 176 0.08 0.08 0 176 1 0.15 0.18 90 2 123 "HapMap,submitter,freq,cluster" Tolerant 0.5 2.83 87 moderately conservative 250800 22q13.2-q13.31 diaphorase (NADH) (cytochrome b-5 reductase) 2366 rs1800458 TTR 7276 18 27426863 NM_000371 NP_000362 A/G G26S plus 2420552 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 83 0.08 0.11 0.06 131 2 123 "by submitter,freq" Benign 0.107 44 Tolerant 0.8 3.17 31 moderately conservative 176300 18q12.1 "transthyretin (prealbumin, amyloidosis type I)" 2367 rs1800458 TTR 7276 18 27426863 NM_000371 NP_000362 A/G G26S plus 24686660 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.11 0.06 131 2 123 "by submitter,freq" Benign 0.107 44 Tolerant 0.8 3.17 31 moderately conservative 176300 18q12.1 "transthyretin (prealbumin, amyloidosis type I)" 2368 rs1800497 ANKK1 255239 11 112776038 NM_178510 NP_848605 C/T E713K minus 5586480 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.13 0.18 0.07 228 3 0.26 0.07 593 7 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.59 2.91 21 moderately conservative 608774 11q23.2 ankyrin repeat and kinase domain containing 1 2369 rs1800497 ANKK1 255239 11 112776038 NM_178510 NP_848605 C/T E713K minus 6826700 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.23 0.18 0.07 228 3 0.26 0.07 593 7 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.59 2.91 21 moderately conservative 608774 11q23.2 ankyrin repeat and kinase domain containing 1 2370 rs1800497 ANKK1 255239 11 112776038 NM_178510 NP_848605 C/T E713K minus 24101885 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.18 0.07 228 3 0.26 0.07 593 7 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.59 2.91 21 moderately conservative 608774 11q23.2 ankyrin repeat and kinase domain containing 1 2371 rs1800520 AIRE 326 21 44534334 NM_000383 NP_000374 C/G S278R plus 2991110 1303 SEQUENOM CEPH CEPH (92) 92 0.19 0.19 0 92 1 96 "by doubleHit,cluster" Potentially damaging 1.379 14 Tolerant 0.58 2.98 33 moderately radical 607358 21q22.3 autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy) 2372 rs1800566 NQO1 1728 16 68302646 NM_000903 NP_000894 C/T P187S minus 5586808 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.18 0.18 0.05 320 4 0.28 0.1 430 6 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.8 7 Tolerant 0.34 2.79 36 moderately conservative 125860 16q22.1 "NAD(P)H dehydrogenase, quinone 1" 2373 rs1800566 NQO1 1728 16 68302646 NM_000903 NP_000894 C/T P187S minus 5586808 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.22 0.18 0.05 320 4 0.28 0.1 430 6 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.8 7 Tolerant 0.34 2.79 36 moderately conservative 125860 16q22.1 "NAD(P)H dehydrogenase, quinone 1" 2374 rs1800566 NQO1 1728 16 68302646 NM_000903 NP_000894 C/T P187S minus 16725653 1303 SEQUENOM CEPH CEPH (92) 92 0.19 0.18 0.05 320 4 0.28 0.1 430 6 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.8 7 Tolerant 0.34 2.79 36 moderately conservative 125860 16q22.1 "NAD(P)H dehydrogenase, quinone 1" 2375 rs1800566 NQO1 1728 16 68302646 NM_000903 NP_000894 C/T P187S minus 23984542 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.18 0.05 320 4 0.28 0.1 430 6 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.8 7 Tolerant 0.34 2.79 36 moderately conservative 125860 16q22.1 "NAD(P)H dehydrogenase, quinone 1" 2376 rs1800956 ENG 2022 9 127666175 NM_000118 NP_000109 C/G D366H minus 4925819 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.01 0.01 0 120 1 0.06 0.02 1574 3 123 "HapMap,freq,cluster" Possibly damaging 1.672 5 Intolerant 0.02 2.93 14 moderately conservative 131195 9q33-q34.1 endoglin (Osler-Rendu-Weber syndrome 1) 2377 rs1800974 ITGA7 3679 12 54375624 NM_002206 NP_002197 A/G R651H minus 3236448 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.49 0.48 0.02 166 2 0.07 0.06 1584 3 123 "HapMap,doubleHit,freq,cluster" Potentially damaging 1.312 6 conservative 600536 12q13 "integrin, alpha 7" 2378 rs1800974 ITGA7 3679 12 54375624 NM_002206 NP_002197 A/G R651H minus 24454183 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.48 0.02 166 2 0.07 0.06 1584 3 123 "HapMap,doubleHit,freq,cluster" Potentially damaging 1.312 6 conservative 600536 12q13 "integrin, alpha 7" 2379 rs1801019 UMPS 7372 3 125939432 NM_000373 NP_000364 C/G G213A plus 3177761 619 WICVAR MITOGPOP6 CORIELL Mixed 56 0.18 0.2 0.03 148 2 0.25 0 1498 1 120 "by cluster,freq" Potentially damaging 1.319 10 Tolerant 0.79 2.83 19 moderately conservative 258900 3q13 uridine monophosphate synthetase (orotate phosphoribosyl transferase and orotidine-5'-decarboxylase) 2380 rs1801019 UMPS 7372 3 125939432 NM_000373 NP_000364 C/G G213A plus 10068017 1303 SEQUENOM CEPH CEPH (92) 92 0.22 0.2 0.03 148 2 0.25 0 1498 1 120 "by cluster,freq" Potentially damaging 1.319 10 Tolerant 0.79 2.83 19 moderately conservative 258900 3q13 uridine monophosphate synthetase (orotate phosphoribosyl transferase and orotidine-5'-decarboxylase) 2381 rs1801105 HNMT 3176 2 138593381 NM_006895 NP_008826 C/T T105I plus 24273695 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.08 0.03 228 2 123 "by cluster,freq" Possibly damaging 1.641 6 moderately conservative 605238 2q22.1 histamine N-methyltransferase 2382 rs1801114 CSF2RB 1439 22 35658304 NM_000395 NP_000386 A/G V652M plus 3172729 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 60 0.02 0.03 0.01 152 2 0.04 0 46 1 123 "by cluster,freq" Benign 0.687 6 conservative 138981 22q13.1 "colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)" 2383 rs1801114 CSF2RB 1439 22 35658304 NM_000395 NP_000386 A/G V652M plus 3172729 1303 SEQUENOM CEPH CEPH (92) 92 0.03 0.03 0.01 152 2 0.04 0 46 1 123 "by cluster,freq" Benign 0.687 6 conservative 138981 22q13.1 "colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)" 2384 rs1801122 CSF2RB 1439 22 35658157 NM_000395 NP_000386 A/C P603T plus 24803546 1303 SEQUENOM CEPH CEPH (92) 184 0.06 0.06 0 184 1 123 by freq Probably damaging 2.1 6 conservative 138981 22q13.1 "colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)" 2385 rs1801131 MTHFR 4524 1 11788742 NM_005957 NP_005948 A/C E429A minus 5586779 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.37 0.34 0.06 110 2 0.27 0.05 1030 7 123 "by cluster,freq" Possibly damaging 1.717 5 moderately radical 607093 1p36.3 "5,10-methylenetetrahydrofolate reductase (NADPH)" 2386 rs1801131 MTHFR 4524 1 11788742 NM_005957 NP_005948 A/C E429A minus 24238726 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.34 0.06 110 2 0.27 0.05 1030 7 123 "by cluster,freq" Possibly damaging 1.717 5 moderately radical 607093 1p36.3 "5,10-methylenetetrahydrofolate reductase (NADPH)" 2387 rs1801133 MTHFR 4524 1 11790644 NM_005957 NP_005948 C/T A222V minus 2978066 506 NCBI NIHPDR NIHPDR 74 0.22 0.29 0.06 422 7 0.35 0.07 2586 11 123 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.227 6 Intolerant 0.01 2.75 36 moderately conservative 607093 1p36.3 "5,10-methylenetetrahydrofolate reductase (NADPH)" 2388 rs1801133 MTHFR 4524 1 11790644 NM_005957 NP_005948 C/T A222V minus 5586780 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.37 0.29 0.06 422 7 0.35 0.07 2586 11 123 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.227 6 Intolerant 0.01 2.75 36 moderately conservative 607093 1p36.3 "5,10-methylenetetrahydrofolate reductase (NADPH)" 2389 rs1801133 MTHFR 4524 1 11790644 NM_005957 NP_005948 C/T A222V minus 9880738 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.25 0.29 0.06 422 7 0.35 0.07 2586 11 123 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.227 6 Intolerant 0.01 2.75 36 moderately conservative 607093 1p36.3 "5,10-methylenetetrahydrofolate reductase (NADPH)" 2390 rs1801133 MTHFR 4524 1 11790644 NM_005957 NP_005948 C/T A222V minus 9880738 902 AFFY Caucasian 24 0.25 0.29 0.06 422 7 0.35 0.07 2586 11 123 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.227 6 Intolerant 0.01 2.75 36 moderately conservative 607093 1p36.3 "5,10-methylenetetrahydrofolate reductase (NADPH)" 2391 rs1801133 MTHFR 4524 1 11790644 NM_005957 NP_005948 C/T A222V minus 9880738 904 AFFY CEPH 6 0.5 0.29 0.06 422 7 0.35 0.07 2586 11 123 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.227 6 Intolerant 0.01 2.75 36 moderately conservative 607093 1p36.3 "5,10-methylenetetrahydrofolate reductase (NADPH)" 2392 rs1801133 MTHFR 4524 1 11790644 NM_005957 NP_005948 C/T A222V minus 9880738 1303 SEQUENOM CEPH CEPH (92) 92 0.34 0.29 0.06 422 7 0.35 0.07 2586 11 123 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.227 6 Intolerant 0.01 2.75 36 moderately conservative 607093 1p36.3 "5,10-methylenetetrahydrofolate reductase (NADPH)" 2393 rs1801133 MTHFR 4524 1 11790644 NM_005957 NP_005948 C/T A222V minus 23844687 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.29 0.06 422 7 0.35 0.07 2586 11 123 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.227 6 Intolerant 0.01 2.75 36 moderately conservative 607093 1p36.3 "5,10-methylenetetrahydrofolate reductase (NADPH)" 2394 rs1801158 DPYD 1806 1 97693442 NM_000110 NP_000101 A/G S534N minus 24796095 1303 SEQUENOM CEPH CEPH (92) 184 0.05 0.05 0 184 1 123 by freq Intolerant 0.02 3.25 113 conservative 274270 1p22 dihydropyrimidine dehydrogenase 2395 rs1801200 ERBB2 2064 17 35133114 NM_004448 NP_004439 A/G I655V plus 2857309 885 TSC-CSHL HapMap-CEPH-30-trios 114 0.33 0.18 0.09 662 5 0.13 0.02 1778 4 123 "HapMap,freq,cluster" Benign 0.738 19 Tolerant 0.25 2.8 224 conservative 164870 17q21.1 "v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)" 2396 rs1801200 ERBB2 2064 17 35133114 NM_004448 NP_004439 A/G I655V plus 5608570 693 EGP_SNPS PDR90 NIHPDR 164 0.18 0.18 0.09 662 5 0.13 0.02 1778 4 123 "HapMap,freq,cluster" Benign 0.738 19 Tolerant 0.25 2.8 224 conservative 164870 17q21.1 "v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)" 2397 rs1801200 ERBB2 2064 17 35133114 NM_004448 NP_004439 A/G I655V plus 24577730 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.25 0.18 0.09 662 5 0.13 0.02 1778 4 123 "HapMap,freq,cluster" Benign 0.738 19 Tolerant 0.25 2.8 224 conservative 164870 17q21.1 "v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)" 2398 rs1801200 ERBB2 2064 17 35133114 NM_004448 NP_004439 A/G I655V plus 24803553 1303 SEQUENOM CEPH CEPH (92) 184 0.08 0.18 0.09 662 5 0.13 0.02 1778 4 123 "HapMap,freq,cluster" Benign 0.738 19 Tolerant 0.25 2.8 224 conservative 164870 17q21.1 "v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)" 2399 rs1801200 ERBB2 2064 17 35133114 NM_004448 NP_004439 A/G I655V plus 28458517 549 KYUGEN CP CEPH (78) 156 0.16 0.18 0.09 662 5 0.13 0.02 1778 4 123 "HapMap,freq,cluster" Benign 0.738 19 Tolerant 0.25 2.8 224 conservative 164870 17q21.1 "v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)" 2400 rs1801204 ACADL 33 2 210893637 NM_001608 NP_001599 C/G S303T minus 24796174 1303 SEQUENOM CEPH CEPH (92) 184 0.29 0.29 0 184 1 123 by freq Borderline 1.001 10 Tolerant 0.95 2.78 36 moderately conservative 201460 2q34-q35 "acyl-Coenzyme A dehydrogenase, long chain" 2401 rs1801222 CUBN 8029 10 17196157 NM_001081 NP_001072 C/T F253S minus 2947966 1303 SEQUENOM CEPH CEPH (92) 92 0.46 0.4 0.14 130 2 121 "by doubleHit,freq" radical 602997 10p12.31 cubilin (intrinsic factor-cobalamin receptor) 2402 rs1801222 CUBN 8029 10 17196157 NM_001081 NP_001072 C/T F253S minus 3172685 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 38 0.24 0.4 0.14 130 2 121 "by doubleHit,freq" radical 602997 10p12.31 cubilin (intrinsic factor-cobalamin receptor) 2403 rs1801231 CUBN 8029 10 17064509 NM_001081 NP_001072 C/T P1559S minus 19889894 1303 SEQUENOM CEPH CEPH (92) 92 0.12 0.12 0 92 1 121 "by doubleHit,freq,cluster" Tolerant 0.92 2.76 8 moderately conservative 602997 10p12.31 cubilin (intrinsic factor-cobalamin receptor) 2404 rs1801238 CUBN 8029 10 16972496 NM_001081 NP_001072 A/C L2879I minus 3176098 619 WICVAR MITOGPOP6 CORIELL Mixed 30 0.07 0.06 0 262 3 123 "by submitter,freq" Borderline 0.14 2.76 8 conservative 602997 10p12.31 cubilin (intrinsic factor-cobalamin receptor) 2405 rs1801238 CUBN 8029 10 16972496 NM_001081 NP_001072 A/C L2879I minus 24540436 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 262 3 123 "by submitter,freq" Borderline 0.14 2.76 8 conservative 602997 10p12.31 cubilin (intrinsic factor-cobalamin receptor) 2406 rs1801238 CUBN 8029 10 16972496 NM_001081 NP_001072 A/C L2879I minus 24796397 1303 SEQUENOM CEPH CEPH (92) 184 0.06 0.06 0 262 3 123 "by submitter,freq" Borderline 0.14 2.76 8 conservative 602997 10p12.31 cubilin (intrinsic factor-cobalamin receptor) 2407 rs1801239 CUBN 8029 10 16959058 NM_001081 NP_001072 A/G I2984V minus 24540193 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.16 0.16 0 44 1 123 "by submitter,freq" Tolerant 0.84 2.76 8 conservative 602997 10p12.31 cubilin (intrinsic factor-cobalamin receptor) 2408 rs1801243 ATP7B 540 13 51446141 NM_000053 NP_000044 G/T S406A minus 13221772 1303 SEQUENOM CEPH CEPH (92) 92 0.33 0.37 0.09 140 2 0.46 0.07 1588 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.343 20 Tolerant 0.75 2.74 31 moderately conservative 606882 13q14.2-q21 "ATPase, Cu++ transporting, beta polypeptide (Wilson disease)" 2409 rs1801243 ATP7B 540 13 51446141 NM_000053 NP_000044 G/T S406A minus 24448283 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.37 0.09 140 2 0.46 0.07 1588 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.343 20 Tolerant 0.75 2.74 31 moderately conservative 606882 13q14.2-q21 "ATPase, Cu++ transporting, beta polypeptide (Wilson disease)" 2410 rs1801244 ATP7B 540 13 51442806 NM_000053 NP_000044 C/G V456L minus 16604408 1303 SEQUENOM CEPH CEPH (92) 92 0.32 0.37 0.11 140 2 0.31 0.1 94 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.068 20 conservative 606882 13q14.2-q21 "ATPase, Cu++ transporting, beta polypeptide (Wilson disease)" 2411 rs1801244 ATP7B 540 13 51442806 NM_000053 NP_000044 C/G V456L minus 24448235 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.37 0.11 140 2 0.31 0.1 94 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.068 20 conservative 606882 13q14.2-q21 "ATPase, Cu++ transporting, beta polypeptide (Wilson disease)" 2412 rs1801249 ATP7B 540 13 51413355 NM_000053 NP_000044 C/T V1140A minus 24448066 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.46 0 48 1 0.42 0.02 1574 3 123 "by doubleHit,freq,cluster" Benign 0.025 19 Tolerant 0.8 3.06 18 moderately conservative 606882 13q14.2-q21 "ATPase, Cu++ transporting, beta polypeptide (Wilson disease)" 2413 rs1801262 NEUROD1 4760 2 182368961 NM_002500 NP_002491 A/G T45A minus 12586884 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.4 0.37 0.01 1133 3 121 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.886 5 moderately conservative 601724 2q32 neurogenic differentiation 1 2414 rs1801262 NEUROD1 4760 2 182368961 NM_002500 NP_002491 A/G T45A minus 12586884 1303 SEQUENOM CEPH CEPH (92) 92 0.36 0.37 0.01 1133 3 121 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.886 5 moderately conservative 601724 2q32 neurogenic differentiation 1 2415 rs1801262 NEUROD1 4760 2 182368961 NM_002500 NP_002491 A/G T45A minus 12587271 928 IBARROSO ELY UK (Ely region of East Anglia) 921 0.37 0.37 0.01 1133 3 121 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.886 5 moderately conservative 601724 2q32 neurogenic differentiation 1 2416 rs1801265 DPYD 1806 1 98060906 NM_000110 NP_000101 C/T R29C minus 19100782 1303 SEQUENOM CEPH CEPH (92) 92 0.25 0.22 0.05 140 2 0.24 0.23 94 2 123 "by doubleHit,freq,cluster" radical 274270 1p22 dihydropyrimidine dehydrogenase 2417 rs1801265 DPYD 1806 1 98060906 NM_000110 NP_000101 C/T R29C minus 23739939 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.22 0.05 140 2 0.24 0.23 94 2 123 "by doubleHit,freq,cluster" radical 274270 1p22 dihydropyrimidine dehydrogenase 2418 rs1801274 FCGR2A 2212 1 158292800 NM_021642 NP_067674 C/T H165R minus 2707025 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.45 0.05 202 3 0.4 0.07 440 6 123 "by doubleHit,submitter,freq,cluster" Benign 0.639 24 conservative 146790 1q23 "Fc fragment of IgG, low affinity IIa, receptor for (CD32)" 2419 rs1801274 FCGR2A 2212 1 158292800 NM_021642 NP_067674 C/T H165R minus 5586537 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.47 0.45 0.05 202 3 0.4 0.07 440 6 123 "by doubleHit,submitter,freq,cluster" Benign 0.639 24 conservative 146790 1q23 "Fc fragment of IgG, low affinity IIa, receptor for (CD32)" 2420 rs1801274 FCGR2A 2212 1 158292800 NM_021642 NP_067674 C/T H165R minus 23156764 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.45 0.05 202 3 0.4 0.07 440 6 123 "by doubleHit,submitter,freq,cluster" Benign 0.639 24 conservative 146790 1q23 "Fc fragment of IgG, low affinity IIa, receptor for (CD32)" 2421 rs1801275 IL4R 3566 16 27281901 NM_000418 NP_000409 A/G Q576R plus 3172787 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 54 0.2 0.26 0.03 1730 6 0.34 0.1 480 7 123 "by cluster,freq" Benign 0.107 18 conservative 147781 16p11.2-12.1 interleukin 4 receptor 2422 rs1801275 IL4R 3566 16 27281901 NM_000418 NP_000409 A/G Q576R plus 4250598 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 44 0.3 0.26 0.03 1730 6 0.34 0.1 480 7 123 "by cluster,freq" Benign 0.107 18 conservative 147781 16p11.2-12.1 interleukin 4 receptor 2423 rs1801275 IL4R 3566 16 27281901 NM_000418 NP_000409 A/G Q576R plus 4250598 1303 SEQUENOM CEPH CEPH (92) 92 0.37 0.26 0.03 1730 6 0.34 0.1 480 7 123 "by cluster,freq" Benign 0.107 18 conservative 147781 16p11.2-12.1 interleukin 4 receptor 2424 rs1801275 IL4R 3566 16 27281901 NM_000418 NP_000409 A/G Q576R plus 5586673 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.26 0.26 0.03 1730 6 0.34 0.1 480 7 123 "by cluster,freq" Benign 0.107 18 conservative 147781 16p11.2-12.1 interleukin 4 receptor 2425 rs1801275 IL4R 3566 16 27281901 NM_000418 NP_000409 A/G Q576R plus 7986644 683 O_LEUT HUTTERITE USA Caucasians (German ancestry) 1430 0.25 0.26 0.03 1730 6 0.34 0.1 480 7 123 "by cluster,freq" Benign 0.107 18 conservative 147781 16p11.2-12.1 interleukin 4 receptor 2426 rs1801275 IL4R 3566 16 27281901 NM_000418 NP_000409 A/G Q576R plus 23444666 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.26 0.03 1730 6 0.34 0.1 480 7 123 "by cluster,freq" Benign 0.107 18 conservative 147781 16p11.2-12.1 interleukin 4 receptor 2427 rs1801276 IRS1 3667 2 227487426 NM_005544 NP_005535 C/G A512P minus 24796179 1303 SEQUENOM CEPH CEPH (92) 184 0.16 0.11 0.07 368 2 123 by freq Borderline 1.163 6 conservative 147545 2q36 insulin receptor substrate 1 2428 rs1801276 IRS1 3667 2 227487426 NM_005544 NP_005535 C/G A512P minus 24803560 1303 SEQUENOM CEPH CEPH (92) 184 0.06 0.11 0.07 368 2 123 by freq Borderline 1.163 6 conservative 147545 2q36 insulin receptor substrate 1 2429 rs1801278 IRS1 3667 2 227486049 NM_005544 NP_005535 A/G G971R minus 12675509 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.05 0.06 0.01 154 2 0.03 0 1774 4 121 "by cluster,freq" Probably damaging 2.031 6 moderately radical 147545 2q36 insulin receptor substrate 1 2430 rs1801278 IRS1 3667 2 227486049 NM_005544 NP_005535 A/G G971R minus 12675509 1303 SEQUENOM CEPH CEPH (92) 92 0.07 0.06 0.01 154 2 0.03 0 1774 4 121 "by cluster,freq" Probably damaging 2.031 6 moderately radical 147545 2q36 insulin receptor substrate 1 2431 rs1801280 NAT2 10 8 18302134 NM_000015 NP_000006 C/T I114T plus 5586798 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.44 0.44 0.09 288 3 0.27 0.12 432 6 123 "by cluster,freq" Benign 0.768 34 Borderline 0.11 2.85 40 moderately conservative 243400 8p22 N-acetyltransferase 2 (arylamine N-acetyltransferase) 2432 rs1801280 NAT2 10 8 18302134 NM_000015 NP_000006 C/T I114T plus 23737719 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.26 0.44 0.09 288 3 0.27 0.12 432 6 123 "by cluster,freq" Benign 0.768 34 Borderline 0.11 2.85 40 moderately conservative 243400 8p22 N-acetyltransferase 2 (arylamine N-acetyltransferase) 2433 rs1801280 NAT2 10 8 18302134 NM_000015 NP_000006 C/T I114T plus 24796683 1303 SEQUENOM CEPH CEPH (92) 184 0.48 0.44 0.09 288 3 0.27 0.12 432 6 123 "by cluster,freq" Benign 0.768 34 Borderline 0.11 2.85 40 moderately conservative 243400 8p22 N-acetyltransferase 2 (arylamine N-acetyltransferase) 2434 rs1801282 PPARG 5468 3 12368125 NM_015869 NP_056953 C/G P12A plus 5587532 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 4 0.25 0.11 0.02 1139 7 0.05 0.01 426 8 123 "by cluster,freq" conservative 601487 3p25 "peroxisome proliferative activated receptor, gamma" 2435 rs1801282 PPARG 5468 3 12368125 NM_015869 NP_056953 C/G P12A plus 5587532 902 AFFY Caucasian 22 0.09 0.11 0.02 1139 7 0.05 0.01 426 8 123 "by cluster,freq" conservative 601487 3p25 "peroxisome proliferative activated receptor, gamma" 2436 rs1801282 PPARG 5468 3 12368125 NM_015869 NP_056953 C/G P12A plus 5587532 904 AFFY CEPH 8 0.13 0.11 0.02 1139 7 0.05 0.01 426 8 123 "by cluster,freq" conservative 601487 3p25 "peroxisome proliferative activated receptor, gamma" 2437 rs1801282 PPARG 5468 3 12368125 NM_015869 NP_056953 C/G P12A plus 5587532 1303 SEQUENOM CEPH CEPH (92) 92 0.1 0.11 0.02 1139 7 0.05 0.01 426 8 123 "by cluster,freq" conservative 601487 3p25 "peroxisome proliferative activated receptor, gamma" 2438 rs1801282 PPARG 5468 3 12368125 NM_015869 NP_056953 C/G P12A plus 12587275 928 IBARROSO ELY UK (Ely region of East Anglia) 921 0.12 0.11 0.02 1139 7 0.05 0.01 426 8 123 "by cluster,freq" conservative 601487 3p25 "peroxisome proliferative activated receptor, gamma" 2439 rs1801282 PPARG 5468 3 12368125 NM_015869 NP_056953 C/G P12A plus 24301991 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.11 0.02 1139 7 0.05 0.01 426 8 123 "by cluster,freq" conservative 601487 3p25 "peroxisome proliferative activated receptor, gamma" 2440 rs1801282 PPARG 5468 3 12368125 NM_015869 NP_056953 C/G P12A plus 28447437 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 44 0.07 0.11 0.02 1139 7 0.05 0.01 426 8 123 "by cluster,freq" conservative 601487 3p25 "peroxisome proliferative activated receptor, gamma" 2441 rs1801311 NDUFA6 4700 22 40811223 NM_002490 NP_002481 C/T A9V minus 8298715 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.33 0.4 0.11 212 2 120 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.041 9 moderately conservative 602138 22q13.2-q13.31 "NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6, 14kDa" 2442 rs1801311 NDUFA6 4700 22 40811223 NM_002490 NP_002481 C/T A9V minus 8298715 1303 SEQUENOM CEPH CEPH (92) 92 0.49 0.4 0.11 212 2 120 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.041 9 moderately conservative 602138 22q13.2-q13.31 "NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6, 14kDa" 2443 rs1801376 BUB1B 701 15 38265123 NM_001211 NP_001202 A/G R349Q plus 12312147 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.27 0.26 0.03 168 2 0.37 0.03 1566 3 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 602860 15q15 BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast) 2444 rs1801376 BUB1B 701 15 38265123 NM_001211 NP_001202 A/G R349Q plus 24035662 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.26 0.03 168 2 0.37 0.03 1566 3 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 602860 15q15 BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast) 2445 rs1801426 BRCA2 675 13 31870884 NM_000059 NP_000050 A/G I3412V plus 5586309 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.02 0.03 0.01 212 2 0.06 0.04 434 6 123 "by cluster,freq" conservative 600185 13q12.3 "breast cancer 2, early onset" 2446 rs1801426 BRCA2 675 13 31870884 NM_000059 NP_000050 A/G I3412V plus 16356058 693 EGP_SNPS PDR90 NIHPDR 152 0.03 0.03 0.01 212 2 0.06 0.04 434 6 123 "by cluster,freq" conservative 600185 13q12.3 "breast cancer 2, early onset" 2447 rs1801689 APOH 350 17 61641042 NM_000042 NP_000033 G/T C325G minus 24592474 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 123 by freq Probably damaging 3.168 12 radical 138700 17q23-qter apolipoprotein H (beta-2-glycoprotein I) 2448 rs1801690 APOH 350 17 61638747 NM_000042 NP_000033 C/G W335S minus 9807051 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 42 0.02 0.06 0.02 456 4 0.03 0.01 94 2 123 "by cluster,freq" Probably damaging 3.543 11 radical 138700 17q23-qter apolipoprotein H (beta-2-glycoprotein I) 2449 rs1801690 APOH 350 17 61638747 NM_000042 NP_000033 C/G W335S minus 24592426 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.04 0.06 0.02 456 4 0.03 0.01 94 2 123 "by cluster,freq" Probably damaging 3.543 11 radical 138700 17q23-qter apolipoprotein H (beta-2-glycoprotein I) 2450 rs1801690 APOH 350 17 61638747 NM_000042 NP_000033 C/G W335S minus 24796544 1303 SEQUENOM CEPH CEPH (92) 184 0.07 0.06 0.02 456 4 0.03 0.01 94 2 123 "by cluster,freq" Probably damaging 3.543 11 radical 138700 17q23-qter apolipoprotein H (beta-2-glycoprotein I) 2451 rs1801690 APOH 350 17 61638747 NM_000042 NP_000033 C/G W335S minus 24803567 1303 SEQUENOM CEPH CEPH (92) 184 0.06 0.06 0.02 456 4 0.03 0.01 94 2 123 "by cluster,freq" Probably damaging 3.543 11 radical 138700 17q23-qter apolipoprotein H (beta-2-glycoprotein I) 2452 rs1801699 APOB 338 2 21145651 NM_000384 NP_000375 A/G N1914S minus 24242192 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.01 0 92 1 123 "HapMap,submitter,cluster" conservative 107730 2p24-p23 apolipoprotein B (including Ag(x) antigen) 2453 rs1801701 APOB 338 2 21140479 NM_000384 NP_000375 A/G R3638Q minus 24796145 1303 SEQUENOM CEPH CEPH (92) 184 0.13 0.13 0 184 1 0.1 0 94 1 123 "by cluster,freq" conservative 107730 2p24-p23 apolipoprotein B (including Ag(x) antigen) 2454 rs1801702 APOB 338 2 21137137 NM_000384 NP_000375 C/G R4270T minus 6424043 1303 SEQUENOM CEPH CEPH (92) 92 0.08 0.08 0 92 1 0.08 0.04 574 7 123 "by cluster,freq" moderately conservative 107730 2p24-p23 apolipoprotein B (including Ag(x) antigen) 2455 rs1801714 ICAM1 3383 19 10256208 NM_000201 NP_000192 C/T P352L plus 3176193 619 WICVAR MITOGPOP6 CORIELL Mixed 40 0.03 0.03 0 80 2 113 "by cluster,freq" Probably damaging 2.293 13 Borderline 0.16 2.85 21 moderately conservative 147840 19p13.3-p13.2 "intercellular adhesion molecule 1 (CD54), human rhinovirus receptor" 2456 rs1801714 ICAM1 3383 19 10256208 NM_000201 NP_000192 C/T P352L plus 7985496 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 40 0.03 0.03 0 80 2 113 "by cluster,freq" Probably damaging 2.293 13 Borderline 0.16 2.85 21 moderately conservative 147840 19p13.3-p13.2 "intercellular adhesion molecule 1 (CD54), human rhinovirus receptor" 2457 rs1801725 CASR 846 3 123486447 NM_000388 NP_000379 G/T A986S plus 5606251 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.15 0.15 0.01 290 3 0.09 0.06 434 6 123 "by cluster,freq" Benign 0.105 10 moderately conservative 601199 3q21-q24 "calcium-sensing receptor (hypocalciuric hypercalcemia 1, severe neonatal hyperparathyroidism)" 2458 rs1801725 CASR 846 3 123486447 NM_000388 NP_000379 G/T A986S plus 24317505 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.17 0.15 0.01 290 3 0.09 0.06 434 6 123 "by cluster,freq" Benign 0.105 10 moderately conservative 601199 3q21-q24 "calcium-sensing receptor (hypocalciuric hypercalcemia 1, severe neonatal hyperparathyroidism)" 2459 rs1801725 CASR 846 3 123486447 NM_000388 NP_000379 G/T A986S plus 24795982 1303 SEQUENOM CEPH CEPH (92) 184 0.15 0.15 0.01 290 3 0.09 0.06 434 6 123 "by cluster,freq" Benign 0.105 10 moderately conservative 601199 3q21-q24 "calcium-sensing receptor (hypocalciuric hypercalcemia 1, severe neonatal hyperparathyroidism)" 2460 rs1801726 CASR 846 3 123486522 NM_000388 NP_000379 C/G E1011Q plus 5606250 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.03 0.04 0.02 108 2 0.03 0.04 1516 6 123 "by doubleHit,submitter,freq,cluster" Benign 0.675 6 conservative 601199 3q21-q24 "calcium-sensing receptor (hypocalciuric hypercalcemia 1, severe neonatal hyperparathyroidism)" 2461 rs1801726 CASR 846 3 123486522 NM_000388 NP_000379 C/G E1011Q plus 23264216 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.04 0.02 108 2 0.03 0.04 1516 6 123 "by doubleHit,submitter,freq,cluster" Benign 0.675 6 conservative 601199 3q21-q24 "calcium-sensing receptor (hypocalciuric hypercalcemia 1, severe neonatal hyperparathyroidism)" 2462 rs1802002 CDIPT 10423 16 29778058 NM_006319 NP_006310 C/T R199C minus 24796504 1303 SEQUENOM CEPH CEPH (92) 184 0.05 0.05 0 184 1 123 by freq Borderline 0.14 2.8 19 radical 605893 16p12.1 CDP-diacylglycerol--inositol 3-phosphatidyltransferase (phosphatidylinositol synthase) 2463 rs1802073 SFRP4 6424 7 37720404 NM_003014 NP_003005 A/C P320T minus 3844710 1303 SEQUENOM CEPH CEPH (92) 92 0.33 0.34 0.01 140 2 0.41 0 92 2 123 "by doubleHit,freq,cluster" conservative 606570 7p14.1 secreted frizzled-related protein 4 2464 rs1802073 SFRP4 6424 7 37720404 NM_003014 NP_003005 A/C P320T minus 23395019 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.34 0.01 140 2 0.41 0 92 2 123 "by doubleHit,freq,cluster" conservative 606570 7p14.1 secreted frizzled-related protein 4 2465 rs1802074 SFRP4 6424 7 37720343 NM_003014 NP_003005 A/G R340K minus 24796330 1303 SEQUENOM CEPH CEPH (92) 184 0.42 0.42 0 184 1 123 by freq conservative 606570 7p14.1 secreted frizzled-related protein 4 2466 rs1802617 ZNF137 7696 19 57792397 NM_003438 NP_003429 G/T Q181H plus 10928225 1303 SEQUENOM CEPH CEPH (92) 92 0.34 0.34 0 92 1 0.24 0 1492 1 121 "by doubleHit,freq,cluster" Potentially damaging 1.338 20 Intolerant 0 2.75 368 conservative 604079 19q13.4 zinc finger protein 137 (clone pHZ-30) 2467 rs1802668 DLG1 1739 3 198409670 NM_004087 NP_004078 A/G K140R minus 24645157 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.08 0.01 232 2 123 by freq Borderline 1.219 15 conservative 601014 3q29 "discs, large homolog 1 (Drosophila)" 2468 rs1802668 DLG1 1739 3 198409670 NM_004087 NP_004078 A/G K140R minus 24796205 1303 SEQUENOM CEPH CEPH (92) 184 0.08 0.08 0.01 232 2 123 by freq Borderline 1.219 15 conservative 601014 3q29 "discs, large homolog 1 (Drosophila)" 2469 rs1803155 AADAC 13 3 153028299 NM_001086 NP_001077 A/G V281I plus 3377328 1303 SEQUENOM CEPH CEPH (92) 92 0.27 0.27 0 92 1 0.42 0 1494 1 121 "by doubleHit,freq,cluster" Benign 0.986 6 conservative 600338 3q21.3-q25.2 arylacetamide deacetylase (esterase) 2470 rs1803274 BCHE 590 3 166973982 NM_000055 NP_000046 A/G A567T minus 24385183 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.17 0 48 1 0.11 0.05 94 2 123 "by cluster,freq" Benign 0.386 19 Borderline 0.14 2.92 30 moderately conservative 177400 3q26.1-q26.2 butyrylcholinesterase 2471 rs1803843 CDKN3 1033 14 53954343 NM_005192 NP_005183 C/T S159F plus 24796473 1303 SEQUENOM CEPH CEPH (92) 184 0.07 0.07 0 184 1 123 by freq Benign 0.166 12 Intolerant 0.01 2.86 49 radical 123832 14q22 cyclin-dependent kinase inhibitor 3 (CDK2-associated dual specificity phosphatase) 2472 rs1804020 ZFML 27332 2 71565830 NM_014497 NP_055312 A/G V1726M plus 21655471 1303 SEQUENOM CEPH CEPH (92) 92 0.22 0.22 0 92 1 121 "by doubleHit,freq" conservative 2p13.2-p13.1 NP220 nuclear protein 2473 rs1804062 AKR1C3 8644 10 5128623 NM_003739 NP_003730 G/T E36X plus 24796396 1303 SEQUENOM CEPH CEPH (92) 184 0.14 0.14 0 184 1 123 by freq Probably damaging Intolerant radical 603966 10p15-p14 "aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II)" 2474 rs1804118 TTR 7276 18 27432605 NM_000371 NP_000362 A/C T138N plus 2424851 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 83 0.22 0.22 0 83 1 0.23 0 83 1 123 by freq Possibly damaging 1.67 50 Intolerant 0 2.9 35 moderately conservative 176300 18q12.1 "transthyretin (prealbumin, amyloidosis type I)" 2475 rs1804160 PCK1 5105 20 55572771 NM_002591 NP_002582 A/G V368I plus 24451455 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.02 0 46 1 123 by freq Benign 0.49 53 Borderline 0.15 2.77 291 conservative 261680 20q13.31 phosphoenolpyruvate carboxykinase 1 (soluble) 2476 rs1804515 TMSB10 9168 2 85044819 NM_021103 NP_066926 G/T M7R plus 24803613 1303 SEQUENOM CEPH CEPH (92) 184 0.2 0.2 0 184 1 123 by freq moderately conservative 188399 2p11.2 "thymosin, beta 10" 2477 rs1804785 ACO2 50 22 40249076 NM_001098 NP_001089 G/T A768S plus 24803614 1303 SEQUENOM CEPH CEPH (92) 184 0.02 0.02 0 184 1 123 by freq Benign 0.689 61 Intolerant 0.03 2.82 59 moderately conservative 100850 22q13.2-q13.31 "aconitase 2, mitochondrial" 2478 rs1805002 CCKBR 887 11 6247696 NM_176875 NP_795344 A/G V125I plus 12586737 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.04 0.05 0.01 168 2 0.02 0 46 1 123 "HapMap,submitter,freq,cluster" Tolerant 0.23 2.8 30 conservative 118445 11p15.4 cholecystokinin B receptor 2479 rs1805002 CCKBR 887 11 6247696 NM_176875 NP_795344 A/G V125I plus 24513918 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.05 0.01 168 2 0.02 0 46 1 123 "HapMap,submitter,freq,cluster" Tolerant 0.23 2.8 30 conservative 118445 11p15.4 cholecystokinin B receptor 2480 rs1805005 MC1R 4157 16 88513345 NM_002386 NP_002377 G/T V60L plus 3173165 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 60 0.03 0.06 0.06 106 2 106 "by cluster,freq" Possibly damaging 1.501 210 Tolerant 0.28 2.8 286 conservative 155555 16q24.3 melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor) 2481 rs1805005 MC1R 4157 16 88513345 NM_002386 NP_002377 G/T V60L plus 4472754 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.11 0.06 0.06 106 2 106 "by cluster,freq" Possibly damaging 1.501 210 Tolerant 0.28 2.8 286 conservative 155555 16q24.3 melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor) 2482 rs1805007 MC1R 4157 16 88513618 NM_002386 NP_002377 C/T R151C plus 4472756 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.11 0.11 0 92 2 123 "by cluster,freq" Probably damaging 2.899 206 Intolerant 0 2.79 280 radical 155555 16q24.3 melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor) 2483 rs1805007 MC1R 4157 16 88513618 NM_002386 NP_002377 C/T R151C plus 24695277 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.11 0.11 0 92 2 123 "by cluster,freq" Probably damaging 2.899 206 Intolerant 0 2.79 280 radical 155555 16q24.3 melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor) 2484 rs1805008 MC1R 4157 16 88513645 NM_002386 NP_002377 C/T R160W plus 4472758 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.09 0.09 0 46 1 110 "by cluster,freq" Benign 0.183 207 Intolerant 0.01 2.8 283 moderately radical 155555 16q24.3 melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor) 2485 rs1805011 IL4R 3566 16 27281373 NM_000418 NP_000409 A/C E400A plus 4250592 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.13 0.13 0 108 2 0.27 0.13 384 5 119 "by doubleHit,freq,cluster" Benign 0.264 18 moderately radical 147781 16p11.2-12.1 interleukin 4 receptor 2486 rs1805011 IL4R 3566 16 27281373 NM_000418 NP_000409 A/C E400A plus 5586670 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.13 0.13 0 108 2 0.27 0.13 384 5 119 "by doubleHit,freq,cluster" Benign 0.264 18 moderately radical 147781 16p11.2-12.1 interleukin 4 receptor 2487 rs1805012 IL4R 3566 16 27281465 NM_000418 NP_000409 C/T C431R plus 4250594 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.13 0.13 0 108 2 0.1 0.04 386 5 116 "by cluster,freq" Potentially damaging 1.467 18 radical 147781 16p11.2-12.1 interleukin 4 receptor 2488 rs1805012 IL4R 3566 16 27281465 NM_000418 NP_000409 C/T C431R plus 5586671 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.13 0.13 0 108 2 0.1 0.04 386 5 116 "by cluster,freq" Potentially damaging 1.467 18 radical 147781 16p11.2-12.1 interleukin 4 receptor 2489 rs1805013 IL4R 3566 16 27281481 NM_000418 NP_000409 C/T S436L plus 4250627 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.09 0.07 0.02 108 2 0.03 0.01 296 3 123 "by cluster,freq" Benign 0.129 18 moderately radical 147781 16p11.2-12.1 interleukin 4 receptor 2490 rs1805013 IL4R 3566 16 27281481 NM_000418 NP_000409 C/T S436L plus 5586672 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.06 0.07 0.02 108 2 0.03 0.01 296 3 123 "by cluster,freq" Benign 0.129 18 moderately radical 147781 16p11.2-12.1 interleukin 4 receptor 2491 rs1805015 IL4R 3566 16 27281681 NM_000418 NP_000409 C/T S503P plus 3176232 619 WICVAR MITOGPOP6 CORIELL Mixed 46 0.02 0.18 0.12 182 3 0.31 0 48 1 102 by freq Benign 0.283 18 moderately conservative 147781 16p11.2-12.1 interleukin 4 receptor 2492 rs1805015 IL4R 3566 16 27281681 NM_000418 NP_000409 C/T S503P plus 4250597 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 44 0.2 0.18 0.12 182 3 0.31 0 48 1 102 by freq Benign 0.283 18 moderately conservative 147781 16p11.2-12.1 interleukin 4 receptor 2493 rs1805015 IL4R 3566 16 27281681 NM_000418 NP_000409 C/T S503P plus 4250597 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.18 0.12 182 3 0.31 0 48 1 102 by freq Benign 0.283 18 moderately conservative 147781 16p11.2-12.1 interleukin 4 receptor 2494 rs1805016 IL4R 3566 16 27282428 NM_000418 NP_000409 G/T S752A plus 4250601 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.09 0.08 0.01 156 3 0.14 0.07 430 6 123 "by cluster,freq" Potentially damaging 1.323 18 moderately conservative 147781 16p11.2-12.1 interleukin 4 receptor 2495 rs1805016 IL4R 3566 16 27282428 NM_000418 NP_000409 G/T S752A plus 5586674 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.08 0.08 0.01 156 3 0.14 0.07 430 6 123 "by cluster,freq" Potentially damaging 1.323 18 moderately conservative 147781 16p11.2-12.1 interleukin 4 receptor 2496 rs1805016 IL4R 3566 16 27282428 NM_000418 NP_000409 G/T S752A plus 23444700 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0.01 156 3 0.14 0.07 430 6 123 "by cluster,freq" Potentially damaging 1.323 18 moderately conservative 147781 16p11.2-12.1 interleukin 4 receptor 2497 rs1805017 PLA2G7 7941 6 46792181 NM_005084 NP_005075 A/G R92H minus 24622434 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.33 0.06 232 2 0.23 0.01 92 2 123 "by submitter,freq" Benign 0.639 8 Tolerant 0.53 2.85 22 conservative 601690 6p21.2-p12 "phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)" 2498 rs1805017 PLA2G7 7941 6 46792181 NM_005084 NP_005075 A/G R92H minus 24796315 1303 SEQUENOM CEPH CEPH (92) 184 0.35 0.33 0.06 232 2 0.23 0.01 92 2 123 "by submitter,freq" Benign 0.639 8 Tolerant 0.53 2.85 22 conservative 601690 6p21.2-p12 "phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)" 2499 rs1805018 PLA2G7 7941 6 46787262 NM_005084 NP_005075 C/T I198T minus 22377263 1303 SEQUENOM CEPH CEPH (92) 92 0.12 0.09 0.05 140 2 0.19 0.03 1584 3 123 "by doubleHit,submitter,freq,cluster" Borderline 1.136 8 Tolerant 0.65 2.76 24 moderately conservative 601690 6p21.2-p12 "phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)" 2500 rs1805018 PLA2G7 7941 6 46787262 NM_005084 NP_005075 C/T I198T minus 23675804 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.09 0.05 140 2 0.19 0.03 1584 3 123 "by doubleHit,submitter,freq,cluster" Borderline 1.136 8 Tolerant 0.65 2.76 24 moderately conservative 601690 6p21.2-p12 "phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)" 2501 rs1805034 TNFRSF11A 8792 18 58178221 NM_003839 NP_003830 C/T A192V plus 12439382 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.47 0.46 0.02 168 2 0.41 0.09 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 603499 18q22.1 "tumor necrosis factor receptor superfamily, member 11a, activator of NFKB" 2502 rs1805034 TNFRSF11A 8792 18 58178221 NM_003839 NP_003830 C/T A192V plus 23488962 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.46 0.02 168 2 0.41 0.09 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 603499 18q22.1 "tumor necrosis factor receptor superfamily, member 11a, activator of NFKB" 2503 rs1805074 DMGDH 29958 5 78360108 NM_013391 NP_037523 C/T S646P minus 23392777 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.27 0 48 1 0.31 0.15 92 2 123 "by submitter,freq,cluster" Potentially damaging 1.316 7 Tolerant 0.21 2.79 17 moderately conservative 605849 5q14.1 dimethylglycine dehydrogenase 2504 rs1805075 IGF2R 3482 6 160475618 NM_000876 NP_000867 A/G N2020S plus 12585941 693 EGP_SNPS PDR90 NIHPDR 180 0.14 0.12 0.06 228 2 0.33 0 48 1 123 by freq Potentially damaging 1.37 17 Tolerant 0.34 2.94 29 conservative 147280 6q26 insulin-like growth factor 2 receptor 2505 rs1805075 IGF2R 3482 6 160475618 NM_000876 NP_000867 A/G N2020S plus 24053426 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.12 0.06 228 2 0.33 0 48 1 123 by freq Potentially damaging 1.37 17 Tolerant 0.34 2.94 29 conservative 147280 6q26 insulin-like growth factor 2 receptor 2506 rs1805086 GDF8 2660 2 190750583 NM_005259 NP_005250 A/G K153R minus 2426001 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 83 0.05 0.05 0 83 1 0.21 0.18 266 5 123 "by submitter,freq,cluster" Benign 0.153 53 Tolerant 0.62 2.84 89 conservative 601788 2q32.2 growth differentiation factor 8 2507 rs1805087 MTR 4548 1 233374541 NM_000254 NP_000245 A/G D919G plus 2961149 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 83 0.19 0.22 0.06 371 6 0.2 0.03 1812 7 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.004 57 Tolerant 0.37 2.8 51 moderately conservative 156570 1q43 5-methyltetrahydrofolate-homocysteine methyltransferase 2508 rs1805087 MTR 4548 1 233374541 NM_000254 NP_000245 A/G D919G plus 2961149 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.17 0.22 0.06 371 6 0.2 0.03 1812 7 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.004 57 Tolerant 0.37 2.8 51 moderately conservative 156570 1q43 5-methyltetrahydrofolate-homocysteine methyltransferase 2509 rs1805087 MTR 4548 1 233374541 NM_000254 NP_000245 A/G D919G plus 2961149 902 AFFY Caucasian 22 0.32 0.22 0.06 371 6 0.2 0.03 1812 7 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.004 57 Tolerant 0.37 2.8 51 moderately conservative 156570 1q43 5-methyltetrahydrofolate-homocysteine methyltransferase 2510 rs1805087 MTR 4548 1 233374541 NM_000254 NP_000245 A/G D919G plus 2961149 904 AFFY CEPH 6 0.33 0.22 0.06 371 6 0.2 0.03 1812 7 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.004 57 Tolerant 0.37 2.8 51 moderately conservative 156570 1q43 5-methyltetrahydrofolate-homocysteine methyltransferase 2511 rs1805087 MTR 4548 1 233374541 NM_000254 NP_000245 A/G D919G plus 14457700 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.22 0.06 371 6 0.2 0.03 1812 7 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.004 57 Tolerant 0.37 2.8 51 moderately conservative 156570 1q43 5-methyltetrahydrofolate-homocysteine methyltransferase 2512 rs1805087 MTR 4548 1 233374541 NM_000254 NP_000245 A/G D919G plus 24276502 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.22 0.06 371 6 0.2 0.03 1812 7 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.004 57 Tolerant 0.37 2.8 51 moderately conservative 156570 1q43 5-methyltetrahydrofolate-homocysteine methyltransferase 2513 rs1805097 IRS2 8660 13 109233232 NM_003749 NP_003740 A/G G1057D minus 12266409 1303 SEQUENOM CEPH CEPH (92) 92 0.21 0.21 0 92 1 119 "by doubleHit,freq,cluster" moderately conservative 600797 13q34 insulin receptor substrate 2 2514 rs1805107 CDX2 1045 13 27435317 NM_001265 NP_001256 C/T P293S minus 12587362 928 IBARROSO ELY UK (Ely region of East Anglia) 921 0.18 0.18 0 921 1 121 "by doubleHit,freq,cluster" moderately conservative 600297 13q12.3 caudal type homeo box transcription factor 2 2515 rs1805318 PMS2 5395 7 5799848 NM_000535 NP_000526 A/T T597S minus 2667723 506 NCBI NIHPDR NIHPDR 84 0.02 0.03 0.01 202 2 101 "HapMap,freq,cluster" Tolerant 0.79 2.82 12 moderately conservative 600259 7p22.2 PMS2 postmeiotic segregation increased 2 (S. cerevisiae) 2516 rs1805318 PMS2 5395 7 5799848 NM_000535 NP_000526 A/T T597S minus 2667723 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.03 0.03 0.01 202 2 101 "HapMap,freq,cluster" Tolerant 0.79 2.82 12 moderately conservative 600259 7p22.2 PMS2 postmeiotic segregation increased 2 (S. cerevisiae) 2517 rs1805321 PMS2 5395 7 5800229 NM_000535 NP_000526 C/T P470S minus 2667726 506 NCBI NIHPDR NIHPDR 92 0.36 0.32 0.12 366 4 120 "HapMap,freq,cluster" Tolerant 0.73 2.82 12 moderately conservative 600259 7p22.2 PMS2 postmeiotic segregation increased 2 (S. cerevisiae) 2518 rs1805321 PMS2 5395 7 5800229 NM_000535 NP_000526 C/T P470S minus 3172641 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 64 0.09 0.32 0.12 366 4 120 "HapMap,freq,cluster" Tolerant 0.73 2.82 12 moderately conservative 600259 7p22.2 PMS2 postmeiotic segregation increased 2 (S. cerevisiae) 2519 rs1805321 PMS2 5395 7 5800229 NM_000535 NP_000526 C/T P470S minus 5259684 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.33 0.32 0.12 366 4 120 "HapMap,freq,cluster" Tolerant 0.73 2.82 12 moderately conservative 600259 7p22.2 PMS2 postmeiotic segregation increased 2 (S. cerevisiae) 2520 rs1805321 PMS2 5395 7 5800229 NM_000535 NP_000526 C/T P470S minus 5259684 1303 SEQUENOM CEPH CEPH (92) 92 0.41 0.32 0.12 366 4 120 "HapMap,freq,cluster" Tolerant 0.73 2.82 12 moderately conservative 600259 7p22.2 PMS2 postmeiotic segregation increased 2 (S. cerevisiae) 2521 rs1805323 PMS2 5395 7 5800183 NM_000535 NP_000526 A/C T485K minus 2667729 506 NCBI NIHPDR NIHPDR 92 0.05 0.05 0 92 1 101 "by cluster,freq" Intolerant 0.04 2.82 12 moderately conservative 600259 7p22.2 PMS2 postmeiotic segregation increased 2 (S. cerevisiae) 2522 rs1805324 PMS2 5395 7 5799771 NM_000535 NP_000526 A/G M622I minus 2667730 506 NCBI NIHPDR NIHPDR 72 0.03 0.03 0 72 1 101 "by cluster,freq" Tolerant 0.36 2.82 12 conservative 600259 7p22.2 PMS2 postmeiotic segregation increased 2 (S. cerevisiae) 2523 rs1805329 RAD23B 5887 9 107163883 NM_002874 NP_002865 C/T A249V plus 2667735 506 NCBI NIHPDR NIHPDR 86 0.19 0.18 0.03 492 5 0.18 0.06 346 4 120 "HapMap,submitter,freq,cluster" Benign 0.156 12 Tolerant 0.25 2.76 27 moderately conservative 600062 9q31.2 RAD23 homolog B (S. cerevisiae) 2524 rs1805329 RAD23B 5887 9 107163883 NM_002874 NP_002865 C/T A249V plus 3172617 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 48 0.13 0.18 0.03 492 5 0.18 0.06 346 4 120 "HapMap,submitter,freq,cluster" Benign 0.156 12 Tolerant 0.25 2.76 27 moderately conservative 600062 9q31.2 RAD23 homolog B (S. cerevisiae) 2525 rs1805329 RAD23B 5887 9 107163883 NM_002874 NP_002865 C/T A249V plus 5586896 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.21 0.18 0.03 492 5 0.18 0.06 346 4 120 "HapMap,submitter,freq,cluster" Benign 0.156 12 Tolerant 0.25 2.76 27 moderately conservative 600062 9q31.2 RAD23 homolog B (S. cerevisiae) 2526 rs1805329 RAD23B 5887 9 107163883 NM_002874 NP_002865 C/T A249V plus 5586896 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.15 0.18 0.03 492 5 0.18 0.06 346 4 120 "HapMap,submitter,freq,cluster" Benign 0.156 12 Tolerant 0.25 2.76 27 moderately conservative 600062 9q31.2 RAD23 homolog B (S. cerevisiae) 2527 rs1805329 RAD23B 5887 9 107163883 NM_002874 NP_002865 C/T A249V plus 16358632 693 EGP_SNPS PDR90 NIHPDR 176 0.2 0.18 0.03 492 5 0.18 0.06 346 4 120 "HapMap,submitter,freq,cluster" Benign 0.156 12 Tolerant 0.25 2.76 27 moderately conservative 600062 9q31.2 RAD23 homolog B (S. cerevisiae) 2528 rs1805378 NTHL1 4913 16 2034654 NM_002528 NP_002519 C/T I176T minus 2667796 506 NCBI NIHPDR NIHPDR 84 0.01 0.01 0 84 1 102 "by cluster,freq" Intolerant 0 2.73 35 moderately conservative 602656 16p13.3 nth endonuclease III-like 1 (E. coli) 2529 rs1805409 ADPRT 142 1 222884901 NM_001618 NP_001609 A/G A188T minus 2667854 506 NCBI NIHPDR NIHPDR 96 0.01 0.01 0 276 2 113 "by cluster,freq" Borderline 1.016 8 Tolerant 0.57 2.81 20 moderately conservative 173870 1q41-q42 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase) 2530 rs1805409 ADPRT 142 1 222884901 NM_001618 NP_001609 A/G A188T minus 4480415 693 EGP_SNPS PDR90 NIHPDR 180 0.01 0.01 0 276 2 113 "by cluster,freq" Borderline 1.016 8 Tolerant 0.57 2.81 20 moderately conservative 173870 1q41-q42 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase) 2531 rs1805749 KLRG1 10219 12 9036158 NM_005810 NP_005801 A/G W58R minus 2668237 1303 SEQUENOM CEPH CEPH (92) 92 0.37 0.37 0 92 1 92 by freq Tolerant 0.85 2.85 9 moderately radical 604874 12p12-p13 "killer cell lectin-like receptor subfamily G, member 1" 2532 rs1805794 NBS1 4683 8 91059655 NM_002485 NP_002476 C/G E185Q plus 870115 506 NCBI NIHPDR NIHPDR 174 0.33 0.32 0.04 652 6 0.46 0.09 1930 7 123 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.042 8 Tolerant 1 2.95 21 conservative 602667 8q21 Nijmegen breakage syndrome 1 (nibrin) 2533 rs1805794 NBS1 4683 8 91059655 NM_002485 NP_002476 C/G E185Q plus 5586804 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.31 0.32 0.04 652 6 0.46 0.09 1930 7 123 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.042 8 Tolerant 1 2.95 21 conservative 602667 8q21 Nijmegen breakage syndrome 1 (nibrin) 2534 rs1805794 NBS1 4683 8 91059655 NM_002485 NP_002476 C/G E185Q plus 22970225 693 EGP_SNPS PDR90 NIHPDR 156 0.37 0.32 0.04 652 6 0.46 0.09 1930 7 123 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.042 8 Tolerant 1 2.95 21 conservative 602667 8q21 Nijmegen breakage syndrome 1 (nibrin) 2535 rs1805794 NBS1 4683 8 91059655 NM_002485 NP_002476 C/G E185Q plus 22970225 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.28 0.32 0.04 652 6 0.46 0.09 1930 7 123 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.042 8 Tolerant 1 2.95 21 conservative 602667 8q21 Nijmegen breakage syndrome 1 (nibrin) 2536 rs1805794 NBS1 4683 8 91059655 NM_002485 NP_002476 C/G E185Q plus 22970225 1303 SEQUENOM CEPH CEPH (92) 92 0.28 0.32 0.04 652 6 0.46 0.09 1930 7 123 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.042 8 Tolerant 1 2.95 21 conservative 602667 8q21 Nijmegen breakage syndrome 1 (nibrin) 2537 rs1805794 NBS1 4683 8 91059655 NM_002485 NP_002476 C/G E185Q plus 24042204 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.32 0.04 652 6 0.46 0.09 1930 7 123 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.042 8 Tolerant 1 2.95 21 conservative 602667 8q21 Nijmegen breakage syndrome 1 (nibrin) 2538 rs1811237 PCDHB7 56129 5 140534665 NM_018940 NP_061763 A/C V689L minus 2675851 1303 SEQUENOM CEPH CEPH (92) 92 0.11 0.11 0 92 1 120 "by doubleHit,submitter,freq,cluster" Possibly damaging 1.631 103 Intolerant 0 2.78 128 conservative 606333 5q31 protocadherin beta 7 2539 rs1815811 PDZK2 79849 11 118564614 NM_024791 NP_079067 A/G R358Q plus 5574788 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.43 0.44 0.01 164 2 0.23 0.19 94 2 123 "HapMap,doubleHit,freq,cluster" conservative 607146 11q23.3 PDZ domain containing 2 2540 rs1815811 PDZK2 79849 11 118564614 NM_024791 NP_079067 A/G R358Q plus 24569183 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.45 0.44 0.01 164 2 0.23 0.19 94 2 123 "HapMap,doubleHit,freq,cluster" conservative 607146 11q23.3 PDZ domain containing 2 2541 rs1820128 ZNF600 162966 19 57962196 NM_198457 NP_940859 A/G C209R plus 5274133 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.17 0.17 0 120 1 121 "HapMap,doubleHit,freq,cluster" Probably damaging 2.094 15 radical 19q13.42 zinc finger protein 600 2542 rs1820965 TAF1B 9014 2 10010368 NM_005680 NP_005671 A/C E462D minus 19457023 1303 SEQUENOM CEPH CEPH (92) 92 0.22 0.24 0.05 140 2 0.34 0.09 92 2 123 "by doubleHit,submitter,freq,cluster" conservative 604904 2p25 "TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa" 2543 rs1820965 TAF1B 9014 2 10010368 NM_005680 NP_005671 A/C E462D minus 24162698 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.24 0.05 140 2 0.34 0.09 92 2 123 "by doubleHit,submitter,freq,cluster" conservative 604904 2p25 "TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa" 2544 rs1822135 ADPRTL1 143 13 23906630 NM_006437 NP_006428 A/G L1550P plus 2689070 1303 SEQUENOM CEPH CEPH (92) 92 0.05 0.05 0 92 1 121 "by doubleHit,freq,cluster" moderately conservative 607519 13q11 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1 2545 rs1833785 SIGLEC10 89790 19 56609947 NM_033130 NP_149121 G/T R520S plus 23766897 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.29 0.29 0 42 1 0.28 0.13 82 2 123 "by doubleHit,freq,cluster" Benign 0.237 7 Tolerant 0.56 3.01 8 moderately radical 606091 19q13.3 sialic acid binding Ig-like lectin 10 2546 rs1841958 KLRC4 8302 12 10453356 NM_013431 NP_038459 A/C I29S plus 5472183 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.31 0.25 0.1 212 2 0.23 0 1420 1 120 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.968 53 Borderline 0.14 2.86 66 moderately radical 602893 12p13.2-p12.3 "killer cell lectin-like receptor subfamily C, member 4" 2547 rs1841958 KLRC4 8302 12 10453356 NM_013431 NP_038459 A/C I29S plus 5472183 1303 SEQUENOM CEPH CEPH (92) 92 0.17 0.25 0.1 212 2 0.23 0 1420 1 120 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.968 53 Borderline 0.14 2.86 66 moderately radical 602893 12p13.2-p12.3 "killer cell lectin-like receptor subfamily C, member 4" 2548 rs1863703 STK36 27148 2 219369893 NM_015690 NP_056505 A/G K295R plus 2738221 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.04 0 92 1 120 "by doubleHit,freq,cluster" Benign 0.093 5 conservative 607652 2q35 "serine/threonine kinase 36 (fused homolog, Drosophila)" 2549 rs1863704 STK36 27148 2 219388180 NM_015690 NP_056505 A/G G1003D plus 2738222 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.3 0.36 0.13 166 2 100 "HapMap,freq,cluster" Possibly damaging 1.606 5 moderately conservative 607652 2q35 "serine/threonine kinase 36 (fused homolog, Drosophila)" 2550 rs1863704 STK36 27148 2 219388180 NM_015690 NP_056505 A/G G1003D plus 2738222 1303 SEQUENOM CEPH CEPH (92) 46 0.5 0.36 0.13 166 2 100 "HapMap,freq,cluster" Possibly damaging 1.606 5 moderately conservative 607652 2q35 "serine/threonine kinase 36 (fused homolog, Drosophila)" 2551 rs1864345 FRMPD2 143162 10 49090014 NM_152428 NP_689641 C/T K509E plus 2739059 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.3 0.29 0.03 168 2 0.28 0.28 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 10q11.22 FERM and PDZ domain containing 2 2552 rs1864345 FRMPD2 143162 10 49090014 NM_152428 NP_689641 C/T K509E plus 23777530 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.29 0.03 168 2 0.28 0.28 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 10q11.22 FERM and PDZ domain containing 2 2553 rs1866389 THBS4 7060 5 79397021 NM_003248 NP_003239 C/G A387P minus 2741510 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.28 0.25 0.11 216 3 0.05 0.05 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.321 25 Tolerant 0.85 2.75 126 conservative 600715 5q13 thrombospondin 4 2554 rs1866389 THBS4 7060 5 79397021 NM_003248 NP_003239 C/G A387P minus 3172955 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 48 0.08 0.25 0.11 216 3 0.05 0.05 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.321 25 Tolerant 0.85 2.75 126 conservative 600715 5q13 thrombospondin 4 2555 rs1866389 THBS4 7060 5 79397021 NM_003248 NP_003239 C/G A387P minus 24417338 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.25 0.11 216 3 0.05 0.05 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.321 25 Tolerant 0.85 2.75 126 conservative 600715 5q13 thrombospondin 4 2556 rs1868024 MOGAT1 116255 2 223384594 NM_058165 NP_477513 C/T S162P plus 2743545 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.23 0.26 0.06 168 2 0.14 0.01 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.729 8 Tolerant 0.42 2.76 37 moderately conservative 2q36.2 monoacylglycerol O-acyltransferase 1 2557 rs1868024 MOGAT1 116255 2 223384594 NM_058165 NP_477513 C/T S162P plus 24362385 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.26 0.06 168 2 0.14 0.01 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Possibly damaging 1.729 8 Tolerant 0.42 2.76 37 moderately conservative 2q36.2 monoacylglycerol O-acyltransferase 1 2558 rs1870377 KDR 3791 4 55813902 NM_002253 NP_002244 A/T Q472H plus 2746383 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.24 0.07 140 2 0.39 0.06 1548 3 123 "by submitter,freq,cluster" Possibly damaging 1.502 8 Borderline 0.11 3 26 conservative 191306 4q11-q12 kinase insert domain receptor (a type III receptor tyrosine kinase) 2559 rs1870377 KDR 3791 4 55813902 NM_002253 NP_002244 A/T Q472H plus 23961304 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.24 0.07 140 2 0.39 0.06 1548 3 123 "by submitter,freq,cluster" Possibly damaging 1.502 8 Borderline 0.11 3 26 conservative 191306 4q11-q12 kinase insert domain receptor (a type III receptor tyrosine kinase) 2560 rs1877031 STARD3 10948 17 35067606 NM_006804 NP_006795 C/T R117Q minus 2754635 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.31 0.35 0.06 208 2 0.46 0 1492 1 120 "HapMap,doubleHit,freq,cluster" Potentially damaging 1.357 7 Tolerant 0.34 3.1 16 conservative 607048 17q11-q12 START domain containing 3 2561 rs1877031 STARD3 10948 17 35067606 NM_006804 NP_006795 C/T R117Q minus 2754635 1303 SEQUENOM CEPH CEPH (92) 92 0.4 0.35 0.06 208 2 0.46 0 1492 1 120 "HapMap,doubleHit,freq,cluster" Potentially damaging 1.357 7 Tolerant 0.34 3.1 16 conservative 607048 17q11-q12 START domain containing 3 2562 rs1878061 IREM2 342510 17 70121684 NM_181449 NP_852114 C/T G158R plus 24558676 1371 PERLEGEN AFD_EUR_PANEL European American (24) 40 0.4 0.4 0 40 1 0.07 0.06 86 2 123 "by doubleHit,freq,cluster" Borderline 0.18 2.84 16 moderately radical 17q25.2 immune receptor expressed on myeloid cells 2 2563 rs1878326 MFGE8 4240 15 87251591 NM_005928 NP_005919 A/C L76M minus 24508772 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.48 0 48 1 0.48 0.06 1584 3 123 "by doubleHit,freq,cluster" Potentially damaging 1.442 16 conservative 602281 15q25 milk fat globule-EGF factor 8 protein 2564 rs1881420 ALK 238 2 29328132 NM_004304 NP_004295 A/G K1491R minus 2760055 1303 SEQUENOM CEPH CEPH (92) 92 0.23 0.24 0.01 140 2 0.31 0.03 1592 3 123 "by doubleHit,submitter,freq,cluster" conservative 105590 2p23 anaplastic lymphoma kinase (Ki-1) 2565 rs1881420 ALK 238 2 29328132 NM_004304 NP_004295 A/G K1491R minus 23225638 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.24 0.01 140 2 0.31 0.03 1592 3 123 "by doubleHit,submitter,freq,cluster" conservative 105590 2p23 anaplastic lymphoma kinase (Ki-1) 2566 rs1881421 ALK 238 2 29328017 NM_004304 NP_004295 C/G D1529E minus 2760056 1303 SEQUENOM CEPH CEPH (92) 92 0.29 0.32 0.06 140 2 0.31 0.03 1598 3 123 "by doubleHit,submitter,freq,cluster" conservative 105590 2p23 anaplastic lymphoma kinase (Ki-1) 2567 rs1881421 ALK 238 2 29328017 NM_004304 NP_004295 C/G D1529E minus 23225625 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.32 0.06 140 2 0.31 0.03 1598 3 123 "by doubleHit,submitter,freq,cluster" conservative 105590 2p23 anaplastic lymphoma kinase (Ki-1) 2568 rs1884444 IL23R 149233 1 67345833 NM_144701 NP_653302 G/T Q3H plus 2763781 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.44 0.42 0.04 303 5 0.44 0.06 106 3 123 "HapMap,doubleHit,freq,cluster" conservative 607562 1p31.3-p31.2 interleukin-23 receptor 2569 rs1884444 IL23R 149233 1 67345833 NM_144701 NP_653302 G/T Q3H plus 2763781 1303 SEQUENOM CEPH CEPH (92) 92 0.36 0.42 0.04 303 5 0.44 0.06 106 3 123 "HapMap,doubleHit,freq,cluster" conservative 607562 1p31.3-p31.2 interleukin-23 receptor 2570 rs1884444 IL23R 149233 1 67345833 NM_144701 NP_653302 G/T Q3H plus 15355728 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.45 0.42 0.04 303 5 0.44 0.06 106 3 123 "HapMap,doubleHit,freq,cluster" conservative 607562 1p31.3-p31.2 interleukin-23 receptor 2571 rs1884444 IL23R 149233 1 67345833 NM_144701 NP_653302 G/T Q3H plus 15355728 848 IIPGA-WEISS-MARTINEZ E-1 CEPH 3 0.5 0.42 0.04 303 5 0.44 0.06 106 3 123 "HapMap,doubleHit,freq,cluster" conservative 607562 1p31.3-p31.2 interleukin-23 receptor 2572 rs1884444 IL23R 149233 1 67345833 NM_144701 NP_653302 G/T Q3H plus 23689269 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.42 0.04 303 5 0.44 0.06 106 3 123 "HapMap,doubleHit,freq,cluster" conservative 607562 1p31.3-p31.2 interleukin-23 receptor 2573 rs1885137 SERPINA11 256394 14 93982649 XM_170754 XP_170754 G/T E412A plus 2764624 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.43 0.44 0.04 144 2 0.13 0.05 94 2 123 "HapMap,doubleHit,submitter,freq" Intolerant 0.03 2.77 287 moderately radical 14q32.2 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 11" 2574 rs1885137 SERPINA11 256394 14 93982649 XM_170754 XP_170754 G/T E412A plus 24602084 1371 PERLEGEN AFD_EUR_PANEL European American (24) 24 0.5 0.44 0.04 144 2 0.13 0.05 94 2 123 "HapMap,doubleHit,submitter,freq" Intolerant 0.03 2.77 287 moderately radical 14q32.2 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 11" 2575 rs1890908 SYNE2 23224 14 63588788 NM_015180 NP_055995 A/G S2801G plus 24129754 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 0.14 0.1 94 2 123 "by submitter,freq,cluster" moderately conservative 608442 14q23.2 "spectrin repeat containing, nuclear envelope 2" 2576 rs1895245 NMUR2 56923 5 151752248 NM_020167 NP_064552 G/T F315L plus 24458026 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.19 0 48 1 0.06 0.04 94 2 123 "by doubleHit,freq" Possibly damaging 1.775 5 Tolerant 1 2.77 31 conservative 605108 5q33.1 neuromedin U receptor 2 2577 rs1912403 NEDD4 4734 15 53996225 NM_198400 NP_940682 C/T M33V plus 2797203 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.07 0.07 0 120 1 121 "HapMap,doubleHit,submitter,freq" conservative 602278 15q "neural precursor cell expressed, developmentally down-regulated 4" 2578 rs1923185 GMNN 51053 6 24888871 NM_015895 NP_056979 A/C N18T plus 3255127 506 NCBI NIHPDR NIHPDR 166 0.22 0.19 0.08 214 2 0.24 0.16 94 2 123 "by doubleHit,submitter,freq,cluster" moderately conservative 602842 6p22.1 "geminin, DNA replication inhibitor" 2579 rs1923185 GMNN 51053 6 24888871 NM_015895 NP_056979 A/C N18T plus 24166885 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.19 0.08 214 2 0.24 0.16 94 2 123 "by doubleHit,submitter,freq,cluster" moderately conservative 602842 6p22.1 "geminin, DNA replication inhibitor" 2580 rs1932618 BAI3 577 6 69723405 NM_001704 NP_001695 A/G N503S plus 24447601 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.21 0 48 1 0.1 0.02 1590 3 123 "by doubleHit,freq,cluster" conservative 602684 6q12 brain-specific angiogenesis inhibitor 3 2581 rs1933631 CAPN9 10753 1 227221464 NM_006615 NP_006606 A/C K322Q plus 24298094 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.27 0 48 1 0.23 0.01 94 2 123 "by doubleHit,submitter,freq" Benign 0.472 66 Tolerant 0.76 2.85 90 moderately conservative 606401 1q42.11-q42.3 calpain 9 (nCL-4) 2582 rs1940475 MMP8 4317 11 102098458 NM_002424 NP_002415 C/T K87E plus 2831389 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.48 0.47 0.03 168 2 0.3 0.05 1588 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.355 23 Tolerant 0.27 2.76 64 moderately conservative 120355 11q22.3 matrix metalloproteinase 8 (neutrophil collagenase) 2583 rs1940475 MMP8 4317 11 102098458 NM_002424 NP_002415 C/T K87E plus 24072884 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.47 0.03 168 2 0.3 0.05 1588 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.355 23 Tolerant 0.27 2.76 64 moderately conservative 120355 11q22.3 matrix metalloproteinase 8 (neutrophil collagenase) 2584 rs1943330 CDH20 28316 18 57325739 NM_031891 NP_114097 A/C P328H plus 2835524 760 TSC-CSHL CEL_CAUCASIAN CELERA Caucasians (30) 60 0.13 0.14 0.02 646 5 0.03 0.02 166 3 123 "HapMap,doubleHit,submitter,freq" Borderline 1.238 57 Tolerant 0.21 2.77 65 moderately conservative 605807 18q22-q23 "cadherin 20, type 2" 2585 rs1943330 CDH20 28316 18 57325739 NM_031891 NP_114097 A/C P328H plus 2835524 761 TSC-CSHL CEL_CAUCASIAN_CEPH CELERA CEPH Caucasians (661) 328 0.13 0.14 0.02 646 5 0.03 0.02 166 3 123 "HapMap,doubleHit,submitter,freq" Borderline 1.238 57 Tolerant 0.21 2.77 65 moderately conservative 605807 18q22-q23 "cadherin 20, type 2" 2586 rs1943330 CDH20 28316 18 57325739 NM_031891 NP_114097 A/C P328H plus 2835524 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.13 0.14 0.02 646 5 0.03 0.02 166 3 123 "HapMap,doubleHit,submitter,freq" Borderline 1.238 57 Tolerant 0.21 2.77 65 moderately conservative 605807 18q22-q23 "cadherin 20, type 2" 2587 rs1943330 CDH20 28316 18 57325739 NM_031891 NP_114097 A/C P328H plus 2835524 1303 SEQUENOM CEPH CEPH (92) 92 0.18 0.14 0.02 646 5 0.03 0.02 166 3 123 "HapMap,doubleHit,submitter,freq" Borderline 1.238 57 Tolerant 0.21 2.77 65 moderately conservative 605807 18q22-q23 "cadherin 20, type 2" 2588 rs1943330 CDH20 28316 18 57325739 NM_031891 NP_114097 A/C P328H plus 24601004 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.17 0.14 0.02 646 5 0.03 0.02 166 3 123 "HapMap,doubleHit,submitter,freq" Borderline 1.238 57 Tolerant 0.21 2.77 65 moderately conservative 605807 18q22-q23 "cadherin 20, type 2" 2589 rs1949471 DLG1 1739 3 198353552 NM_004087 NP_004078 C/T R278Q plus 2843379 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.26 0 92 1 100 "by cluster,freq" Benign 0.386 30 conservative 601014 3q29 "discs, large homolog 1 (Drosophila)" 2590 rs1950902 MTHFD1 4522 14 63952133 NM_005956 NP_005947 C/T K134R minus 2845017 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.21 0.25 0.07 260 3 0.22 0.02 1588 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.055 41 conservative 172460 14q24 "methylenetetrahydrofolate dehydrogenase (NADP+ dependent), methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase" 2591 rs1950902 MTHFD1 4522 14 63952133 NM_005956 NP_005947 C/T K134R minus 2845017 1303 SEQUENOM CEPH CEPH (92) 92 0.33 0.25 0.07 260 3 0.22 0.02 1588 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.055 41 conservative 172460 14q24 "methylenetetrahydrofolate dehydrogenase (NADP+ dependent), methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase" 2592 rs1950902 MTHFD1 4522 14 63952133 NM_005956 NP_005947 C/T K134R minus 24129796 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.25 0.07 260 3 0.22 0.02 1588 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.055 41 conservative 172460 14q24 "methylenetetrahydrofolate dehydrogenase (NADP+ dependent), methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase" 2593 rs1953758 ATRNL1 26033 10 117065165 NM_207303 NP_997186 A/G S989N plus 23279759 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.07 0 42 1 123 "by cluster,freq" Benign 0.184 21 Borderline 0.14 3.14 17 conservative 10q26 attractin-like 1 2594 rs1968090 ZNF543 125919 19 62531379 NM_213598 NP_998763 A/T L246H plus 2871875 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 84 0.3 0.29 0.01 204 2 0.38 0.11 168 2 121 "HapMap,freq,cluster" Tolerant 0.3 2.76 26 moderately conservative 19q13.43 zinc finger protein 543 2595 rs1968090 ZNF543 125919 19 62531379 NM_213598 NP_998763 A/T L246H plus 2871875 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.28 0.29 0.01 204 2 0.38 0.11 168 2 121 "HapMap,freq,cluster" Tolerant 0.3 2.76 26 moderately conservative 19q13.43 zinc finger protein 543 2596 rs1974777 GEMIN5 25929 5 154271602 NM_015465 NP_056280 A/G R682Q minus 2879379 1303 SEQUENOM CEPH CEPH (92) 92 0.1 0.1 0 140 2 0.22 0.11 92 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.387 8 conservative 607005 5q33.2 gem (nuclear organelle) associated protein 5 2597 rs1974777 GEMIN5 25929 5 154271602 NM_015465 NP_056280 A/G R682Q minus 23470849 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 140 2 0.22 0.11 92 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.387 8 conservative 607005 5q33.2 gem (nuclear organelle) associated protein 5 2598 rs1975937 ZNF540 163255 19 42783772 NM_152606 NP_689819 A/T D53V plus 2880679 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.18 0.19 0.01 260 3 0.39 0.02 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Probably damaging 2.639 5 Intolerant 0 2.79 23 radical 19q13.13 zinc finger protein 540 2599 rs1975937 ZNF540 163255 19 42783772 NM_152606 NP_689819 A/T D53V plus 2880679 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.19 0.01 260 3 0.39 0.02 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Probably damaging 2.639 5 Intolerant 0 2.79 23 radical 19q13.13 zinc finger protein 540 2600 rs1975937 ZNF540 163255 19 42783772 NM_152606 NP_689819 A/T D53V plus 23986128 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.19 0.01 260 3 0.39 0.02 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Probably damaging 2.639 5 Intolerant 0 2.79 23 radical 19q13.13 zinc finger protein 540 2601 rs1983346 KNTC2 10403 18 2606457 NM_006101 NP_006092 C/G A605P plus 2888739 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.4 0.09 140 2 0.15 0.03 94 2 123 "by submitter,freq" Borderline 1.188 6 Tolerant 0.27 2.81 12 conservative 607272 18p11.31 kinetochore associated 2 2602 rs1983346 KNTC2 10403 18 2606457 NM_006101 NP_006092 C/G A605P plus 24469002 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.4 0.09 140 2 0.15 0.03 94 2 123 "by submitter,freq" Borderline 1.188 6 Tolerant 0.27 2.81 12 conservative 607272 18p11.31 kinetochore associated 2 2603 rs1983609 PARVB 29780 22 42814769 NM_013327 NP_037459 C/T V58A plus 8018984 1303 SEQUENOM CEPH CEPH (92) 92 0.24 0.24 0 92 1 120 "by doubleHit,freq,cluster" Benign 0.143 20 moderately conservative 608121 22q13.2-q13.33 "parvin, beta" 2604 rs1983864 LOXL4 84171 10 100007443 NM_032211 NP_115587 A/C D405A minus 24093087 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.35 0 48 1 0.46 0.08 1592 3 123 "by doubleHit,freq,cluster" Probably damaging 2.289 15 moderately radical 607318 10q24 lysyl oxidase-like 4 2605 rs1990760 IFIH1 64135 2 162949558 NM_022168 NP_071451 C/T A946T plus 2902594 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.39 0.38 0.01 212 2 0.22 0 1494 1 121 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.62 2.82 26 moderately conservative 606951 2p24.3-q24.3 melanoma differentiation associated protein-5 2606 rs1990760 IFIH1 64135 2 162949558 NM_022168 NP_071451 C/T A946T plus 2902594 1303 SEQUENOM CEPH CEPH (92) 92 0.37 0.38 0.01 212 2 0.22 0 1494 1 121 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.62 2.82 26 moderately conservative 606951 2p24.3-q24.3 melanoma differentiation associated protein-5 2607 rs1991517 TSHR 7253 14 80680336 NM_000369 NP_000360 C/G E727D plus 2903573 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.08 0.1 0.05 326 4 0.12 0.11 94 2 123 "HapMap,submitter,freq,cluster" Benign 0.268 21 conservative 603372 14q31 thyroid stimulating hormone receptor 2608 rs1991517 TSHR 7253 14 80680336 NM_000369 NP_000360 C/G E727D plus 2903573 1303 SEQUENOM CEPH CEPH (92) 92 0.17 0.1 0.05 326 4 0.12 0.11 94 2 123 "HapMap,submitter,freq,cluster" Benign 0.268 21 conservative 603372 14q31 thyroid stimulating hormone receptor 2609 rs1991517 TSHR 7253 14 80680336 NM_000369 NP_000360 C/G E727D plus 3172741 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 66 0.08 0.1 0.05 326 4 0.12 0.11 94 2 123 "HapMap,submitter,freq,cluster" Benign 0.268 21 conservative 603372 14q31 thyroid stimulating hormone receptor 2610 rs1991517 TSHR 7253 14 80680336 NM_000369 NP_000360 C/G E727D plus 24104812 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.1 0.05 326 4 0.12 0.11 94 2 123 "HapMap,submitter,freq,cluster" Benign 0.268 21 conservative 603372 14q31 thyroid stimulating hormone receptor 2611 rs1995641 TGM4 7047 3 44918393 NM_003241 NP_003232 A/G E313K plus 10036569 885 TSC-CSHL HapMap-CEPH-30-trios 114 0.47 0.4 0.11 206 2 0.17 0 1496 1 116 "HapMap,doubleHit,freq,cluster" moderately conservative 600585 3p22-p21.33 transglutaminase 4 (prostate) 2612 rs1995641 TGM4 7047 3 44918393 NM_003241 NP_003232 A/G E313K plus 10036569 1303 SEQUENOM CEPH CEPH (92) 92 0.32 0.4 0.11 206 2 0.17 0 1496 1 116 "HapMap,doubleHit,freq,cluster" moderately conservative 600585 3p22-p21.33 transglutaminase 4 (prostate) 2613 rs1997660 PGBD1 84547 6 28377642 NM_032507 NP_115896 C/T I678V minus 23916072 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.33 0 48 1 0.3 0.26 92 2 123 "by doubleHit,freq,cluster" conservative 6p21.33 piggyBac transposable element derived 1 2614 rs1998206 ROS1 6098 6 117832141 NM_002944 NP_002935 A/C T145P minus 12675615 775 SNP500CANCER CAUC1 Caucasian (31) 58 0.09 0.11 0.03 106 2 0.17 0.03 408 6 123 "by doubleHit,freq,cluster" Possibly damaging 1.711 6 conservative 165020 6q22 v-ros UR2 sarcoma virus oncogene homolog 1 (avian) 2615 rs1998206 ROS1 6098 6 117832141 NM_002944 NP_002935 A/C T145P minus 23338423 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.11 0.03 106 2 0.17 0.03 408 6 123 "by doubleHit,freq,cluster" Possibly damaging 1.711 6 conservative 165020 6q22 v-ros UR2 sarcoma virus oncogene homolog 1 (avian) 2616 rs1999240 MYO3A 53904 10 26503136 NM_017433 NP_059129 A/C R1313S plus 2913174 760 TSC-CSHL CEL_CAUCASIAN CELERA Caucasians (30) 60 0.45 0.46 0.04 408 6 0.3 0.06 1768 8 123 "by doubleHit,submitter,freq,cluster" moderately radical 606808 10p11.1 myosin IIIA 2617 rs1999240 MYO3A 53904 10 26503136 NM_017433 NP_059129 A/C R1313S plus 2913174 761 TSC-CSHL CEL_CAUCASIAN_CEPH CELERA CEPH Caucasians (661) 186 0.49 0.46 0.04 408 6 0.3 0.06 1768 8 123 "by doubleHit,submitter,freq,cluster" moderately radical 606808 10p11.1 myosin IIIA 2618 rs1999240 MYO3A 53904 10 26503136 NM_017433 NP_059129 A/C R1313S plus 2913174 902 AFFY Caucasian 12 0.5 0.46 0.04 408 6 0.3 0.06 1768 8 123 "by doubleHit,submitter,freq,cluster" moderately radical 606808 10p11.1 myosin IIIA 2619 rs1999240 MYO3A 53904 10 26503136 NM_017433 NP_059129 A/C R1313S plus 2913174 904 AFFY CEPH 10 0.4 0.46 0.04 408 6 0.3 0.06 1768 8 123 "by doubleHit,submitter,freq,cluster" moderately radical 606808 10p11.1 myosin IIIA 2620 rs1999240 MYO3A 53904 10 26503136 NM_017433 NP_059129 A/C R1313S plus 2913174 1303 SEQUENOM CEPH CEPH (92) 92 0.4 0.46 0.04 408 6 0.3 0.06 1768 8 123 "by doubleHit,submitter,freq,cluster" moderately radical 606808 10p11.1 myosin IIIA 2621 rs1999240 MYO3A 53904 10 26503136 NM_017433 NP_059129 A/C R1313S plus 24688626 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.46 0.04 408 6 0.3 0.06 1768 8 123 "by doubleHit,submitter,freq,cluster" moderately radical 606808 10p11.1 myosin IIIA 2622 rs2000813 LIPG 9388 18 45347862 NM_006033 NP_006024 C/T T111I plus 2915222 1303 SEQUENOM CEPH CEPH (92) 92 0.28 0.31 0.05 136 2 0.28 0.19 86 2 123 "by cluster,freq" Borderline 1.222 9 Potentially intolerant 0.06 2.81 37 moderately conservative 603684 18q21.1 "lipase, endothelial" 2623 rs2000813 LIPG 9388 18 45347862 NM_006033 NP_006024 C/T T111I plus 24068059 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.36 0.31 0.05 136 2 0.28 0.19 86 2 123 "by cluster,freq" Borderline 1.222 9 Potentially intolerant 0.06 2.81 37 moderately conservative 603684 18q21.1 "lipase, endothelial" 2624 rs2001301 LRRFIP1 9208 2 238453609 NM_004735 NP_004726 C/T N394S minus 2915846 1303 SEQUENOM CEPH CEPH (92) 92 0.22 0.22 0 92 1 119 "by doubleHit,cluster" conservative 603256 2q37.3 leucine rich repeat (in FLII) interacting protein 1 2625 rs2001490 CML2 51471 2 73839753 NM_016347 NP_057431 C/G G112A plus 2916040 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.47 0 92 1 121 "by doubleHit,submitter" Benign 0.437 22 moderately conservative 608190 2p13.1 putative N-acetyltransferase Camello 2 2626 rs2003783 KLK3 354 19 56053284 NM_001648 NP_001639 G/T L132I minus 2918710 1303 SEQUENOM CEPH CEPH (92) 92 0.18 0.15 0.06 132 2 0.08 0.03 1590 3 123 "by doubleHit,freq,cluster" Benign 0.917 75 Tolerant 1 2.75 84 conservative 176820 19q13.41 "kallikrein 3, (prostate specific antigen)" 2627 rs2003783 KLK3 354 19 56053284 NM_001648 NP_001639 G/T L132I minus 23623364 1371 PERLEGEN AFD_EUR_PANEL European American (24) 40 0.08 0.15 0.06 132 2 0.08 0.03 1590 3 123 "by doubleHit,freq,cluster" Benign 0.917 75 Tolerant 1 2.75 84 conservative 176820 19q13.41 "kallikrein 3, (prostate specific antigen)" 2628 rs2005771 PASK 23178 2 241786146 NM_015148 NP_055963 C/T G725D plus 2922697 1303 SEQUENOM CEPH CEPH (92) 92 0.02 0.02 0 92 1 0.18 0 1496 1 98 "by cluster,freq" moderately conservative 607505 2q37.3 PAS domain containing serine/threonine kinase 2629 rs2006846 P2RXL1 9127 22 19694130 NM_005446 NP_005437 G/T V28G plus 2855759 1303 SEQUENOM CEPH CEPH (92) 92 0.11 0.11 0 92 1 92 by freq Intolerant 0 2.78 64 moderately radical 608077 22q11.21 "purinergic receptor P2X-like 1, orphan receptor" 2630 rs2014055 MRC2 9902 17 58095649 NM_006039 NP_006030 C/T V43I minus 2858471 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.14 0.18 0.08 168 2 0.03 0.01 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.54 2.8 17 conservative 17q24.1 "mannose receptor, C type 2" 2631 rs2014055 MRC2 9902 17 58095649 NM_006039 NP_006030 C/T V43I minus 24569784 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.18 0.08 168 2 0.03 0.01 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 0.54 2.8 17 conservative 17q24.1 "mannose receptor, C type 2" 2632 rs2014377 SIX5 147912 19 50961153 NM_175875 NP_787071 C/G L556V minus 2923565 1303 SEQUENOM CEPH CEPH (92) 92 0.15 0.15 0 92 1 121 "by doubleHit,cluster" conservative 600963 19q13.32 sine oculis homeobox homolog 5 (Drosophila) 2633 rs2014576 SIX5 147912 19 50960916 NM_175875 NP_787071 C/T P635S minus 2918742 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.48 0.48 0 120 1 0.3 0 1314 1 120 "HapMap,doubleHit,freq,cluster" moderately conservative 600963 19q13.32 sine oculis homeobox homolog 5 (Drosophila) 2634 rs2019552 DPEP1 1800 16 88231866 NM_004413 NP_004404 C/G E351Q plus 24205571 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.21 0.21 0 42 1 0.32 0.04 1518 3 123 "by doubleHit,freq,cluster" Borderline 1.015 10 Tolerant 0.21 2.76 36 conservative 179780 16q24.3 dipeptidase 1 (renal) 2635 rs2020872 MLH1 4292 3 37010136 NM_000249 NP_000240 A/G I32V plus 2923976 506 NCBI NIHPDR NIHPDR 82 0.02 0.01 0.01 238 2 111 "by cluster,freq" Benign 0.3 8 Intolerant 0.04 2.83 15 conservative 120436 3p21.3 "mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)" 2636 rs2020872 MLH1 4292 3 37010136 NM_000249 NP_000240 A/G I32V plus 6312911 693 EGP_SNPS PDR90 NIHPDR 156 0.01 0.01 0.01 238 2 111 "by cluster,freq" Benign 0.3 8 Intolerant 0.04 2.83 15 conservative 120436 3p21.3 "mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)" 2637 rs2020873 MLH1 4292 3 37067029 NM_000249 NP_000240 C/T H718Y plus 2923977 506 NCBI NIHPDR NIHPDR 88 0.03 0.03 0 88 1 119 "HapMap,freq,cluster" Possibly damaging 1.834 7 Intolerant 0 2.82 16 moderately conservative 120436 3p21.3 "mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)" 2638 rs2020874 PGR 5241 11 100467733 NM_000926 NP_000917 G/T R625I minus 2923978 506 NCBI NIHPDR NIHPDR 80 0.18 0.18 0 80 1 123 "by cluster,freq" Potentially damaging 1.427 13 Intolerant 0 2.77 394 moderately conservative 607311 11q22-q23 progesterone receptor 2639 rs2020880 PGR 5241 11 100417938 NM_000926 NP_000917 C/T S865L minus 2923987 506 NCBI NIHPDR NIHPDR 88 0.01 0.06 0.11 360 3 120 "by cluster,freq" Possibly damaging 1.568 7 Tolerant 0.25 2.77 360 moderately radical 607311 11q22-q23 progesterone receptor 2640 rs2020880 PGR 5241 11 100417938 NM_000926 NP_000917 C/T S865L minus 16343523 693 EGP_SNPS PDR90 NIHPDR 180 0.01 0.06 0.11 360 3 120 "by cluster,freq" Possibly damaging 1.568 7 Tolerant 0.25 2.77 360 moderately radical 607311 11q22-q23 progesterone receptor 2641 rs2020880 PGR 5241 11 100417938 NM_000926 NP_000917 C/T S865L minus 16343523 1303 SEQUENOM CEPH CEPH (92) 92 0.22 0.06 0.11 360 3 120 "by cluster,freq" Possibly damaging 1.568 7 Tolerant 0.25 2.77 360 moderately radical 607311 11q22-q23 progesterone receptor 2642 rs2020893 MGMT 4255 10 131224594 NM_002412 NP_002403 A/G E30K plus 3256189 506 NCBI NIHPDR NIHPDR 844 0.01 0.05 0.17 936 2 100 "by cluster,freq" Potentially damaging 1.46 7 Tolerant 0.88 2.79 29 moderately conservative 156569 10q26 O-6-methylguanine-DNA methyltransferase 2643 rs2020893 MGMT 4255 10 131224594 NM_002412 NP_002403 A/G E30K plus 3256189 1303 SEQUENOM CEPH CEPH (92) 92 0.42 0.05 0.17 936 2 100 "by cluster,freq" Potentially damaging 1.46 7 Tolerant 0.88 2.79 29 moderately conservative 156569 10q26 O-6-methylguanine-DNA methyltransferase 2644 rs2020908 MSH6 2956 2 47937959 NM_000179 NP_000170 C/G L396V plus 2924019 506 NCBI NIHPDR NIHPDR 88 0.01 0.01 0 268 2 103 "by cluster,freq" Borderline 1.21 9 Borderline 0.11 2.82 15 conservative 600678 2p16 mutS homolog 6 (E. coli) 2645 rs2020908 MSH6 2956 2 47937959 NM_000179 NP_000170 C/G L396V plus 4384594 693 EGP_SNPS PDR90 NIHPDR 180 0.01 0.01 0 268 2 103 "by cluster,freq" Borderline 1.21 9 Borderline 0.11 2.82 15 conservative 600678 2p16 mutS homolog 6 (E. coli) 2646 rs2020914 MSH6 2956 2 47939429 NM_000179 NP_000170 A/G I886V plus 2924027 506 NCBI NIHPDR NIHPDR 80 0.01 0.01 0 248 2 103 "by cluster,freq" Benign 0.119 9 Borderline 0.12 2.83 15 conservative 600678 2p16 mutS homolog 6 (E. coli) 2647 rs2020914 MSH6 2956 2 47939429 NM_000179 NP_000170 A/G I886V plus 4384598 693 EGP_SNPS PDR90 NIHPDR 168 0.01 0.01 0 248 2 103 "by cluster,freq" Benign 0.119 9 Borderline 0.12 2.83 15 conservative 600678 2p16 mutS homolog 6 (E. coli) 2648 rs2020916 GSR 2936 8 30666320 NM_000637 NP_000628 A/C P271H minus 2924031 506 NCBI NIHPDR NIHPDR 80 0.33 0.33 0 80 1 98 "HapMap,freq,cluster" Possibly damaging 1.645 27 moderately conservative 138300 8p21.1 glutathione reductase 2649 rs2020924 PLAT 5327 8 42155734 NM_000931 NP_000922 C/T L285P minus 9807084 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 44 0.14 0.13 0.01 92 2 0.15 0 48 1 123 "by doubleHit,freq,cluster" moderately conservative 173370 8p12 "plasminogen activator, tissue" 2650 rs2020924 PLAT 5327 8 42155734 NM_000931 NP_000922 C/T L285P minus 24028471 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0.01 92 2 0.15 0 48 1 123 "by doubleHit,freq,cluster" moderately conservative 173370 8p12 "plasminogen activator, tissue" 2651 rs2020955 ERCC4 2072 16 13946160 NM_005236 NP_005227 C/T S662P plus 2924078 506 NCBI NIHPDR NIHPDR 82 0.04 0.05 0.01 258 2 103 "HapMap,freq,cluster" Benign 0.337 11 moderately conservative 133520 16p13.3-p13.11 "excision repair cross-complementing rodent repair deficiency, complementation group 4" 2652 rs2020955 ERCC4 2072 16 13946160 NM_005236 NP_005227 C/T S662P plus 4384450 693 EGP_SNPS PDR90 NIHPDR 176 0.06 0.05 0.01 258 2 103 "HapMap,freq,cluster" Benign 0.337 11 moderately conservative 133520 16p13.3-p13.11 "excision repair cross-complementing rodent repair deficiency, complementation group 4" 2653 rs2020957 ERCC4 2072 16 13949571 NM_005236 NP_005227 A/G I873V plus 2924080 506 NCBI NIHPDR NIHPDR 88 0.02 0.01 0.01 254 2 113 "by cluster,freq" Benign 0.929 10 Tolerant 0.49 2.81 14 conservative 133520 16p13.3-p13.11 "excision repair cross-complementing rodent repair deficiency, complementation group 4" 2654 rs2020957 ERCC4 2072 16 13949571 NM_005236 NP_005227 A/G I873V plus 4384474 693 EGP_SNPS PDR90 NIHPDR 166 0.01 0.01 0.01 254 2 113 "by cluster,freq" Benign 0.929 10 Tolerant 0.49 2.81 14 conservative 133520 16p13.3-p13.11 "excision repair cross-complementing rodent repair deficiency, complementation group 4" 2655 rs2020959 ERCC4 2072 16 13949123 NM_005236 NP_005227 A/C C723X plus 2924082 506 NCBI NIHPDR NIHPDR 84 0.01 0.01 0 264 2 103 "by cluster,freq" Probably damaging Intolerant radical 133520 16p13.3-p13.11 "excision repair cross-complementing rodent repair deficiency, complementation group 4" 2656 rs2020959 ERCC4 2072 16 13949123 NM_005236 NP_005227 A/C C723X plus 4384470 693 EGP_SNPS PDR90 NIHPDR 180 0.01 0.01 0 264 2 103 "by cluster,freq" Probably damaging Intolerant radical 133520 16p13.3-p13.11 "excision repair cross-complementing rodent repair deficiency, complementation group 4" 2657 rs2020961 ERCC4 2072 16 13928033 NM_005236 NP_005227 C/T A168V plus 2924085 506 NCBI NIHPDR NIHPDR 88 0.01 0.01 0 262 2 103 "by cluster,freq" Potentially damaging 1.438 11 Tolerant 0.57 2.81 14 moderately conservative 133520 16p13.3-p13.11 "excision repair cross-complementing rodent repair deficiency, complementation group 4" 2658 rs2020961 ERCC4 2072 16 13928033 NM_005236 NP_005227 C/T A168V plus 4384327 693 EGP_SNPS PDR90 NIHPDR 174 0.01 0.01 0 262 2 103 "by cluster,freq" Potentially damaging 1.438 11 Tolerant 0.57 2.81 14 moderately conservative 133520 16p13.3-p13.11 "excision repair cross-complementing rodent repair deficiency, complementation group 4" 2659 rs2024320 DPPA3 359787 12 7759114 NM_199286 NP_954980 C/G E51Q plus 2932601 885 TSC-CSHL HapMap-CEPH-30-trios 100 0.18 0.18 0 100 1 121 "HapMap,doubleHit,submitter,freq" conservative 608408 12p13.31 developmental pluripotency associated 3 2660 rs2032567 LAMA4 3910 6 112564083 NM_002290 NP_002281 C/T G1110S plus 2941527 1303 SEQUENOM CEPH CEPH (92) 92 0.23 0.23 0.01 138 2 0.15 0.13 88 2 123 "by doubleHit,submitter,freq,cluster" Borderline 1.186 8 moderately conservative 600133 6q21 "laminin, alpha 4" 2661 rs2032567 LAMA4 3910 6 112564083 NM_002290 NP_002281 C/T G1110S plus 23392187 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.22 0.23 0.01 138 2 0.15 0.13 88 2 123 "by doubleHit,submitter,freq,cluster" Borderline 1.186 8 moderately conservative 600133 6q21 "laminin, alpha 4" 2662 rs2032729 ZNF24 7572 18 31171642 NM_006965 NP_008896 A/G N220S minus 2941706 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.08 0.12 0.07 260 3 0.23 0.08 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 194534 18q12 zinc finger protein 24 (KOX 17) 2663 rs2032729 ZNF24 7572 18 31171642 NM_006965 NP_008896 A/G N220S minus 2941706 1303 SEQUENOM CEPH CEPH (92) 92 0.19 0.12 0.07 260 3 0.23 0.08 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 194534 18q12 zinc finger protein 24 (KOX 17) 2664 rs2032729 ZNF24 7572 18 31171642 NM_006965 NP_008896 A/G N220S minus 24187710 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.12 0.07 260 3 0.23 0.08 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 194534 18q12 zinc finger protein 24 (KOX 17) 2665 rs2034310 NKIR 146722 17 70203523 NM_139018 NP_620587 C/T Q218R plus 2943391 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.18 0.18 0 120 1 120 "HapMap,doubleHit,freq,cluster" Tolerant 1 3.24 13 conservative 17q25.2 NK inhibitory receptor precursor 2666 rs2034891 SIGLECL1 89858 19 56696559 NM_053003 NP_443729 G/T P81T plus 2944024 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 80 0.04 0.05 0.01 176 2 0.15 0.11 156 2 111 "by doubleHit,cluster" conservative 606094 19q13.4 SIGLEC-like 1 2667 rs2034891 SIGLECL1 89858 19 56696559 NM_053003 NP_443729 G/T P81T plus 2944024 782 TSC-CSHL WICGR6_CAUCASIAN_POOLED WICGR Caucasian (48) 96 0.06 0.05 0.01 176 2 0.15 0.11 156 2 111 "by doubleHit,cluster" conservative 606094 19q13.4 SIGLEC-like 1 2668 rs2041385 TAPBPL 55080 12 6432554 NM_018009 NP_060479 C/T A42V plus 2951026 1303 SEQUENOM CEPH CEPH (92) 92 0.35 0.24 0.09 318 3 0.2 0.06 92 2 123 "by submitter,freq,cluster" moderately conservative 607081 12p13.31 TAP binding protein-like 2669 rs2041385 TAPBPL 55080 12 6432554 NM_018009 NP_060479 C/T A42V plus 16340831 693 EGP_SNPS PDR90 NIHPDR 178 0.18 0.24 0.09 318 3 0.2 0.06 92 2 123 "by submitter,freq,cluster" moderately conservative 607081 12p13.31 TAP binding protein-like 2670 rs2041385 TAPBPL 55080 12 6432554 NM_018009 NP_060479 C/T A42V plus 24697326 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.24 0.09 318 3 0.2 0.06 92 2 123 "by submitter,freq,cluster" moderately conservative 607081 12p13.31 TAP binding protein-like 2671 rs2041387 TAPBPL 55080 12 6433084 NM_018009 NP_060479 C/T A169V plus 24207405 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.18 0.18 0 44 1 0.22 0.02 88 2 123 "by doubleHit,submitter,freq,cluster" moderately conservative 607081 12p13.31 TAP binding protein-like 2672 rs2043211 CARD8 22900 19 53429518 NM_014959 NP_055774 A/T C10X plus 2952971 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.31 0.36 0.07 258 3 0.4 0.03 1586 3 123 "HapMap,doubleHit,submitter,freq,cluster" Probably damaging Intolerant radical 19q13.33 "caspase recruitment domain family, member 8" 2673 rs2043211 CARD8 22900 19 53429518 NM_014959 NP_055774 A/T C10X plus 2952971 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.36 0.07 258 3 0.4 0.03 1586 3 123 "HapMap,doubleHit,submitter,freq,cluster" Probably damaging Intolerant radical 19q13.33 "caspase recruitment domain family, member 8" 2674 rs2043211 CARD8 22900 19 53429518 NM_014959 NP_055774 A/T C10X plus 24109677 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.36 0.07 258 3 0.4 0.03 1586 3 123 "HapMap,doubleHit,submitter,freq,cluster" Probably damaging Intolerant radical 19q13.33 "caspase recruitment domain family, member 8" 2675 rs2044502 ZFP29 54993 15 82965002 NM_181877 NP_870992 C/G S190T minus 2954383 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.15 0.15 0 120 1 116 "HapMap,doubleHit,freq,cluster" Borderline 0.16 2.82 141 moderately conservative 15q25.2 zinc finger protein 29 2676 rs2045732 TDRD7 23424 9 97273961 NM_014290 NP_055105 C/T V150A plus 2955702 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.48 0.48 0 168 2 0.48 0.03 1592 3 123 "HapMap,doubleHit,freq,cluster" moderately conservative 9q22.33 tudor domain containing 7 2677 rs2045732 TDRD7 23424 9 97273961 NM_014290 NP_055105 C/T V150A plus 24539267 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.48 0 168 2 0.48 0.03 1592 3 123 "HapMap,doubleHit,freq,cluster" moderately conservative 9q22.33 tudor domain containing 7 2678 rs2052937 GPR113 165082 2 26448345 NM_153835 NP_722577 C/T A404T plus 2963464 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.33 0.33 0 120 1 121 "HapMap,doubleHit,submitter,freq,cluster" Borderline 0.19 3.05 29 moderately conservative 2p24.1 G protein-coupled receptor 113 2679 rs2057413 SETDB2 83852 13 48955098 NM_031915 NP_114121 A/G V473M plus 2968316 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.25 0.29 0.06 211 2 121 "HapMap,doubleHit,submitter,freq,cluster" conservative 607865 13q14 "SET domain, bifurcated 2" 2680 rs2057413 SETDB2 83852 13 48955098 NM_031915 NP_114121 A/G V473M plus 2968316 1303 SEQUENOM CEPH CEPH (92) 91 0.34 0.29 0.06 211 2 121 "HapMap,doubleHit,submitter,freq,cluster" conservative 607865 13q14 "SET domain, bifurcated 2" 2681 rs2059696 LY75 4065 2 160499033 NM_002349 NP_002340 A/G Y1391H plus 24313263 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.33 0 48 1 0.15 0.11 94 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.364 5 moderately conservative 604524 2q24 lymphocyte antigen 75 2682 rs2061690 PBXIP1 57326 1 151732153 NM_020524 NP_065385 C/T G357D plus 2972903 1303 SEQUENOM CEPH CEPH (92) 92 0.49 0.49 0 92 1 0.08 0 1474 1 120 "by doubleHit,freq,cluster" moderately conservative 1q22 pre-B-cell leukemia transcription factor interacting protein 1 2683 rs2062988 DHTKD1 55526 10 12183111 NM_018706 NP_061176 C/G I607M plus 2974308 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.17 0.2 0.06 166 2 0.26 0.03 1350 3 123 "HapMap,doubleHit,freq,cluster" Probably damaging 2.055 8 Tolerant 0.48 2.74 54 conservative 10p14 dehydrogenase E1 and transketolase domain containing 1 2684 rs2062988 DHTKD1 55526 10 12183111 NM_018706 NP_061176 C/G I607M plus 23243374 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.2 0.06 166 2 0.26 0.03 1350 3 123 "HapMap,doubleHit,freq,cluster" Probably damaging 2.055 8 Tolerant 0.48 2.74 54 conservative 10p14 dehydrogenase E1 and transketolase domain containing 1 2685 rs2066455 PMS1 5378 2 190554278 NM_000534 NP_000525 C/G E720D plus 2978048 506 NCBI NIHPDR NIHPDR 84 0.01 0.01 0 264 2 114 "by cluster,freq" conservative 600258 2q31.1 PMS1 postmeiotic segregation increased 1 (S. cerevisiae) 2686 rs2066455 PMS1 5378 2 190554278 NM_000534 NP_000525 C/G E720D plus 7986962 693 EGP_SNPS PDR90 NIHPDR 180 0.01 0.01 0 264 2 114 "by cluster,freq" conservative 600258 2q31.1 PMS1 postmeiotic segregation increased 1 (S. cerevisiae) 2687 rs2066456 PMS1 5378 2 190554013 NM_000534 NP_000525 A/G N632S plus 2978049 506 NCBI NIHPDR NIHPDR 84 0.01 0.01 0 260 2 114 "by cluster,freq" conservative 600258 2q31.1 PMS1 postmeiotic segregation increased 1 (S. cerevisiae) 2688 rs2066456 PMS1 5378 2 190554013 NM_000534 NP_000525 A/G N632S plus 7986961 693 EGP_SNPS PDR90 NIHPDR 176 0.01 0.01 0 260 2 114 "by cluster,freq" conservative 600258 2q31.1 PMS1 postmeiotic segregation increased 1 (S. cerevisiae) 2689 rs2066459 PMS1 5378 2 190534218 NM_000534 NP_000525 A/G R202K plus 2978053 506 NCBI NIHPDR NIHPDR 72 0.01 0.03 0.03 344 3 114 "by cluster,freq" Tolerant 0.85 2.77 59 conservative 600258 2q31.1 PMS1 postmeiotic segregation increased 1 (S. cerevisiae) 2690 rs2066459 PMS1 5378 2 190534218 NM_000534 NP_000525 A/G R202K plus 7986900 693 EGP_SNPS PDR90 NIHPDR 180 0.01 0.03 0.03 344 3 114 "by cluster,freq" Tolerant 0.85 2.77 59 conservative 600258 2q31.1 PMS1 postmeiotic segregation increased 1 (S. cerevisiae) 2691 rs2066459 PMS1 5378 2 190534218 NM_000534 NP_000525 A/G R202K plus 7986900 1303 SEQUENOM CEPH CEPH (92) 92 0.07 0.03 0.03 344 3 114 "by cluster,freq" Tolerant 0.85 2.77 59 conservative 600258 2q31.1 PMS1 postmeiotic segregation increased 1 (S. cerevisiae) 2692 rs2066479 HSD17B3 3293 9 96077365 NM_000197 NP_000188 A/G G289S minus 2978076 506 NCBI NIHPDR NIHPDR 80 0.09 0.07 0.03 300 4 0.22 0.05 1934 7 123 "by cluster,freq" Tolerant 0.87 2.9 15 moderately conservative 605573 9q22 hydroxysteroid (17-beta) dehydrogenase 3 2693 rs2066479 HSD17B3 3293 9 96077365 NM_000197 NP_000188 A/G G289S minus 5586587 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.06 0.07 0.03 300 4 0.22 0.05 1934 7 123 "by cluster,freq" Tolerant 0.87 2.9 15 moderately conservative 605573 9q22 hydroxysteroid (17-beta) dehydrogenase 3 2694 rs2066479 HSD17B3 3293 9 96077365 NM_000197 NP_000188 A/G G289S minus 12584274 693 EGP_SNPS PDR90 NIHPDR 114 0.07 0.07 0.03 300 4 0.22 0.05 1934 7 123 "by cluster,freq" Tolerant 0.87 2.9 15 moderately conservative 605573 9q22 hydroxysteroid (17-beta) dehydrogenase 3 2695 rs2066479 HSD17B3 3293 9 96077365 NM_000197 NP_000188 A/G G289S minus 24174312 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.02 0.07 0.03 300 4 0.22 0.05 1934 7 123 "by cluster,freq" Tolerant 0.87 2.9 15 moderately conservative 605573 9q22 hydroxysteroid (17-beta) dehydrogenase 3 2696 rs2066480 HSD17B3 3293 9 96143851 NM_000197 NP_000188 A/G V31I minus 2978077 506 NCBI NIHPDR NIHPDR 74 0.03 0.02 0.01 368 3 0.08 0 48 1 123 "HapMap,freq,cluster" Tolerant 0.4 2.88 16 conservative 605573 9q22 hydroxysteroid (17-beta) dehydrogenase 3 2697 rs2066480 HSD17B3 3293 9 96143851 NM_000197 NP_000188 A/G V31I minus 12584142 693 EGP_SNPS PDR90 NIHPDR 174 0.03 0.02 0.01 368 3 0.08 0 48 1 123 "HapMap,freq,cluster" Tolerant 0.4 2.88 16 conservative 605573 9q22 hydroxysteroid (17-beta) dehydrogenase 3 2698 rs2066480 HSD17B3 3293 9 96143851 NM_000197 NP_000188 A/G V31I minus 12584142 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.01 0.02 0.01 368 3 0.08 0 48 1 123 "HapMap,freq,cluster" Tolerant 0.4 2.88 16 conservative 605573 9q22 hydroxysteroid (17-beta) dehydrogenase 3 2699 rs2066575 DLEU1 10301 13 49554583 NM_005887 NP_005878 A/T C4S plus 4045551 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.23 0.23 0.03 260 3 0.25 0.22 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately radical 605765 13q14.3 "deleted in lymphocytic leukemia, 1" 2700 rs2066575 DLEU1 10301 13 49554583 NM_005887 NP_005878 A/T C4S plus 14647001 1303 SEQUENOM CEPH CEPH (92) 92 0.21 0.23 0.03 260 3 0.25 0.22 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately radical 605765 13q14.3 "deleted in lymphocytic leukemia, 1" 2701 rs2066575 DLEU1 10301 13 49554583 NM_005887 NP_005878 A/T C4S plus 24002084 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.23 0.03 260 3 0.25 0.22 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately radical 605765 13q14.3 "deleted in lymphocytic leukemia, 1" 2702 rs2066703 ATP10A 57194 15 23513151 NM_024490 NP_077816 C/T T532M minus 2978369 524 LDN AUTISM USA (autistic probands) 20 0.15 0.09 0.04 280 4 0.11 0 46 1 123 "HapMap,submitter,freq" Possibly damaging 1.711 7 Potentially intolerant 0.06 2.92 13 moderately conservative 605855 15q11-q13 "ATPase, Class V, type 10A" 2703 rs2066703 ATP10A 57194 15 23513151 NM_024490 NP_077816 C/T T532M minus 2978369 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.06 0.09 0.04 280 4 0.11 0 46 1 123 "HapMap,submitter,freq" Possibly damaging 1.711 7 Potentially intolerant 0.06 2.92 13 moderately conservative 605855 15q11-q13 "ATPase, Class V, type 10A" 2704 rs2066703 ATP10A 57194 15 23513151 NM_024490 NP_077816 C/T T532M minus 2978369 1303 SEQUENOM CEPH CEPH (92) 92 0.12 0.09 0.04 280 4 0.11 0 46 1 123 "HapMap,submitter,freq" Possibly damaging 1.711 7 Potentially intolerant 0.06 2.92 13 moderately conservative 605855 15q11-q13 "ATPase, Class V, type 10A" 2705 rs2066703 ATP10A 57194 15 23513151 NM_024490 NP_077816 C/T T532M minus 23748339 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.09 0.04 280 4 0.11 0 46 1 123 "HapMap,submitter,freq" Possibly damaging 1.711 7 Potentially intolerant 0.06 2.92 13 moderately conservative 605855 15q11-q13 "ATPase, Class V, type 10A" 2706 rs2066704 ATP10A 57194 15 23504535 NM_024490 NP_077816 A/G A784T minus 2978370 524 LDN AUTISM USA (autistic probands) 20 0.2 0.11 0.06 280 4 0.11 0 46 1 123 "HapMap,submitter,freq,cluster" Borderline 1.003 7 Tolerant 0.72 2.94 13 moderately conservative 605855 15q11-q13 "ATPase, Class V, type 10A" 2707 rs2066704 ATP10A 57194 15 23504535 NM_024490 NP_077816 A/G A784T minus 2978370 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.06 0.11 0.06 280 4 0.11 0 46 1 123 "HapMap,submitter,freq,cluster" Borderline 1.003 7 Tolerant 0.72 2.94 13 moderately conservative 605855 15q11-q13 "ATPase, Class V, type 10A" 2708 rs2066704 ATP10A 57194 15 23504535 NM_024490 NP_077816 A/G A784T minus 2978370 1303 SEQUENOM CEPH CEPH (92) 92 0.17 0.11 0.06 280 4 0.11 0 46 1 123 "HapMap,submitter,freq,cluster" Borderline 1.003 7 Tolerant 0.72 2.94 13 moderately conservative 605855 15q11-q13 "ATPase, Class V, type 10A" 2709 rs2066704 ATP10A 57194 15 23504535 NM_024490 NP_077816 A/G A784T minus 23748312 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.11 0.06 280 4 0.11 0 46 1 123 "HapMap,submitter,freq,cluster" Borderline 1.003 7 Tolerant 0.72 2.94 13 moderately conservative 605855 15q11-q13 "ATPase, Class V, type 10A" 2710 rs2066791 RFC1 5981 4 39132915 NM_002913 NP_002904 A/G I598V minus 2978462 506 NCBI NIHPDR NIHPDR 84 0.01 0.01 0 84 1 98 "by submitter,cluster" Benign 0.711 8 Borderline 0.2 2.8 19 conservative 102579 4p14-p13 "replication factor C (activator 1) 1, 145kDa" 2711 rs2066807 STAT2 6773 12 55026949 NM_005419 NP_005410 C/G M594I minus 2978483 506 NCBI NIHPDR NIHPDR 56 0.07 0.06 0.01 324 3 120 "by cluster,freq" Benign 0.557 5 Tolerant 0.53 2.8 87 conservative 600556 12q13.13 "signal transducer and activator of transcription 2, 113kDa" 2712 rs2066807 STAT2 6773 12 55026949 NM_005419 NP_005410 C/G M594I minus 16361231 693 EGP_SNPS PDR90 NIHPDR 176 0.07 0.06 0.01 324 3 120 "by cluster,freq" Benign 0.557 5 Tolerant 0.53 2.8 87 conservative 600556 12q13.13 "signal transducer and activator of transcription 2, 113kDa" 2713 rs2066807 STAT2 6773 12 55026949 NM_005419 NP_005410 C/G M594I minus 16361231 1303 SEQUENOM CEPH CEPH (92) 92 0.05 0.06 0.01 324 3 120 "by cluster,freq" Benign 0.557 5 Tolerant 0.53 2.8 87 conservative 600556 12q13.13 "signal transducer and activator of transcription 2, 113kDa" 2714 rs2066809 STAT2 6773 12 55029049 NM_005419 NP_005410 G/T S501I minus 2978485 506 NCBI NIHPDR NIHPDR 76 0.01 0.01 0 76 1 98 "HapMap,cluster" Possibly damaging 1.773 6 Intolerant 0 2.79 85 moderately radical 600556 12q13.13 "signal transducer and activator of transcription 2, 113kDa" 2715 rs2066811 STAT2 6773 12 55029264 NM_005419 NP_005410 A/G I464V minus 2978489 506 NCBI NIHPDR NIHPDR 76 0.05 0.06 0.01 254 2 120 "by cluster,freq" Benign 0.989 6 Potentially intolerant 0.09 2.79 84 conservative 600556 12q13.13 "signal transducer and activator of transcription 2, 113kDa" 2716 rs2066811 STAT2 6773 12 55029264 NM_005419 NP_005410 A/G I464V minus 16361225 693 EGP_SNPS PDR90 NIHPDR 178 0.06 0.06 0.01 254 2 120 "by cluster,freq" Benign 0.989 6 Potentially intolerant 0.09 2.79 84 conservative 600556 12q13.13 "signal transducer and activator of transcription 2, 113kDa" 2717 rs2066815 STAT2 6773 12 55029311 NM_005419 NP_005410 C/T T448M minus 2978493 506 NCBI NIHPDR NIHPDR 76 0.01 0.02 0.01 254 2 120 "by cluster,freq" Possibly damaging 1.711 6 Intolerant 0 2.8 83 moderately conservative 600556 12q13.13 "signal transducer and activator of transcription 2, 113kDa" 2718 rs2066815 STAT2 6773 12 55029311 NM_005419 NP_005410 C/T T448M minus 16361224 693 EGP_SNPS PDR90 NIHPDR 178 0.02 0.02 0.01 254 2 120 "by cluster,freq" Possibly damaging 1.711 6 Intolerant 0 2.8 83 moderately conservative 600556 12q13.13 "signal transducer and activator of transcription 2, 113kDa" 2719 rs2066816 STAT2 6773 12 55036270 NM_005419 NP_005410 G/T Q66H minus 2978495 506 NCBI NIHPDR NIHPDR 82 0.28 0.28 0 82 1 98 "HapMap,freq,cluster" Possibly damaging 1.657 5 Intolerant 0 2.81 78 conservative 600556 12q13.13 "signal transducer and activator of transcription 2, 113kDa" 2720 rs2066827 CDKN1B 1027 12 12762366 NM_004064 NP_004055 G/T V109G plus 2978511 506 NCBI NIHPDR NIHPDR 82 0.27 0.28 0.05 746 7 0.19 0.21 92 2 123 "HapMap,freq,cluster" Benign 0.183 15 Tolerant 0.41 2.81 34 moderately radical 600778 12p13.1-p12 "cyclin-dependent kinase inhibitor 1B (p27, Kip1)" 2721 rs2066827 CDKN1B 1027 12 12762366 NM_004064 NP_004055 G/T V109G plus 3176696 619 WICVAR MITOGPOP6 CORIELL Mixed 62 0.4 0.28 0.05 746 7 0.19 0.21 92 2 123 "HapMap,freq,cluster" Benign 0.183 15 Tolerant 0.41 2.81 34 moderately radical 600778 12p13.1-p12 "cyclin-dependent kinase inhibitor 1B (p27, Kip1)" 2722 rs2066827 CDKN1B 1027 12 12762366 NM_004064 NP_004055 G/T V109G plus 4329016 693 EGP_SNPS PDR90 NIHPDR 178 0.28 0.28 0.05 746 7 0.19 0.21 92 2 123 "HapMap,freq,cluster" Benign 0.183 15 Tolerant 0.41 2.81 34 moderately radical 600778 12p13.1-p12 "cyclin-dependent kinase inhibitor 1B (p27, Kip1)" 2723 rs2066827 CDKN1B 1027 12 12762366 NM_004064 NP_004055 G/T V109G plus 4329016 885 TSC-CSHL HapMap-CEPH-30-trios 108 0.21 0.28 0.05 746 7 0.19 0.21 92 2 123 "HapMap,freq,cluster" Benign 0.183 15 Tolerant 0.41 2.81 34 moderately radical 600778 12p13.1-p12 "cyclin-dependent kinase inhibitor 1B (p27, Kip1)" 2724 rs2066827 CDKN1B 1027 12 12762366 NM_004064 NP_004055 G/T V109G plus 4329016 1303 SEQUENOM CEPH CEPH (92) 92 0.25 0.28 0.05 746 7 0.19 0.21 92 2 123 "HapMap,freq,cluster" Benign 0.183 15 Tolerant 0.41 2.81 34 moderately radical 600778 12p13.1-p12 "cyclin-dependent kinase inhibitor 1B (p27, Kip1)" 2725 rs2066827 CDKN1B 1027 12 12762366 NM_004064 NP_004055 G/T V109G plus 5607385 693 EGP_SNPS PDR90 NIHPDR 178 0.29 0.28 0.05 746 7 0.19 0.21 92 2 123 "HapMap,freq,cluster" Benign 0.183 15 Tolerant 0.41 2.81 34 moderately radical 600778 12p13.1-p12 "cyclin-dependent kinase inhibitor 1B (p27, Kip1)" 2726 rs2066827 CDKN1B 1027 12 12762366 NM_004064 NP_004055 G/T V109G plus 24702910 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.35 0.28 0.05 746 7 0.19 0.21 92 2 123 "HapMap,freq,cluster" Benign 0.183 15 Tolerant 0.41 2.81 34 moderately radical 600778 12p13.1-p12 "cyclin-dependent kinase inhibitor 1B (p27, Kip1)" 2727 rs2066828 CDKN1B 1027 12 12762083 NM_004064 NP_004055 C/T R15W plus 2978512 506 NCBI NIHPDR NIHPDR 86 0.01 0.01 0 446 3 113 "by cluster,freq" Probably damaging 2.257 15 Intolerant 0 3.19 27 moderately radical 600778 12p13.1-p12 "cyclin-dependent kinase inhibitor 1B (p27, Kip1)" 2728 rs2066828 CDKN1B 1027 12 12762083 NM_004064 NP_004055 C/T R15W plus 4329015 693 EGP_SNPS PDR90 NIHPDR 180 0.01 0.01 0 446 3 113 "by cluster,freq" Probably damaging 2.257 15 Intolerant 0 3.19 27 moderately radical 600778 12p13.1-p12 "cyclin-dependent kinase inhibitor 1B (p27, Kip1)" 2729 rs2066828 CDKN1B 1027 12 12762083 NM_004064 NP_004055 C/T R15W plus 5607384 693 EGP_SNPS PDR90 NIHPDR 180 0.01 0.01 0 446 3 113 "by cluster,freq" Probably damaging 2.257 15 Intolerant 0 3.19 27 moderately radical 600778 12p13.1-p12 "cyclin-dependent kinase inhibitor 1B (p27, Kip1)" 2730 rs2066842 CARD15 64127 16 49302125 NM_022162 NP_071445 C/T P268S plus 2978533 594 CEPH EUCAUC French Caucasians (10 individuals with crohn's disease and 2 unaffected individuals were used as controls) 24 0.46 0.36 0.06 274 6 0.05 0.03 142 3 123 "by submitter,freq,cluster" Potentially damaging 1.429 18 Borderline 0.16 2.98 29 moderately conservative 605956 16p12-q21 "caspase recruitment domain family, member 15" 2731 rs2066842 CARD15 64127 16 49302125 NM_022162 NP_071445 C/T P268S plus 2978533 1303 SEQUENOM CEPH CEPH (92) 92 0.42 0.36 0.06 274 6 0.05 0.03 142 3 123 "by submitter,freq,cluster" Potentially damaging 1.429 18 Borderline 0.16 2.98 29 moderately conservative 605956 16p12-q21 "caspase recruitment domain family, member 15" 2732 rs2066842 CARD15 64127 16 49302125 NM_022162 NP_071445 C/T P268S plus 2992219 611 GKT-CGM CD_UK-POP UK (crohn's disease) (32) 64 0.33 0.36 0.06 274 6 0.05 0.03 142 3 123 "by submitter,freq,cluster" Potentially damaging 1.429 18 Borderline 0.16 2.98 29 moderately conservative 605956 16p12-q21 "caspase recruitment domain family, member 15" 2733 rs2066842 CARD15 64127 16 49302125 NM_022162 NP_071445 C/T P268S plus 7987091 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.3 0.36 0.06 274 6 0.05 0.03 142 3 123 "by submitter,freq,cluster" Potentially damaging 1.429 18 Borderline 0.16 2.98 29 moderately conservative 605956 16p12-q21 "caspase recruitment domain family, member 15" 2734 rs2066842 CARD15 64127 16 49302125 NM_022162 NP_071445 C/T P268S plus 7987091 848 IIPGA-WEISS-MARTINEZ E-1 CEPH 6 0.33 0.36 0.06 274 6 0.05 0.03 142 3 123 "by submitter,freq,cluster" Potentially damaging 1.429 18 Borderline 0.16 2.98 29 moderately conservative 605956 16p12-q21 "caspase recruitment domain family, member 15" 2735 rs2066842 CARD15 64127 16 49302125 NM_022162 NP_071445 C/T P268S plus 24523863 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.36 0.06 274 6 0.05 0.03 142 3 123 "by submitter,freq,cluster" Potentially damaging 1.429 18 Borderline 0.16 2.98 29 moderately conservative 605956 16p12-q21 "caspase recruitment domain family, member 15" 2736 rs2066844 CARD15 64127 16 49303427 NM_022162 NP_071445 C/T R702W plus 2978536 594 CEPH EUCAUC French Caucasians (10 individuals with crohn's disease and 2 unaffected individuals were used as controls) 24 0.17 0.08 0.06 238 5 0.02 0 250 2 123 "by cluster,freq" Possibly damaging 1.868 18 Intolerant 0.02 2.92 34 moderately radical 605956 16p12-q21 "caspase recruitment domain family, member 15" 2737 rs2066844 CARD15 64127 16 49303427 NM_022162 NP_071445 C/T R702W plus 2992222 611 GKT-CGM CD_UK-POP UK (crohn's disease) (32) 64 0.14 0.08 0.06 238 5 0.02 0 250 2 123 "by cluster,freq" Possibly damaging 1.868 18 Intolerant 0.02 2.92 34 moderately radical 605956 16p12-q21 "caspase recruitment domain family, member 15" 2738 rs2066844 CARD15 64127 16 49303427 NM_022162 NP_071445 C/T R702W plus 7987100 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.03 0.08 0.06 238 5 0.02 0 250 2 123 "by cluster,freq" Possibly damaging 1.868 18 Intolerant 0.02 2.92 34 moderately radical 605956 16p12-q21 "caspase recruitment domain family, member 15" 2739 rs2066844 CARD15 64127 16 49303427 NM_022162 NP_071445 C/T R702W plus 8819693 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.06 0.08 0.06 238 5 0.02 0 250 2 123 "by cluster,freq" Possibly damaging 1.868 18 Intolerant 0.02 2.92 34 moderately radical 605956 16p12-q21 "caspase recruitment domain family, member 15" 2740 rs2066844 CARD15 64127 16 49303427 NM_022162 NP_071445 C/T R702W plus 24523902 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.08 0.06 238 5 0.02 0 250 2 123 "by cluster,freq" Possibly damaging 1.868 18 Intolerant 0.02 2.92 34 moderately radical 605956 16p12-q21 "caspase recruitment domain family, member 15" 2741 rs2066845 CARD15 64127 16 49314041 NM_022162 NP_071445 C/G G908R plus 2978537 594 CEPH EUCAUC French Caucasians (10 individuals with crohn's disease and 2 unaffected individuals were used as controls) 20 0.15 0.04 0.04 250 4 0.01 0.01 252 2 123 "HapMap,freq,cluster" Probably damaging 2.031 18 Tolerant 0.21 2.84 31 moderately radical 605956 16p12-q21 "caspase recruitment domain family, member 15" 2742 rs2066845 CARD15 64127 16 49314041 NM_022162 NP_071445 C/G G908R plus 2978537 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.02 0.04 0.04 250 4 0.01 0.01 252 2 123 "HapMap,freq,cluster" Probably damaging 2.031 18 Tolerant 0.21 2.84 31 moderately radical 605956 16p12-q21 "caspase recruitment domain family, member 15" 2743 rs2066845 CARD15 64127 16 49314041 NM_022162 NP_071445 C/G G908R plus 2992223 611 GKT-CGM CD_UK-POP UK (crohn's disease) (32) 64 0.06 0.04 0.04 250 4 0.01 0.01 252 2 123 "HapMap,freq,cluster" Probably damaging 2.031 18 Tolerant 0.21 2.84 31 moderately radical 605956 16p12-q21 "caspase recruitment domain family, member 15" 2744 rs2066845 CARD15 64127 16 49314041 NM_022162 NP_071445 C/G G908R plus 24524028 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.04 0.04 0.04 250 4 0.01 0.01 252 2 123 "HapMap,freq,cluster" Probably damaging 2.031 18 Tolerant 0.21 2.84 31 moderately radical 605956 16p12-q21 "caspase recruitment domain family, member 15" 2745 rs2066853 AHR 196 7 17152350 NM_001621 NP_001612 A/G R554K plus 2978548 593 IMB-FU-BERLIN CAUCASIAN German Caucasians 199 0.16 0.1 0.05 509 4 0.32 0.13 566 5 123 "by doubleHit,freq,cluster" Benign 0.331 37 Tolerant 1 2.92 56 conservative 600253 7p15 aryl hydrocarbon receptor 2746 rs2066853 AHR 196 7 17152350 NM_001621 NP_001612 A/G R554K plus 5586223 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.08 0.1 0.05 509 4 0.32 0.13 566 5 123 "by doubleHit,freq,cluster" Benign 0.331 37 Tolerant 1 2.92 56 conservative 600253 7p15 aryl hydrocarbon receptor 2747 rs2066853 AHR 196 7 17152350 NM_001621 NP_001612 A/G R554K plus 5586223 1303 SEQUENOM CEPH CEPH (92) 92 0.06 0.1 0.05 509 4 0.32 0.13 566 5 123 "by doubleHit,freq,cluster" Benign 0.331 37 Tolerant 1 2.92 56 conservative 600253 7p15 aryl hydrocarbon receptor 2748 rs2066853 AHR 196 7 17152350 NM_001621 NP_001612 A/G R554K plus 28461207 549 KYUGEN CP CEPH (78) 156 0.07 0.1 0.05 509 4 0.32 0.13 566 5 123 "by doubleHit,freq,cluster" Benign 0.331 37 Tolerant 1 2.92 56 conservative 600253 7p15 aryl hydrocarbon receptor 2749 rs2067019 TJP3 27134 19 3679609 NM_014428 NP_055243 A/G R38H plus 2993969 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.28 0.28 0 120 1 121 "HapMap,doubleHit,freq,cluster" Borderline 0.16 2.91 23 conservative 19p13.3 tight junction protein 3 (zona occludens 3) 2750 rs2069860 IL6 3569 7 22544278 NM_000600 NP_000591 A/T D162V plus 2981987 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.04 0.04 0 94 2 123 "by cluster,freq" Possibly damaging 1.69 23 Borderline 0.17 2.95 39 radical 147620 7p21 "interleukin 6 (interferon, beta 2)" 2751 rs2069860 IL6 3569 7 22544278 NM_000600 NP_000591 A/T D162V plus 24395612 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 94 2 123 "by cluster,freq" Possibly damaging 1.69 23 Borderline 0.17 2.95 39 radical 147620 7p21 "interleukin 6 (interferon, beta 2)" 2752 rs2069885 IL9 3578 5 135256064 NM_000590 NP_000581 C/T T117M minus 2982016 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 42 0.12 0.13 0.03 210 3 0.12 0.01 92 2 123 "HapMap,submitter,freq,cluster" moderately conservative 146931 5q31.1 interleukin 9 2753 rs2069885 IL9 3578 5 135256064 NM_000590 NP_000581 C/T T117M minus 17067099 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.11 0.13 0.03 210 3 0.12 0.01 92 2 123 "HapMap,submitter,freq,cluster" moderately conservative 146931 5q31.1 interleukin 9 2754 rs2069885 IL9 3578 5 135256064 NM_000590 NP_000581 C/T T117M minus 24665721 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.13 0.03 210 3 0.12 0.01 92 2 123 "HapMap,submitter,freq,cluster" moderately conservative 146931 5q31.1 interleukin 9 2755 rs2070094 BARD1 580 2 215457761 NM_000465 NP_000456 A/G V507M minus 5606240 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.37 0.41 0.04 246 2 0.36 0.04 342 4 123 "by doubleHit,freq,cluster" Intolerant 0.04 2.79 355 conservative 601593 2q34-q35 BRCA1 associated RING domain 1 2756 rs2070094 BARD1 580 2 215457761 NM_000465 NP_000456 A/G V507M minus 24795955 1303 SEQUENOM CEPH CEPH (92) 184 0.43 0.41 0.04 246 2 0.36 0.04 342 4 123 "by doubleHit,freq,cluster" Intolerant 0.04 2.79 355 conservative 601593 2q34-q35 BRCA1 associated RING domain 1 2757 rs2070132 ZNF146 7705 19 41419205 NM_007145 NP_009076 A/G R8K plus 24683112 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.43 0.43 0 44 1 0.4 0.05 84 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.451 2080 conservative 601505 19q13.1 zinc finger protein 146 2758 rs2070150 ATF6 22926 1 158492934 NM_007348 NP_031374 C/G A145P plus 4427215 1303 SEQUENOM CEPH CEPH (92) 92 0.03 0.05 0.03 140 2 0.22 0.25 94 2 123 "by cluster,freq" Benign 0.465 5 conservative 605537 1q22-q23 activating transcription factor 6 2759 rs2070150 ATF6 22926 1 158492934 NM_007348 NP_031374 C/G A145P plus 23843006 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.05 0.03 140 2 0.22 0.25 94 2 123 "by cluster,freq" Benign 0.465 5 conservative 605537 1q22-q23 activating transcription factor 6 2760 rs2070180 HCLS1 3059 3 122834028 NM_005335 NP_005326 A/G E361K minus 4407542 1303 SEQUENOM CEPH CEPH (92) 92 0.33 0.33 0 92 1 120 by freq Tolerant 0.51 2.95 24 moderately conservative 601306 3q13 hematopoietic cell-specific Lyn substrate 1 2761 rs2070215 MCM7 4176 7 99341448 NM_005916 NP_005907 A/G N144S minus 3255186 506 NCBI NIHPDR NIHPDR 164 0.17 0.23 0.07 376 3 120 "HapMap,freq,cluster" Benign 0.154 14 Tolerant 1 2.82 30 conservative 600592 7q21.3-q22.1 MCM7 minichromosome maintenance deficient 7 (S. cerevisiae) 2762 rs2070215 MCM7 4176 7 99341448 NM_005916 NP_005907 A/G N144S minus 20309717 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.29 0.23 0.07 376 3 120 "HapMap,freq,cluster" Benign 0.154 14 Tolerant 1 2.82 30 conservative 600592 7q21.3-q22.1 MCM7 minichromosome maintenance deficient 7 (S. cerevisiae) 2763 rs2070215 MCM7 4176 7 99341448 NM_005916 NP_005907 A/G N144S minus 20309717 1303 SEQUENOM CEPH CEPH (92) 92 0.27 0.23 0.07 376 3 120 "HapMap,freq,cluster" Benign 0.154 14 Tolerant 1 2.82 30 conservative 600592 7q21.3-q22.1 MCM7 minichromosome maintenance deficient 7 (S. cerevisiae) 2764 rs2070235 MYBL2 4605 20 41764871 NM_002466 NP_002457 A/G S427G plus 3172553 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 54 0.19 0.14 0.08 102 2 0.18 0.02 1590 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.179 6 Tolerant 0.38 2.84 19 moderately conservative 601415 20q13.1 v-myb myeloblastosis viral oncogene homolog (avian)-like 2 2765 rs2070235 MYBL2 4605 20 41764871 NM_002466 NP_002457 A/G S427G plus 23648539 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.14 0.08 102 2 0.18 0.02 1590 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.179 6 Tolerant 0.38 2.84 19 moderately conservative 601415 20q13.1 v-myb myeloblastosis viral oncogene homolog (avian)-like 2 2766 rs2070317 BPIL3 128859 20 31085744 NM_174897 NP_777557 A/G V97I plus 24533889 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.46 0 48 1 0.22 0.05 1392 3 123 "by doubleHit,submitter,freq,cluster" Tolerant 1 2.87 13 conservative 20q11.22 bactericidal/permeability-increasing protein-like 3 2767 rs2070417 TIAM1 7074 21 31560420 NM_003253 NP_003244 A/C G247V plus 2983649 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.12 0.12 0 118 1 98 "HapMap,freq,cluster" moderately radical 600687 21q22.11 T-cell lymphoma invasion and metastasis 1 2768 rs2070426 PCNT2 5116 21 46674912 NM_006031 NP_006022 C/G Q2659H plus 12501025 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.4 0.4 0 118 1 0.28 0 1280 1 120 "HapMap,doubleHit,freq,cluster" conservative 605925 21q22.3 pericentrin 2 (kendrin) 2769 rs2070507 PPM1F 9647 22 20602125 NM_014634 NP_055449 A/C L420R plus 24212133 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.27 0.06 1380 3 123 "by doubleHit,freq,cluster" Potentially intolerant 0.1 2.81 48 moderately radical 22q11.22 protein phosphatase 1F (PP2C domain containing) 2770 rs2070745 FPR1 2357 19 56941759 NM_002029 NP_002020 C/G V101L minus 24686736 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.43 0.43 0 46 1 0.36 0.06 92 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.633 28 Tolerant 0.38 2.82 31 conservative 136537 19q13.4 formyl peptide receptor 1 2771 rs2070862 SERPINF2 5345 17 1595044 NM_000934 NP_000925 C/T A2V plus 2984258 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.28 0.28 0 118 1 0.16 0 1486 1 98 "HapMap,freq,cluster" moderately conservative 262850 17p13 "serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2" 2772 rs2070959 UGT1A6 54578 2 234384191 NM_001072 NP_001063 A/G T181A plus 5239097 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.27 0.28 0.01 166 2 0.25 0.03 1576 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.423 76 Tolerant 0.53 2.85 156 moderately conservative 606431 2q37 "UDP glycosyltransferase 1 family, polypeptide A6" 2773 rs2070959 UGT1A6 54578 2 234384191 NM_001072 NP_001063 A/G T181A plus 24281282 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.28 0.01 166 2 0.25 0.03 1576 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.423 76 Tolerant 0.53 2.85 156 moderately conservative 606431 2q37 "UDP glycosyltransferase 1 family, polypeptide A6" 2774 rs2071214 BIRC5 332 17 73731186 NM_001168 NP_001159 A/G E129K plus 24106544 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.21 0.05 1188 3 123 "by cluster,freq" Potentially damaging 1.285 9 moderately conservative 603352 17q25 baculoviral IAP repeat-containing 5 (survivin) 2775 rs2071421 ARSA 410 22 49354560 NM_000487 NP_000478 A/G N350S minus 3294278 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.14 0.18 0.05 344 3 0.29 0.17 92 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.493 7 Intolerant 0.03 2.75 21 conservative 607574 22q13.33 arylsulfatase A 2776 rs2071421 ARSA 410 22 49354560 NM_000487 NP_000478 A/G N350S minus 8485025 693 EGP_SNPS PDR90 NIHPDR 176 0.22 0.18 0.05 344 3 0.29 0.17 92 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.493 7 Intolerant 0.03 2.75 21 conservative 607574 22q13.33 arylsulfatase A 2777 rs2071421 ARSA 410 22 49354560 NM_000487 NP_000478 A/G N350S minus 23795637 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.18 0.05 344 3 0.29 0.17 92 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.493 7 Intolerant 0.03 2.75 21 conservative 607574 22q13.33 arylsulfatase A 2778 rs2071543 PSMB8 5696 6 32919607 NM_148919 NP_683720 A/C Q49K minus 23718210 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.14 0.01 1584 3 123 "by cluster,freq" moderately conservative 177046 6p21.3 "proteasome (prosome, macropain) subunit, beta type, 8 (large multifunctional protease 7)" 2779 rs2071587 FOXN1 8456 17 23875729 NM_003593 NP_003584 C/T R69C plus 19361492 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.13 0.15 0.04 166 2 0.22 0 1508 2 123 "HapMap,freq,cluster" Benign 0 5 radical 600838 17q11-q12 forkhead box N1 2780 rs2071587 FOXN1 8456 17 23875729 NM_003593 NP_003584 C/T R69C plus 24126107 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.2 0.15 0.04 166 2 0.22 0 1508 2 123 "HapMap,freq,cluster" Benign 0 5 radical 600838 17q11-q12 forkhead box N1 2781 rs2071676 CA9 768 9 35664053 NM_001216 NP_001207 A/G V33M plus 2985365 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.31 0.3 0.01 168 2 0.44 0.06 1584 3 123 "HapMap,doubleHit,freq,cluster" conservative 603179 9p13-p12 carbonic anhydrase IX 2782 rs2071676 CA9 768 9 35664053 NM_001216 NP_001207 A/G V33M plus 24085687 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.3 0.01 168 2 0.44 0.06 1584 3 123 "HapMap,doubleHit,freq,cluster" conservative 603179 9p13-p12 carbonic anhydrase IX 2783 rs2071747 HMOX1 3162 22 34101739 NM_002133 NP_002124 C/G D7H plus 12675419 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.05 0.05 0 62 1 0.04 0 292 3 118 "by cluster,freq" Borderline 1.206 10 Borderline 0.11 3.23 12 moderately conservative 141250 22q13.1 heme oxygenase (decycling) 1 2784 rs2071915 TMEM8 58986 16 366433 NM_021259 NP_067082 C/T I310V plus 24398620 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.48 0.48 0 46 1 0.31 0.03 1376 3 123 "by doubleHit,freq,cluster" Benign 0.13 5 conservative 16p13.3 transmembrane protein 8 (five membrane-spanning domains) 2785 rs2071921 SAC 55811 1 164557143 NM_018417 NP_060887 C/T I697V plus 23180018 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.42 0 48 1 0.27 0.05 780 3 123 "by doubleHit,submitter,freq,cluster" conservative 605205 1q24 testicular soluble adenylyl cyclase 2786 rs2072123 DGCR2 9993 22 17401167 NM_005137 NP_005128 C/T V473A minus 2985997 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.39 0.4 0.03 168 2 0.3 0.02 1022 3 123 "HapMap,freq,cluster" Benign 0.36 10 moderately conservative 600594 22q11.21 DiGeorge syndrome critical region gene 2 2787 rs2072123 DGCR2 9993 22 17401167 NM_005137 NP_005128 C/T V473A minus 24701428 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.4 0.03 168 2 0.3 0.02 1022 3 123 "HapMap,freq,cluster" Benign 0.36 10 moderately conservative 600594 22q11.21 DiGeorge syndrome critical region gene 2 2788 rs2072174 ZNF596 169270 8 186274 NM_173539 NP_775810 G/T V470G plus 23937416 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.35 0.08 1374 3 123 "by cluster,freq" Borderline 0.16 2.77 29 moderately radical 8p23.3 zinc finger protein 596 2789 rs2072193 PLA2G3 50487 22 29858350 NM_015715 NP_056530 C/G S322R minus 24212274 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.32 0.07 1376 3 123 "by cluster,freq" moderately radical 22q11.2-q13.2 "phospholipase A2, group III" 2790 rs2072446 NGFR 4804 17 44942818 NM_002507 NP_002498 C/T S205L plus 15356315 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.05 0.05 0 40 1 0.1 0.02 1160 2 120 "by cluster,freq" Possibly damaging 1.773 6 moderately radical 162010 17q21-q22 "nerve growth factor receptor (TNFR superfamily, member 16)" 2791 rs2072493 TLR5 7100 1 2899958 NM_003268 NP_003259 A/G N592S minus 7988265 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.2 0.21 0.06 124 5 0.32 0.07 1648 6 123 "by submitter,freq,cluster" Tolerant 0.78 2.82 10 conservative 603031 1q41-q42 toll-like receptor 5 2792 rs2072493 TLR5 7100 1 2899958 NM_003268 NP_003259 A/G N592S minus 7988265 848 IIPGA-WEISS-MARTINEZ E-1 CEPH 6 0.17 0.21 0.06 124 5 0.32 0.07 1648 6 123 "by submitter,freq,cluster" Tolerant 0.78 2.82 10 conservative 603031 1q41-q42 toll-like receptor 5 2793 rs2072493 TLR5 7100 1 2899958 NM_003268 NP_003259 A/G N592S minus 7988265 902 AFFY Caucasian 24 0.29 0.21 0.06 124 5 0.32 0.07 1648 6 123 "by submitter,freq,cluster" Tolerant 0.78 2.82 10 conservative 603031 1q41-q42 toll-like receptor 5 2794 rs2072493 TLR5 7100 1 2899958 NM_003268 NP_003259 A/G N592S minus 7988265 904 AFFY CEPH 12 0.08 0.21 0.06 124 5 0.32 0.07 1648 6 123 "by submitter,freq,cluster" Tolerant 0.78 2.82 10 conservative 603031 1q41-q42 toll-like receptor 5 2795 rs2072493 TLR5 7100 1 2899958 NM_003268 NP_003259 A/G N592S minus 24600736 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.21 0.21 0.06 124 5 0.32 0.07 1648 6 123 "by submitter,freq,cluster" Tolerant 0.78 2.82 10 conservative 603031 1q41-q42 toll-like receptor 5 2796 rs2072579 SART3 9733 12 107457329 NM_014706 NP_055521 C/G D23E plus 2986632 885 TSC-CSHL HapMap-CEPH-30-trios 112 0.19 0.19 0 112 1 0.3 0 1482 1 123 "HapMap,freq,cluster" Benign 0.675 5 conservative 12q24.1 squamous cell carcinoma antigen recognised by T cells 3 2797 rs2072767 UNC93A 54346 6 167689847 NM_018974 NP_061847 A/G V292I plus 24021110 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.29 0 48 1 0.23 0.02 1592 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.835 5 Tolerant 1 2.79 22 conservative 607995 6q27 unc-93 homolog A (C. elegans) 2798 rs2073342 RNASE3 6037 14 20430056 NM_002935 NP_002926 C/G T124R plus 12298829 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.27 0.27 0 116 1 121 "HapMap,doubleHit,freq,cluster" Benign 0.843 40 Tolerant 1 2.85 119 moderately conservative 131398 14q24-q31 "ribonuclease, RNase A family, 3 (eosinophil cationic protein)" 2799 rs2073376 PCNT2 5116 21 46676181 NM_006031 NP_006022 A/G Q2792R plus 10991096 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.31 0.34 0.07 158 2 0.28 0.01 1594 3 123 "HapMap,doubleHit,freq,cluster" conservative 605925 21q22.3 pericentrin 2 (kendrin) 2800 rs2073376 PCNT2 5116 21 46676181 NM_006031 NP_006022 A/G Q2792R plus 24533411 1371 PERLEGEN AFD_EUR_PANEL European American (24) 40 0.43 0.34 0.07 158 2 0.28 0.01 1594 3 123 "HapMap,doubleHit,freq,cluster" conservative 605925 21q22.3 pericentrin 2 (kendrin) 2801 rs2073380 PCNT2 5116 21 46688185 NM_006031 NP_006022 A/C R3245S plus 24074539 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.44 0.08 1590 3 123 "by cluster,freq" moderately radical 605925 21q22.3 pericentrin 2 (kendrin) 2802 rs2073440 HDC 3067 15 48321806 NM_002112 NP_002103 A/C E644D minus 23373131 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.04 0.03 846 3 123 "by submitter,freq,cluster" Borderline 1.042 6 conservative 142704 15q21-q22 histidine decarboxylase 2803 rs2073478 ALDH1B1 219 9 38386065 NM_000692 NP_000683 G/T R107L plus 3172732 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 36 0.47 0.41 0.04 296 4 0.33 0.03 1378 3 123 "HapMap,doubleHit,freq,cluster" Probably damaging 2.21 129 Intolerant 0.01 2.83 146 moderately radical 100670 9p11.1 "aldehyde dehydrogenase 1 family, member B1" 2804 rs2073478 ALDH1B1 219 9 38386065 NM_000692 NP_000683 G/T R107L plus 3172732 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.43 0.41 0.04 296 4 0.33 0.03 1378 3 123 "HapMap,doubleHit,freq,cluster" Probably damaging 2.21 129 Intolerant 0.01 2.83 146 moderately radical 100670 9p11.1 "aldehyde dehydrogenase 1 family, member B1" 2805 rs2073478 ALDH1B1 219 9 38386065 NM_000692 NP_000683 G/T R107L plus 19799525 1303 SEQUENOM CEPH CEPH (92) 92 0.37 0.41 0.04 296 4 0.33 0.03 1378 3 123 "HapMap,doubleHit,freq,cluster" Probably damaging 2.21 129 Intolerant 0.01 2.83 146 moderately radical 100670 9p11.1 "aldehyde dehydrogenase 1 family, member B1" 2806 rs2073478 ALDH1B1 219 9 38386065 NM_000692 NP_000683 G/T R107L plus 23587937 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.41 0.04 296 4 0.33 0.03 1378 3 123 "HapMap,doubleHit,freq,cluster" Probably damaging 2.21 129 Intolerant 0.01 2.83 146 moderately radical 100670 9p11.1 "aldehyde dehydrogenase 1 family, member B1" 2807 rs2073618 TNFRSF11B 4982 8 120033233 NM_002546 NP_002537 C/G N3K minus 11960719 902 AFFY Caucasian 24 0.38 0.39 0.05 248 4 0.28 0.05 1432 5 123 "by doubleHit,submitter,freq,cluster" Possibly damaging 1.497 5 moderately conservative 602643 8q24 "tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin)" 2808 rs2073618 TNFRSF11B 4982 8 120033233 NM_002546 NP_002537 C/G N3K minus 11960719 904 AFFY CEPH 10 0.4 0.39 0.05 248 4 0.28 0.05 1432 5 123 "by doubleHit,submitter,freq,cluster" Possibly damaging 1.497 5 moderately conservative 602643 8q24 "tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin)" 2809 rs2073618 TNFRSF11B 4982 8 120033233 NM_002546 NP_002537 C/G N3K minus 16358800 693 EGP_SNPS PDR90 NIHPDR 166 0.37 0.39 0.05 248 4 0.28 0.05 1432 5 123 "by doubleHit,submitter,freq,cluster" Possibly damaging 1.497 5 moderately conservative 602643 8q24 "tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin)" 2810 rs2073618 TNFRSF11B 4982 8 120033233 NM_002546 NP_002537 C/G N3K minus 24690828 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.39 0.05 248 4 0.28 0.05 1432 5 123 "by doubleHit,submitter,freq,cluster" Possibly damaging 1.497 5 moderately conservative 602643 8q24 "tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin)" 2811 rs2073852 ATBF1 463 16 71550168 NM_006885 NP_008816 C/G E460Q minus 2988330 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.02 0.03 0.02 164 2 0.22 0 1352 2 123 "HapMap,freq,cluster" conservative 104155 16q22.3-q23.1 AT-binding transcription factor 1 2812 rs2073852 ATBF1 463 16 71550168 NM_006885 NP_008816 C/G E460Q minus 24112511 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.05 0.03 0.02 164 2 0.22 0 1352 2 123 "HapMap,freq,cluster" conservative 104155 16q22.3-q23.1 AT-binding transcription factor 1 2813 rs2073924 GBGT1 26301 9 133067296 NM_021996 NP_068836 C/T L20F minus 2988431 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.15 0.14 0.03 168 2 0.43 0.08 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 606074 9q34.13-q34.3 "globoside alpha-1,3-N-acetylgalactosaminyltransferase 1" 2814 rs2073924 GBGT1 26301 9 133067296 NM_021996 NP_068836 C/T L20F minus 24073144 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.14 0.03 168 2 0.43 0.08 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 606074 9q34.13-q34.3 "globoside alpha-1,3-N-acetylgalactosaminyltransferase 1" 2815 rs2074078 ZNF154 7710 19 62905764 NM_003444 NP_003435 A/C G122V plus 24076048 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.45 0.09 1590 3 123 "by doubleHit,freq,cluster" Benign 0.034 10 Intolerant 0 2.84 101 moderately radical 604085 19q13.4 zinc finger protein 154 (pHZ-92) 2816 rs2074158 LGP2 79132 17 37510689 NM_024119 NP_077024 A/G Q425R minus 23630049 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.19 0 48 1 0.25 0.06 94 2 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.52 2.78 20 conservative 17q21.31 likely ortholog of mouse D11lgp2 2817 rs2074160 LGP2 79132 17 37509338 NM_024119 NP_077024 A/G R523Q minus 14302546 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.05 0.05 0 120 1 0.13 0 1488 1 119 "HapMap,freq,cluster" Tolerant 0.51 2.78 21 conservative 17q21.31 likely ortholog of mouse D11lgp2 2818 rs2074654 RAMP3 10268 7 44990255 NM_005856 NP_005847 A/G W56R minus 24055392 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.11 0.02 1552 3 123 "by cluster,freq" Probably damaging 3.543 9 Intolerant 0 2.87 23 moderately radical 605155 7p13-p12 receptor (calcitonin) activity modifying protein 3 2819 rs2074734 PLA2G3 50487 22 29860549 NM_015715 NP_056530 C/G E116Q minus 8002619 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.04 0.03 0.01 168 2 0.27 0.28 92 2 123 "HapMap,doubleHit,freq,cluster" conservative 22q11.2-q13.2 "phospholipase A2, group III" 2820 rs2074734 PLA2G3 50487 22 29860549 NM_015715 NP_056530 C/G E116Q minus 24212280 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.03 0.01 168 2 0.27 0.28 92 2 123 "HapMap,doubleHit,freq,cluster" conservative 22q11.2-q13.2 "phospholipase A2, group III" 2821 rs2074735 PLA2G3 50487 22 29860426 NM_015715 NP_056530 C/G L157V minus 3179448 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.04 0.04 0 120 1 0.34 0 1484 1 98 "HapMap,freq,cluster" conservative 22q11.2-q13.2 "phospholipase A2, group III" 2822 rs2074890 TRIM16 10626 17 15495286 NM_006470 NP_006461 G/T E121D minus 2989730 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.03 0.03 0.01 168 2 0.22 0.02 978 3 123 "HapMap,submitter,freq,cluster" Benign 0.675 6 Tolerant 0.68 2.79 8 conservative 17p11.2 tripartite motif-containing 16 2823 rs2074890 TRIM16 10626 17 15495286 NM_006470 NP_006461 G/T E121D minus 23639313 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.03 0.01 168 2 0.22 0.02 978 3 123 "HapMap,submitter,freq,cluster" Benign 0.675 6 Tolerant 0.68 2.79 8 conservative 17p11.2 tripartite motif-containing 16 2824 rs2075252 LRP2 4036 2 169836492 NM_004525 NP_004516 A/G K4094E minus 23903223 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.29 0 48 1 0.43 0.09 1172 3 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.98 2.76 21 moderately conservative 600073 2q24-q31 low density lipoprotein-related protein 2 2825 rs2075352 TATDN2 9797 3 10286939 XM_376203 XP_376203 C/T P358L plus 2990394 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.08 0.07 138 2 0.3 0.02 1550 3 123 "by cluster,freq" moderately conservative 3p25.3 TatD DNase domain containing 1 2826 rs2075352 TATDN2 9797 3 10286939 XM_376203 XP_376203 C/T P358L plus 23656303 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.15 0.08 0.07 138 2 0.3 0.02 1550 3 123 "by cluster,freq" moderately conservative 3p25.3 TatD DNase domain containing 1 2827 rs2075662 COL15A1 1306 9 98827789 NM_001855 NP_001846 A/G R163H plus 6538731 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.13 0.13 0 168 2 0.29 0.02 1380 3 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 120325 9q21-q22 "collagen, type XV, alpha 1" 2828 rs2075662 COL15A1 1306 9 98827789 NM_001855 NP_001846 A/G R163H plus 23503487 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 168 2 0.29 0.02 1380 3 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 120325 9q21-q22 "collagen, type XV, alpha 1" 2829 rs2075803 SIGLEC9 27180 19 56320341 NM_014441 NP_055256 A/G K100E plus 3608040 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.49 0.49 0 120 1 0.44 0 1492 1 121 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.243 19 Tolerant 0.25 2.83 28 moderately conservative 605640 19q13.41 sialic acid binding Ig-like lectin 9 2830 rs2075820 CARD4 10392 7 30265477 NM_006092 NP_006083 A/G E266K minus 7987180 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.05 0.09 0.08 94 3 0.43 0.06 1370 4 123 "by submitter,freq,cluster" Intolerant 0.04 2.94 23 moderately conservative 605980 7p15-p14 "caspase recruitment domain family, member 4" 2831 rs2075820 CARD4 10392 7 30265477 NM_006092 NP_006083 A/G E266K minus 7987180 848 IIPGA-WEISS-MARTINEZ E-1 CEPH 6 0.33 0.09 0.08 94 3 0.43 0.06 1370 4 123 "by submitter,freq,cluster" Intolerant 0.04 2.94 23 moderately conservative 605980 7p15-p14 "caspase recruitment domain family, member 4" 2832 rs2075820 CARD4 10392 7 30265477 NM_006092 NP_006083 A/G E266K minus 23453667 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.09 0.08 94 3 0.43 0.06 1370 4 123 "by submitter,freq,cluster" Intolerant 0.04 2.94 23 moderately conservative 605980 7p15-p14 "caspase recruitment domain family, member 4" 2833 rs2076222 LAMB3 3914 1 206180324 NM_000228 NP_000219 G/T A926D plus 24155055 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.27 0.06 1520 3 123 "by submitter,freq,cluster" Intolerant 0.02 3.14 12 moderately radical 150310 1q32 "laminin, beta 3" 2834 rs2076349 LAMB3 3914 1 206188625 NM_000228 NP_000219 C/T V527M plus 23692332 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.42 0.02 1588 3 123 "by doubleHit,freq,cluster" Borderline 1.07 5 conservative 150310 1q32 "laminin, beta 3" 2835 rs2076405 TGM6 343641 20 2323262 NM_198994 NP_945345 C/T M58V minus 24067102 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.4 0.08 1586 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.47 11 conservative 20p13 transglutaminase y 2836 rs2076472 APOBEC2 10930 6 41137320 NM_006789 NP_006780 C/T I136T plus 2991883 902 AFFY Caucasian 22 0.23 0.3 0.13 34 2 0.22 0.14 54 2 121 "by cluster,freq" Borderline 0.16 2.71 83 moderately conservative 604797 6p21 "apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 2" 2837 rs2076472 APOBEC2 10930 6 41137320 NM_006789 NP_006780 C/T I136T plus 2991883 904 AFFY CEPH 12 0.42 0.3 0.13 34 2 0.22 0.14 54 2 121 "by cluster,freq" Borderline 0.16 2.71 83 moderately conservative 604797 6p21 "apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 2" 2838 rs2076485 UBD 10537 6 29631931 NM_006398 NP_006389 C/T I68T minus 24341524 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.25 0 48 1 0.1 0.11 92 2 123 "by doubleHit,submitter,freq,cluster" Intolerant 0.05 3.04 390 moderately conservative 606050 6p21.3 ubiquitin D 2839 rs2076559 ENTPD6 955 20 25135213 NM_001247 NP_001238 A/G S14N plus 24615042 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.44 0 48 1 0.38 0.04 1584 3 123 "by cluster,freq" conservative 603160 20p11.2-p11.22 ectonucleoside triphosphate diphosphohydrolase 6 (putative function) 2840 rs2076671 APOL5 80831 22 34447430 NM_030642 NP_085145 C/T T272M plus 8006495 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.3 0.3 0 120 1 0.45 0 1504 1 114 "HapMap,doubleHit,freq,cluster" Potentially intolerant 0.06 2.85 32 moderately conservative 607255 22q13.1 "apolipoprotein L, 5" 2841 rs2076672 APOL5 80831 22 34447583 NM_030642 NP_085145 C/T T323M plus 2992134 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.2 0.2 0 120 1 98 "HapMap,freq,cluster" Intolerant 0 2.85 32 moderately conservative 607255 22q13.1 "apolipoprotein L, 5" 2842 rs2076673 APOL5 80831 22 34449360 NM_030642 NP_085145 C/G S406C plus 8006497 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.3 0.3 0 120 1 0.44 0 1486 1 121 "HapMap,doubleHit,submitter,freq,cluster" moderately radical 607255 22q13.1 "apolipoprotein L, 5" 2843 rs2076742 ATP10A 57194 15 23477291 NM_024490 NP_077816 C/G W1172C minus 2992226 524 LDN AUTISM USA (autistic probands) 460 0.1 0.1 0.01 506 2 0.15 0.11 92 2 123 "by doubleHit,freq,cluster" Probably damaging 3.318 7 Intolerant 0.01 2.78 16 radical 605855 15q11-q13 "ATPase, Class V, type 10A" 2844 rs2076742 ATP10A 57194 15 23477291 NM_024490 NP_077816 C/G W1172C minus 24186754 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.07 0.1 0.01 506 2 0.15 0.11 92 2 123 "by doubleHit,freq,cluster" Probably damaging 3.318 7 Intolerant 0.01 2.78 16 radical 605855 15q11-q13 "ATPase, Class V, type 10A" 2845 rs2076744 ATP10A 57194 15 23477272 NM_024490 NP_077816 A/G A1179T minus 2992228 524 LDN AUTISM USA (autistic probands) 460 0.15 0.15 0 460 1 120 "by cluster,freq" Borderline 1.003 7 Borderline 0.19 2.78 16 moderately conservative 605855 15q11-q13 "ATPase, Class V, type 10A" 2846 rs2076745 ATP10A 57194 15 23477245 NM_024490 NP_077816 A/G I1188V minus 2992229 524 LDN AUTISM USA (autistic probands) 460 0.01 0.01 0 460 1 96 by freq Benign 0.711 7 Tolerant 0.54 2.78 16 conservative 605855 15q11-q13 "ATPase, Class V, type 10A" 2847 rs2077268 RYR3 6263 15 31661043 NM_001036 NP_001027 C/T V494I minus 2992857 902 AFFY Caucasian 24 0.13 0.11 0.08 84 3 0.14 0.12 166 5 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.52 3.24 51 conservative 180903 15q14-q15 ryanodine receptor 3 2848 rs2077268 RYR3 6263 15 31661043 NM_001036 NP_001027 C/T V494I minus 2992857 904 AFFY CEPH 12 0.25 0.11 0.08 84 3 0.14 0.12 166 5 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.52 3.24 51 conservative 180903 15q14-q15 ryanodine receptor 3 2849 rs2077268 RYR3 6263 15 31661043 NM_001036 NP_001027 C/T V494I minus 23661902 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.11 0.08 84 3 0.14 0.12 166 5 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.52 3.24 51 conservative 180903 15q14-q15 ryanodine receptor 3 2850 rs2104772 TNC 3371 9 114888339 NM_002160 NP_002151 A/T I1677L minus 3023389 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.42 0.34 0.1 260 3 0.47 0.02 1592 3 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 187380 9q33 tenascin C (hexabrachion) 2851 rs2104772 TNC 3371 9 114888339 NM_002160 NP_002151 A/T I1677L minus 17247672 1303 SEQUENOM CEPH CEPH (92) 92 0.23 0.34 0.1 260 3 0.47 0.02 1592 3 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 187380 9q33 tenascin C (hexabrachion) 2852 rs2104772 TNC 3371 9 114888339 NM_002160 NP_002151 A/T I1677L minus 24058053 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.34 0.1 260 3 0.47 0.02 1592 3 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 187380 9q33 tenascin C (hexabrachion) 2853 rs2104978 TEP1 7011 14 19906873 NM_007110 NP_009041 A/G H2562R minus 3023623 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.03 0.05 0.02 220 3 123 "HapMap,doubleHit,freq" conservative 601686 14q11.2 telomerase-associated protein 1 2854 rs2104978 TEP1 7011 14 19906873 NM_007110 NP_009041 A/G H2562R minus 3172667 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 54 0.07 0.05 0.02 220 3 123 "HapMap,doubleHit,freq" conservative 601686 14q11.2 telomerase-associated protein 1 2855 rs2104978 TEP1 7011 14 19906873 NM_007110 NP_009041 A/G H2562R minus 24720763 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.05 0.02 220 3 123 "HapMap,doubleHit,freq" conservative 601686 14q11.2 telomerase-associated protein 1 2856 rs2107732 CCM2 83605 7 44851218 NM_031443 NP_113631 A/G V53I plus 24461668 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.02 0 46 1 123 by freq Benign 0.089 5 conservative 607929 7p13 cerebral cavernous malformation 2 2857 rs2108978 AKAP10 11216 17 19802050 NM_007202 NP_009133 A/G R249H minus 3028319 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.41 0.43 0.04 164 2 0.26 0.21 70 2 123 "HapMap,doubleHit,submitter,freq,cluster" Probably damaging 2.298 6 conservative 604694 17p11.1 A kinase (PRKA) anchor protein 10 2858 rs2108978 AKAP10 11216 17 19802050 NM_007202 NP_009133 A/G R249H minus 24577184 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.48 0.43 0.04 164 2 0.26 0.21 70 2 123 "HapMap,doubleHit,submitter,freq,cluster" Probably damaging 2.298 6 conservative 604694 17p11.1 A kinase (PRKA) anchor protein 10 2859 rs2111543 ZNF546 339327 19 45211745 NM_178544 NP_848639 C/G R243T plus 3031260 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.03 0.03 0 120 1 96 "HapMap,freq" Intolerant 0.05 2.75 50 moderately conservative 19q13.2 zinc finger protein 546 2860 rs2111544 ZNF546 339327 19 45211775 NM_178544 NP_848639 C/T A253V plus 3031261 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.03 0.03 0 120 1 96 "HapMap,freq" Tolerant 0.41 2.77 50 moderately conservative 19q13.2 zinc finger protein 546 2861 rs2116665 GPD2 2820 2 157231757 NM_000408 NP_000399 C/T R264H minus 23264641 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.23 0 48 1 0.23 0.05 1576 3 123 "by doubleHit,freq,cluster" Benign 0.551 11 conservative 138430 2q24.1 glycerol-3-phosphate dehydrogenase 2 (mitochondrial) 2862 rs2125579 ZNF235 9310 19 49484541 NM_004234 NP_004225 G/T H296P plus 3048653 639 TSC-CSHL TSC_42_C TSC Caucasian (42) 80 0.45 0.46 0.02 128 2 0.31 0.14 260 4 123 "by doubleHit,submitter,freq,cluster" Probably damaging 2.532 17 Intolerant 0.05 2.81 29 moderately conservative 604749 19q13.2 zinc finger protein 235 2863 rs2125579 ZNF235 9310 19 49484541 NM_004234 NP_004225 G/T H296P plus 24627427 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.46 0.02 128 2 0.31 0.14 260 4 123 "by doubleHit,submitter,freq,cluster" Probably damaging 2.532 17 Intolerant 0.05 2.81 29 moderately conservative 604749 19q13.2 zinc finger protein 235 2864 rs2131107 DAG1 1605 3 49523012 NM_004393 NP_004384 C/G S14W minus 3175980 619 WICVAR MITOGPOP6 CORIELL Mixed 46 0.07 0.07 0 46 1 121 "HapMap,freq,cluster" Probably damaging 3.312 12 radical 128239 3p21 dystroglycan 1 (dystrophin-associated glycoprotein 1) 2865 rs2135720 PCDH15 65217 10 55425497 NM_033056 NP_149045 A/G R929Q minus 24115648 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.21 0 48 1 0.3 0.23 94 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.084 5 Tolerant 0.59 2.74 39 conservative 605514 10p11.2-q21 protocadherin 15 2866 rs2152143 MKI67 4288 10 129796970 NM_002417 NP_002408 A/G G1042S minus 24598791 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.25 0 48 1 0.1 0.06 94 2 123 "by doubleHit,freq" Tolerant 0.79 3.17 6 moderately conservative 176741 10q25-qter antigen identified by monoclonal antibody Ki-67 2867 rs2155587 PORIMIN 114908 11 101778094 NM_052932 NP_443164 A/G V52M minus 3086005 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.1 0.09 0.01 166 2 0.02 0 92 2 123 "HapMap,submitter,freq" conservative 606356 11q22.1 pro-oncosis receptor inducing membrane injury gene 2868 rs2155587 PORIMIN 114908 11 101778094 NM_052932 NP_443164 A/G V52M minus 24528991 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.09 0.01 166 2 0.02 0 92 2 123 "HapMap,submitter,freq" conservative 606356 11q22.1 pro-oncosis receptor inducing membrane injury gene 2869 rs2165627 PTPRB 5787 12 69270162 NM_002837 NP_002828 G/T D415E minus 118890 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.16 0.15 0.02 168 2 0.15 0 46 1 123 "HapMap,submitter,freq,cluster" Benign 0.069 5 Tolerant 1 2.97 11 conservative 176882 12q15-q21 "protein tyrosine phosphatase, receptor type, B" 2870 rs2165627 PTPRB 5787 12 69270162 NM_002837 NP_002828 G/T D415E minus 23660784 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.15 0.02 168 2 0.15 0 46 1 123 "HapMap,submitter,freq,cluster" Benign 0.069 5 Tolerant 1 2.97 11 conservative 176882 12q15-q21 "protein tyrosine phosphatase, receptor type, B" 2871 rs2167079 ACP2 53 11 47226831 NM_001610 NP_001601 A/G R29Q minus 3100463 1303 SEQUENOM CEPH CEPH (92) 92 0.17 0.27 0.11 248 2 0.24 0 200 1 123 "by doubleHit,freq,cluster" Potentially damaging 1.245 5 Tolerant 0.46 2.92 69 conservative 171650 11p11.2-p11.11 "acid phosphatase 2, lysosomal" 2872 rs2167079 ACP2 53 11 47226831 NM_001610 NP_001601 A/G R29Q minus 28461438 549 KYUGEN CP CEPH (78) 156 0.33 0.27 0.11 248 2 0.24 0 200 1 123 "by doubleHit,freq,cluster" Potentially damaging 1.245 5 Tolerant 0.46 2.92 69 conservative 171650 11p11.2-p11.11 "acid phosphatase 2, lysosomal" 2873 rs2171492 CPA4 51200 7 129544691 NM_016352 NP_057436 G/T G303C plus 3105982 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 18 0.33 0.33 0 18 1 0.33 0.05 1632 4 116 "by doubleHit,submitter,freq,cluster" Benign 0.936 37 Intolerant 0.05 2.76 52 radical 607635 7q32 carboxypeptidase A4 2874 rs2180314 GSTA2 2939 6 52725690 NM_000846 NP_000837 C/G S112T plus 3117044 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.43 0.43 0 106 2 0.28 0.07 46 2 121 "by doubleHit,freq" Benign 0.182 61 moderately conservative 138360 6p12.1 glutathione S-transferase A2 2875 rs2180314 GSTA2 2939 6 52725690 NM_000846 NP_000837 C/G S112T plus 3117044 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 92 0.43 0.43 0 106 2 0.28 0.07 46 2 121 "by doubleHit,freq" Benign 0.182 61 moderately conservative 138360 6p12.1 glutathione S-transferase A2 2876 rs2180792 PNN 5411 14 38719985 NM_002687 NP_002678 A/T T441S plus 24579539 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.04 0.04 0 46 1 0.02 0 1590 3 123 "by doubleHit,freq,cluster" Benign 0.957 10 moderately conservative 603154 14q13.3 "pinin, desmosome associated protein" 2877 rs2184953 FLG 2312 1 149093855 XM_048104 XP_048104 A/G Y2194H plus 3122822 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.16 0.2 0.11 150 3 0.44 0.07 70 3 120 "HapMap,doubleHit,freq,cluster" Tolerant 0.52 3.13 11 moderately conservative 135940 1q21 filaggrin 2878 rs2184953 FLG 2312 1 149093855 XM_048104 XP_048104 A/G Y2194H plus 3122822 902 AFFY Caucasian 22 0.41 0.2 0.11 150 3 0.44 0.07 70 3 120 "HapMap,doubleHit,freq,cluster" Tolerant 0.52 3.13 11 moderately conservative 135940 1q21 filaggrin 2879 rs2184953 FLG 2312 1 149093855 XM_048104 XP_048104 A/G Y2194H plus 3122822 904 AFFY CEPH 12 0.17 0.2 0.11 150 3 0.44 0.07 70 3 120 "HapMap,doubleHit,freq,cluster" Tolerant 0.52 3.13 11 moderately conservative 135940 1q21 filaggrin 2880 rs2185379 PRDM1 639 6 106642946 NM_001198 NP_001189 A/G G38S plus 23323991 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.12 0.03 1558 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.041 6 moderately conservative 603423 6q21-q22.1 "PR domain containing 1, with ZNF domain" 2881 rs2186797 TMEM16A 55107 11 69685418 NM_018043 NP_060513 C/T F582S plus 24539341 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.02 0 46 1 123 by freq Possibly damaging 1.885 9 Intolerant 0 2.75 27 radical 11q13.2 transmembrane protein 16A 2882 rs2188736 ZNF154 7710 19 62905585 NM_003444 NP_003435 C/G L182V plus 3127769 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.21 0.21 0 118 1 108 "HapMap,doubleHit,freq" Borderline 1.208 16 Tolerant 0.29 2.78 110 conservative 604085 19q13.4 zinc finger protein 154 (pHZ-92) 2883 rs2193587 DGKG 1608 3 187472798 NM_001346 NP_001337 A/G R316K minus 3133286 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.14 0.14 0.01 202 3 0.17 0.14 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.318 19 conservative 601854 3q27-q28 "diacylglycerol kinase, gamma 90kDa" 2884 rs2193587 DGKG 1608 3 187472798 NM_001346 NP_001337 A/G R316K minus 3175900 619 WICVAR MITOGPOP6 CORIELL Mixed 38 0.13 0.14 0.01 202 3 0.17 0.14 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.318 19 conservative 601854 3q27-q28 "diacylglycerol kinase, gamma 90kDa" 2885 rs2193587 DGKG 1608 3 187472798 NM_001346 NP_001337 A/G R316K minus 24135420 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.13 0.14 0.01 202 3 0.17 0.14 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.318 19 conservative 601854 3q27-q28 "diacylglycerol kinase, gamma 90kDa" 2886 rs2227279 BDKRB2 624 14 95777479 NM_000623 NP_000614 A/G G354E plus 3176441 619 WICVAR MITOGPOP6 CORIELL Mixed 30 0.07 0.07 0 30 1 0.04 0 46 1 98 by freq Possibly damaging 1.769 13 Tolerant 0.27 2.86 223 moderately conservative 113503 14q32.1-q32.2 bradykinin receptor B2 2887 rs2227297 PDE4B 5142 1 66550278 NM_002600 NP_002591 A/T S703C plus 3177303 619 WICVAR MITOGPOP6 CORIELL Mixed 52 0.02 0.02 0 96 2 98 by freq Possibly damaging 1.556 39 moderately radical 600127 1p31 "phosphodiesterase 4B, cAMP-specific (phosphodiesterase E4 dunce homolog, Drosophila)" 2888 rs2227297 PDE4B 5142 1 66550278 NM_002600 NP_002591 A/T S703C plus 3178125 619 WICVAR MITOGPOP6 CORIELL Mixed 44 0.02 0.02 0 96 2 98 by freq Possibly damaging 1.556 39 moderately radical 600127 1p31 "phosphodiesterase 4B, cAMP-specific (phosphodiesterase E4 dunce homolog, Drosophila)" 2889 rs2227309 CASP7 840 10 115479157 NM_033340 NP_203126 A/G R249K plus 3177083 619 WICVAR MITOGPOP6 CORIELL Mixed 44 0.43 0.35 0.09 142 3 0.17 0.14 94 2 123 "by doubleHit,freq,cluster" conservative 601761 10q25 "caspase 7, apoptosis-related cysteine protease" 2890 rs2227309 CASP7 840 10 115479157 NM_033340 NP_203126 A/G R249K plus 3177085 619 WICVAR MITOGPOP6 CORIELL Mixed 50 0.38 0.35 0.09 142 3 0.17 0.14 94 2 123 "by doubleHit,freq,cluster" conservative 601761 10q25 "caspase 7, apoptosis-related cysteine protease" 2891 rs2227309 CASP7 840 10 115479157 NM_033340 NP_203126 A/G R249K plus 24123614 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.35 0.09 142 3 0.17 0.14 94 2 123 "by doubleHit,freq,cluster" conservative 601761 10q25 "caspase 7, apoptosis-related cysteine protease" 2892 rs2227564 PLAU 5328 10 75343107 NM_002658 NP_002649 C/T L141P plus 3172132 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 44 0.34 0.28 0.08 104 2 0.21 0.05 1540 2 121 "by cluster,freq" Possibly damaging 1.917 12 moderately conservative 191840 10q24 "plasminogen activator, urokinase" 2893 rs2227564 PLAU 5328 10 75343107 NM_002658 NP_002649 C/T L141P plus 3172890 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 60 0.23 0.28 0.08 104 2 0.21 0.05 1540 2 121 "by cluster,freq" Possibly damaging 1.917 12 moderately conservative 191840 10q24 "plasminogen activator, urokinase" 2894 rs2227567 PLAU 5328 10 75343754 NM_002658 NP_002649 A/C K231Q plus 3176308 619 WICVAR MITOGPOP6 CORIELL Mixed 68 0.01 0.01 0 68 1 0.13 0.15 94 2 123 by freq Benign 0.034 24 Tolerant 0.58 2.78 38 moderately conservative 191840 10q24 "plasminogen activator, urokinase" 2895 rs2227832 F2R 2149 5 76064575 NM_001992 NP_001983 G/T V257L plus 3172438 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 38 0.03 0.03 0 76 2 119 "by cluster,freq" Benign 0.503 8 Potentially intolerant 0.06 2.79 25 conservative 187930 5q13 coagulation factor II (thrombin) receptor 2896 rs2227832 F2R 2149 5 76064575 NM_001992 NP_001983 G/T V257L plus 14339392 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 38 0.03 0.03 0 76 2 119 "by cluster,freq" Benign 0.503 8 Potentially intolerant 0.06 2.79 25 conservative 187930 5q13 coagulation factor II (thrombin) receptor 2897 rs2227869 ERCC5 2073 13 102313086 NM_000123 NP_000114 C/G C529S plus 3172479 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 66 0.08 0.04 0.03 418 4 0.06 0.02 346 4 113 "HapMap,freq,cluster" Tolerant 0.53 2.9 8 moderately radical 133530 13q22 "excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))" 2898 rs2227869 ERCC5 2073 13 102313086 NM_000123 NP_000114 C/G C529S plus 5586521 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.03 0.04 0.03 418 4 0.06 0.02 346 4 113 "HapMap,freq,cluster" Tolerant 0.53 2.9 8 moderately radical 133530 13q22 "excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))" 2899 rs2227869 ERCC5 2073 13 102313086 NM_000123 NP_000114 C/G C529S plus 5586521 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.06 0.04 0.03 418 4 0.06 0.02 346 4 113 "HapMap,freq,cluster" Tolerant 0.53 2.9 8 moderately radical 133530 13q22 "excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))" 2900 rs2227869 ERCC5 2073 13 102313086 NM_000123 NP_000114 C/G C529S plus 5605249 693 EGP_SNPS PDR90 NIHPDR 170 0.02 0.04 0.03 418 4 0.06 0.02 346 4 113 "HapMap,freq,cluster" Tolerant 0.53 2.9 8 moderately radical 133530 13q22 "excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))" 2901 rs2227902 REST 5978 4 57638028 NM_005612 NP_005603 G/T E692D plus 3172513 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 44 0.14 0.1 0.06 92 2 0.06 0.04 94 2 123 "by cluster,freq" conservative 600571 4q12 RE1-silencing transcription factor 2902 rs2227902 REST 5978 4 57638028 NM_005612 NP_005603 G/T E692D plus 23379726 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.1 0.06 92 2 0.06 0.04 94 2 123 "by cluster,freq" conservative 600571 4q12 RE1-silencing transcription factor 2903 rs2227914 DMC1 11144 22 37259106 NM_007068 NP_008999 A/G M200V minus 3172529 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 48 0.1 0.04 0.04 228 2 0.05 0.04 334 4 123 "HapMap,freq,cluster" Possibly damaging 1.909 61 Tolerant 0.21 2.78 118 conservative 602721 22q13.1 "DMC1 dosage suppressor of mck1 homolog, meiosis-specific homologous recombination (yeast)" 2904 rs2227914 DMC1 11144 22 37259106 NM_007068 NP_008999 A/G M200V minus 16342361 693 EGP_SNPS PDR90 NIHPDR 180 0.03 0.04 0.04 228 2 0.05 0.04 334 4 123 "HapMap,freq,cluster" Possibly damaging 1.909 61 Tolerant 0.21 2.78 118 conservative 602721 22q13.1 "DMC1 dosage suppressor of mck1 homolog, meiosis-specific homologous recombination (yeast)" 2905 rs2227928 ATR 545 3 143764310 NM_001184 NP_001175 C/T M211T minus 3172543 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 54 0.46 0.44 0.02 212 3 0.36 0.15 70 2 123 "HapMap,doubleHit,freq,cluster" moderately conservative 601215 3q22-q24 ataxia telangiectasia and Rad3 related 2906 rs2227928 ATR 545 3 143764310 NM_001184 NP_001175 C/T M211T minus 14210760 885 TSC-CSHL HapMap-CEPH-30-trios 110 0.43 0.44 0.02 212 3 0.36 0.15 70 2 123 "HapMap,doubleHit,freq,cluster" moderately conservative 601215 3q22-q24 ataxia telangiectasia and Rad3 related 2907 rs2227928 ATR 545 3 143764310 NM_001184 NP_001175 C/T M211T minus 23874781 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.44 0.02 212 3 0.36 0.15 70 2 123 "HapMap,doubleHit,freq,cluster" moderately conservative 601215 3q22-q24 ataxia telangiectasia and Rad3 related 2908 rs2227943 BRCA2 675 13 31809278 NM_000059 NP_000050 C/T L929S plus 16355801 693 EGP_SNPS PDR90 NIHPDR 174 0.01 0.01 0 174 1 0.01 0.01 252 2 120 "by cluster,freq" Potentially damaging 1.432 9 moderately radical 600185 13q12.3 "breast cancer 2, early onset" 2909 rs2227944 BRCA2 675 13 31809452 NM_000059 NP_000050 A/T N987I plus 16355804 693 EGP_SNPS PDR90 NIHPDR 174 0.01 0.01 0 174 1 0.01 0.01 252 2 120 "by cluster,freq" Probably damaging 2.165 9 moderately radical 600185 13q12.3 "breast cancer 2, early onset" 2910 rs2227973 RAG1 5896 11 36553889 NM_000448 NP_000439 A/G K820R plus 3172597 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 28 0.32 0.19 0.07 310 4 0.21 0.13 440 6 123 "by submitter,freq,cluster" Benign 0.733 346 conservative 179615 11p13 recombination activating gene 1 2911 rs2227973 RAG1 5896 11 36553889 NM_000448 NP_000439 A/G K820R plus 5606004 693 EGP_SNPS PDR90 NIHPDR 172 0.21 0.19 0.07 310 4 0.21 0.13 440 6 123 "by submitter,freq,cluster" Benign 0.733 346 conservative 179615 11p13 recombination activating gene 1 2912 rs2227973 RAG1 5896 11 36553889 NM_000448 NP_000439 A/G K820R plus 6903927 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.1 0.19 0.07 310 4 0.21 0.13 440 6 123 "by submitter,freq,cluster" Benign 0.733 346 conservative 179615 11p13 recombination activating gene 1 2913 rs2227973 RAG1 5896 11 36553889 NM_000448 NP_000439 A/G K820R plus 24104518 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.19 0.07 310 4 0.21 0.13 440 6 123 "by submitter,freq,cluster" Benign 0.733 346 conservative 179615 11p13 recombination activating gene 1 2914 rs2228006 PMS2 5395 7 5800016 NM_000535 NP_000526 A/G K541E minus 3172636 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 46 0.04 0.04 0 46 1 0.07 0 1480 1 121 "by doubleHit,freq,cluster" moderately conservative 600259 7p22.2 PMS2 postmeiotic segregation increased 2 (S. cerevisiae) 2915 rs2228049 CD14 929 5 139992143 NM_000591 NP_000582 A/G N204D minus 3172683 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 66 0.03 0.03 0 66 1 98 by freq Potentially damaging 1.494 14 Intolerant 0.01 2.76 60 conservative 158120 5q31.1 CD14 antigen 2916 rs2228053 CUBN 8029 10 17185148 NM_001081 NP_001072 C/G I504M minus 3172687 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 56 0.04 0.04 0 56 1 98 by freq Potentially intolerant 0.08 2.84 6 conservative 602997 10p12.31 cubilin (intrinsic factor-cobalamin receptor) 2917 rs2228063 CA2 760 8 86580241 NM_000067 NP_000058 A/G N252D plus 3172698 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 56 0.04 0.04 0 56 1 0.11 0 46 1 123 "HapMap,freq,cluster" Benign 0.513 83 Tolerant 0.22 2.77 62 conservative 259730 8q22 carbonic anhydrase II 2918 rs2228065 ALOX5 240 10 45240512 NM_000698 NP_000689 A/G E254K plus 3172700 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 62 0.06 0.06 0 62 1 0.02 0.01 1774 4 116 "by cluster,freq" Benign 0.755 6 Tolerant 0.95 2.78 33 moderately conservative 152390 10q11.2 arachidonate 5-lipoxygenase 2919 rs2228076 IL17R 23765 22 15963763 NM_014339 NP_055154 C/T A367V plus 3172712 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 64 0.28 0.28 0 64 1 98 by freq moderately conservative 605461 22q11.1 interleukin 17 receptor 2920 rs2228078 GHRHR 2692 7 30792092 NM_000823 NP_000814 C/T M422T plus 3172714 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 48 0.04 0.04 0 48 1 98 by freq Possibly damaging 1.715 9 Tolerant 0.22 2.91 19 moderately conservative 139191 7p14 growth hormone releasing hormone receptor 2921 rs2228093 ALDH1B1 219 9 38386002 NM_000692 NP_000683 C/T A86V plus 3172733 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 44 0.14 0.15 0.01 92 2 0.28 0.29 86 2 123 "by doubleHit,freq,cluster" Possibly damaging 1.913 122 Intolerant 0 2.83 141 moderately conservative 100670 9p11.1 "aldehyde dehydrogenase 1 family, member B1" 2922 rs2228093 ALDH1B1 219 9 38386002 NM_000692 NP_000683 C/T A86V plus 24092964 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0.01 92 2 0.28 0.29 86 2 123 "by doubleHit,freq,cluster" Possibly damaging 1.913 122 Intolerant 0 2.83 141 moderately conservative 100670 9p11.1 "aldehyde dehydrogenase 1 family, member B1" 2923 rs2228139 IL1R1 3554 2 102240167 NM_000877 NP_000868 C/G A124G plus 5111242 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 44 0.11 0.1 0.01 92 2 0.04 0.01 90 2 123 by freq Borderline 1.137 10 Tolerant 0.36 2.77 23 moderately conservative 147810 2q12 "interleukin 1 receptor, type I" 2924 rs2228139 IL1R1 3554 2 102240167 NM_000877 NP_000868 C/G A124G plus 24302787 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0.01 92 2 0.04 0.01 90 2 123 by freq Borderline 1.137 10 Tolerant 0.36 2.77 23 moderately conservative 147810 2q12 "interleukin 1 receptor, type I" 2925 rs2228168 LRP2 4036 2 169894071 NM_004525 NP_004516 C/T I2065T minus 3172821 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 48 0.04 0.04 0 48 1 0.02 0 46 1 123 "HapMap,freq,cluster" Intolerant 0.01 2.76 21 moderately conservative 600073 2q24-q31 low density lipoprotein-related protein 2 2926 rs2228224 GLI 2735 12 56151588 NM_005269 NP_005260 A/G G933D plus 3172886 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 64 0.25 0.29 0.05 224 3 0.47 0.08 1586 3 123 "HapMap,doubleHit,freq,cluster" moderately conservative 165220 12q13.2-q13.3 glioma-associated oncogene homolog (zinc finger protein) 2927 rs2228224 GLI 2735 12 56151588 NM_005269 NP_005260 A/G G933D plus 3172886 885 TSC-CSHL HapMap-CEPH-30-trios 112 0.33 0.29 0.05 224 3 0.47 0.08 1586 3 123 "HapMap,doubleHit,freq,cluster" moderately conservative 165220 12q13.2-q13.3 glioma-associated oncogene homolog (zinc finger protein) 2928 rs2228224 GLI 2735 12 56151588 NM_005269 NP_005260 A/G G933D plus 23451649 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.29 0.05 224 3 0.47 0.08 1586 3 123 "HapMap,doubleHit,freq,cluster" moderately conservative 165220 12q13.2-q13.3 glioma-associated oncogene homolog (zinc finger protein) 2929 rs2228226 GLI 2735 12 56152088 NM_005269 NP_005260 C/G E1100Q plus 3172888 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 46 0.39 0.32 0.06 306 4 0.19 0.01 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 165220 12q13.2-q13.3 glioma-associated oncogene homolog (zinc finger protein) 2930 rs2228226 GLI 2735 12 56152088 NM_005269 NP_005260 C/G E1100Q plus 3172888 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.31 0.32 0.06 306 4 0.19 0.01 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 165220 12q13.2-q13.3 glioma-associated oncogene homolog (zinc finger protein) 2931 rs2228226 GLI 2735 12 56152088 NM_005269 NP_005260 C/G E1100Q plus 15835123 1303 SEQUENOM CEPH CEPH (92) 92 0.36 0.32 0.06 306 4 0.19 0.01 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 165220 12q13.2-q13.3 glioma-associated oncogene homolog (zinc finger protein) 2932 rs2228226 GLI 2735 12 56152088 NM_005269 NP_005260 C/G E1100Q plus 24458951 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.32 0.06 306 4 0.19 0.01 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 165220 12q13.2-q13.3 glioma-associated oncogene homolog (zinc finger protein) 2933 rs2228231 NFATC4 4776 14 23909181 NM_004554 NP_004545 A/G S246N plus 3172893 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 52 0.06 0.06 0 52 1 98 by freq conservative 602699 14q11.2 "nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4" 2934 rs2228243 HRG 3273 3 187877815 NM_000412 NP_000403 A/G H340R plus 3172906 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 66 0.12 0.15 0.03 136 3 0.29 0.05 1646 6 123 "by submitter,freq,cluster" Tolerant 0.23 3.1 21 conservative 142640 3q27 histidine-rich glycoprotein 2935 rs2228243 HRG 3273 3 187877815 NM_000412 NP_000403 A/G H340R plus 3172906 902 AFFY Caucasian 22 0.18 0.15 0.03 136 3 0.29 0.05 1646 6 123 "by submitter,freq,cluster" Tolerant 0.23 3.1 21 conservative 142640 3q27 histidine-rich glycoprotein 2936 rs2228243 HRG 3273 3 187877815 NM_000412 NP_000403 A/G H340R plus 23914253 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.15 0.03 136 3 0.29 0.05 1646 6 123 "by submitter,freq,cluster" Tolerant 0.23 3.1 21 conservative 142640 3q27 histidine-rich glycoprotein 2937 rs2228259 STAT2 6773 12 55034562 NM_005419 NP_005410 C/G C246S minus 3172922 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 64 0.03 0.03 0 64 1 98 by freq Probably damaging 2.718 5 Borderline 0.12 2.81 80 moderately radical 600556 12q13.13 "signal transducer and activator of transcription 2, 113kDa" 2938 rs2228273 ZNF133 7692 20 18244076 NM_003434 NP_003425 A/G G193E plus 3172936 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 48 0.06 0.06 0 48 1 98 by freq Benign 0.094 5 Tolerant 0.41 2.8 32 moderately conservative 604075 20p11.23-20p11.22 zinc finger protein 133 (clone pHZ-13) 2939 rs2228275 ZNF135 7694 19 63271439 NM_003436 NP_003427 C/T S592L plus 3172940 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 58 0.26 0.26 0 58 1 98 by freq Probably damaging 2.038 10 Tolerant 0.64 2.76 37 moderately radical 604077 19q13.4 zinc finger protein 135 (clone pHZ-17) 2940 rs2228277 ZNF135 7694 19 63271184 NM_003436 NP_003427 C/T S507L plus 3172942 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 58 0.22 0.22 0 58 1 98 by freq Possibly damaging 1.498 10 Intolerant 0 2.76 37 moderately radical 604077 19q13.4 zinc finger protein 135 (clone pHZ-17) 2941 rs2228278 ZNF135 7694 19 63271213 NM_003436 NP_003427 A/G T517A plus 3172943 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 58 0.21 0.21 0 58 1 98 by freq Possibly damaging 1.825 10 Intolerant 0.01 2.76 37 moderately conservative 604077 19q13.4 zinc finger protein 135 (clone pHZ-17) 2942 rs2228279 ZNF135 7694 19 63271399 NM_003436 NP_003427 C/G G579R plus 3172944 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 58 0.09 0.09 0 58 1 98 "HapMap,freq" Benign 0.803 10 Tolerant 0.41 2.76 37 moderately radical 604077 19q13.4 zinc finger protein 135 (clone pHZ-17) 2943 rs2228280 ZNF135 7694 19 63271201 NM_003436 NP_003427 C/T Q513X plus 3172945 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 58 0.12 0.12 0 58 1 98 by freq Probably damaging Intolerant radical 604077 19q13.4 zinc finger protein 135 (clone pHZ-17) 2944 rs2228293 S100A6 6277 1 150320249 NM_014624 NP_055439 A/G G90D minus 3172958 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 70 0.03 0.03 0 70 1 98 by freq moderately conservative 114110 1q21 S100 calcium binding protein A6 (calcyclin) 2945 rs2228305 FASN 2194 17 77636081 NM_004104 NP_004095 A/G V1483I minus 3172972 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 66 0.09 0.09 0 66 1 123 by freq Benign 0.106 9 Tolerant 0.38 3.03 11 conservative 600212 17q25 fatty acid synthase 2946 rs2228307 FASN 2194 17 77634184 NM_004104 NP_004095 A/G I1888V minus 3172974 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 66 0.05 0.05 0 66 1 98 by freq Benign 0.711 9 Tolerant 0.51 2.78 17 conservative 600212 17q25 fatty acid synthase 2947 rs2228310 PCCB 5096 3 137499587 NM_000532 NP_000523 C/T P287S plus 3172977 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 70 0.34 0.34 0 70 1 98 by freq Borderline 1.129 88 moderately conservative 232050 3q21-q22 "propionyl Coenzyme A carboxylase, beta polypeptide" 2948 rs2228315 SELPLG 6404 12 107520364 NM_003006 NP_002997 A/G M62I minus 3172984 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 58 0.1 0.09 0.01 220 3 0.26 0 46 1 120 "HapMap,doubleHit,freq,cluster" Tolerant 0.56 3 15 conservative 600738 12q24 selectin P ligand 2949 rs2228315 SELPLG 6404 12 107520364 NM_003006 NP_002997 A/G M62I minus 12568538 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 42 0.1 0.09 0.01 220 3 0.26 0 46 1 120 "HapMap,doubleHit,freq,cluster" Tolerant 0.56 3 15 conservative 600738 12q24 selectin P ligand 2950 rs2228315 SELPLG 6404 12 107520364 NM_003006 NP_002997 A/G M62I minus 12568538 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.09 0.09 0.01 220 3 0.26 0 46 1 120 "HapMap,doubleHit,freq,cluster" Tolerant 0.56 3 15 conservative 600738 12q24 selectin P ligand 2951 rs2228331 GPC1 2817 2 241125518 NM_002081 NP_002072 A/G S500G plus 3173002 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 54 0.2 0.22 0.03 100 2 0.23 0.08 94 2 123 by freq moderately conservative 600395 2q35-q37 glypican 1 2952 rs2228331 GPC1 2817 2 241125518 NM_002081 NP_002072 A/G S500G plus 24170758 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.24 0.22 0.03 100 2 0.23 0.08 94 2 123 by freq moderately conservative 600395 2q35-q37 glypican 1 2953 rs2228337 TGM1 7051 14 23788408 NM_000359 NP_000350 A/T D802V minus 3173008 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 46 0.09 0.09 0 46 1 0.02 0 46 1 123 "HapMap,freq,cluster" Possibly damaging 1.807 8 radical 190195 14q11.2 "transglutaminase 1 (K polypeptide epidermal type I, protein-glutamine-gamma-glutamyltransferase)" 2954 rs2228479 MC1R 4157 16 88513441 NM_002386 NP_002377 A/G V92M plus 3173167 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 58 0.12 0.1 0.04 102 2 120 "by cluster,freq" Benign 0.277 210 Tolerant 0.3 2.8 285 conservative 155555 16q24.3 melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor) 2955 rs2228479 MC1R 4157 16 88513441 NM_002386 NP_002377 A/G V92M plus 4472755 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 44 0.07 0.1 0.04 102 2 120 "by cluster,freq" Benign 0.277 210 Tolerant 0.3 2.8 285 conservative 155555 16q24.3 melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor) 2956 rs2228487 XRCC1 7515 19 48750732 NM_006297 NP_006288 A/G R107H minus 3173176 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 52 0.06 0.06 0 52 1 98 by freq Possibly damaging 1.82 7 conservative 194360 19q13.2 X-ray repair complementing defective repair in Chinese hamster cells 1 2957 rs2228500 PFKM 5213 12 46812979 NM_000289 NP_000280 A/G R100Q plus 3173192 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 58 0.21 0.21 0 58 1 0.2 0 1496 1 102 "by submitter,freq,cluster" Benign 0.327 44 conservative 232800 12q13.3 "phosphofructokinase, muscle" 2958 rs2228510 HERC1 8925 15 61757509 NM_003922 NP_003913 A/G I2220V minus 3173202 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 44 0.23 0.32 0.06 212 3 0.09 0.08 1508 2 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 605109 15q22 hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1 2959 rs2228510 HERC1 8925 15 61757509 NM_003922 NP_003913 A/G I2220V minus 3173202 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.34 0.32 0.06 212 3 0.09 0.08 1508 2 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 605109 15q22 hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1 2960 rs2228510 HERC1 8925 15 61757509 NM_003922 NP_003913 A/G I2220V minus 23518429 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.32 0.06 212 3 0.09 0.08 1508 2 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 605109 15q22 hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1 2961 rs2228516 HERC1 8925 15 61705332 NM_003922 NP_003913 A/G I4394V minus 3173208 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 64 0.03 0.03 0 64 1 98 by freq conservative 605109 15q22 hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1 2962 rs2228526 ERCC6 2074 10 50348723 NM_000124 NP_000115 A/G M1097V minus 3173218 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 54 0.09 0.17 0.05 270 3 0.08 0.06 94 2 123 "by submitter,freq,cluster" conservative 133540 10q11 "excision repair cross-complementing rodent repair deficiency, complementation group 6" 2963 rs2228526 ERCC6 2074 10 50348723 NM_000124 NP_000115 A/G M1097V minus 5609190 693 EGP_SNPS PDR90 NIHPDR 168 0.18 0.17 0.05 270 3 0.08 0.06 94 2 123 "by submitter,freq,cluster" conservative 133540 10q11 "excision repair cross-complementing rodent repair deficiency, complementation group 6" 2964 rs2228526 ERCC6 2074 10 50348723 NM_000124 NP_000115 A/G M1097V minus 24695003 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.17 0.05 270 3 0.08 0.06 94 2 123 "by submitter,freq,cluster" conservative 133540 10q11 "excision repair cross-complementing rodent repair deficiency, complementation group 6" 2965 rs2228527 ERCC6 2074 10 50348375 NM_000124 NP_000115 A/G R1213G minus 3173219 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 62 0.1 0.18 0.04 396 4 0.1 0.08 92 2 123 "HapMap,submitter,freq,cluster" moderately radical 133540 10q11 "excision repair cross-complementing rodent repair deficiency, complementation group 6" 2966 rs2228527 ERCC6 2074 10 50348375 NM_000124 NP_000115 A/G R1213G minus 5609193 693 EGP_SNPS PDR90 NIHPDR 166 0.19 0.18 0.04 396 4 0.1 0.08 92 2 123 "HapMap,submitter,freq,cluster" moderately radical 133540 10q11 "excision repair cross-complementing rodent repair deficiency, complementation group 6" 2967 rs2228527 ERCC6 2074 10 50348375 NM_000124 NP_000115 A/G R1213G minus 5609193 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.2 0.18 0.04 396 4 0.1 0.08 92 2 123 "HapMap,submitter,freq,cluster" moderately radical 133540 10q11 "excision repair cross-complementing rodent repair deficiency, complementation group 6" 2968 rs2228527 ERCC6 2074 10 50348375 NM_000124 NP_000115 A/G R1213G minus 24695002 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.18 0.04 396 4 0.1 0.08 92 2 123 "HapMap,submitter,freq,cluster" moderately radical 133540 10q11 "excision repair cross-complementing rodent repair deficiency, complementation group 6" 2969 rs2228528 ERCC6 2074 10 50402286 NM_000124 NP_000115 A/G G399D minus 3173220 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 68 0.01 0.16 0.14 232 2 0.45 0 726 1 120 "by doubleHit,freq,cluster" Tolerant 0.62 2.92 64 moderately conservative 133540 10q11 "excision repair cross-complementing rodent repair deficiency, complementation group 6" 2970 rs2228528 ERCC6 2074 10 50402286 NM_000124 NP_000115 A/G G399D minus 5609012 693 EGP_SNPS PDR90 NIHPDR 164 0.22 0.16 0.14 232 2 0.45 0 726 1 120 "by doubleHit,freq,cluster" Tolerant 0.62 2.92 64 moderately conservative 133540 10q11 "excision repair cross-complementing rodent repair deficiency, complementation group 6" 2971 rs2228529 ERCC6 2074 10 50337111 NM_000124 NP_000115 A/G Q1413R minus 3173221 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 46 0.26 0.21 0.03 270 3 0.07 0.05 94 2 123 "by doubleHit,submitter,freq,cluster" conservative 133540 10q11 "excision repair cross-complementing rodent repair deficiency, complementation group 6" 2972 rs2228529 ERCC6 2074 10 50337111 NM_000124 NP_000115 A/G Q1413R minus 5609216 693 EGP_SNPS PDR90 NIHPDR 176 0.19 0.21 0.03 270 3 0.07 0.05 94 2 123 "by doubleHit,submitter,freq,cluster" conservative 133540 10q11 "excision repair cross-complementing rodent repair deficiency, complementation group 6" 2973 rs2228529 ERCC6 2074 10 50337111 NM_000124 NP_000115 A/G Q1413R minus 24694991 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.21 0.03 270 3 0.07 0.05 94 2 123 "by doubleHit,submitter,freq,cluster" conservative 133540 10q11 "excision repair cross-complementing rodent repair deficiency, complementation group 6" 2974 rs2228541 SERPINA6 866 14 93845974 NM_001756 NP_001747 G/T S246A minus 3173233 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 42 0.48 0.48 0 42 1 120 "by cluster,freq" Potentially damaging 1.374 10 Borderline 0.14 2.78 49 moderately conservative 122500 14q32.1 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 6" 2975 rs2228545 BMPR2 659 2 203246218 NM_001204 NP_001195 A/G S775N plus 3173237 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 56 0.04 0.03 0.01 176 2 98 "HapMap,freq" conservative 600799 2q33-q34 "bone morphogenetic protein receptor, type II (serine/threonine kinase)" 2976 rs2228545 BMPR2 659 2 203246218 NM_001204 NP_001195 A/G S775N plus 3173237 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.03 0.03 0.01 176 2 98 "HapMap,freq" conservative 600799 2q33-q34 "bone morphogenetic protein receptor, type II (serine/threonine kinase)" 2977 rs2228561 COL7A1 1294 3 48603018 NM_000094 NP_000085 C/T P595L minus 3173254 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 72 0.06 0.11 0.05 232 3 0.03 0.01 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.563 5 moderately conservative 120120 3p21.1 "collagen, type VII, alpha 1 (epidermolysis bullosa, dystrophic, dominant and recessive)" 2978 rs2228561 COL7A1 1294 3 48603018 NM_000094 NP_000085 C/T P595L minus 3550787 885 TSC-CSHL HapMap-CEPH-30-trios 112 0.11 0.11 0.05 232 3 0.03 0.01 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.563 5 moderately conservative 120120 3p21.1 "collagen, type VII, alpha 1 (epidermolysis bullosa, dystrophic, dominant and recessive)" 2979 rs2228561 COL7A1 1294 3 48603018 NM_000094 NP_000085 C/T P595L minus 24326946 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.11 0.05 232 3 0.03 0.01 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.563 5 moderately conservative 120120 3p21.1 "collagen, type VII, alpha 1 (epidermolysis bullosa, dystrophic, dominant and recessive)" 2980 rs2228612 DNMT1 1786 19 10134372 NM_001379 NP_001370 A/G I311V minus 3173310 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 54 0.19 0.19 0 54 1 98 by freq Benign 0.097 13 Tolerant 1 3.16 26 conservative 126375 19p13.2 DNA (cytosine-5-)-methyltransferase 1 2981 rs2228615 ICAM5 7087 19 10264368 NM_003259 NP_003250 A/G A348T plus 3173313 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 44 0.34 0.34 0 44 1 111 "by cluster,freq" moderately conservative 601852 19p13.2 "intercellular adhesion molecule 5, telencephalin" 2982 rs2228637 NRP1 8829 10 33536582 NM_003873 NP_003864 C/G F561L minus 3173336 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 76 0.09 0.09 0 76 1 98 by freq Possibly damaging 1.737 19 Intolerant 0.01 2.82 106 conservative 602069 10p12 neuropilin 1 2983 rs2228638 NRP1 8829 10 33515288 NM_003873 NP_003864 A/G V733I minus 3173338 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 46 0.35 0.25 0.15 76 3 0.18 0.02 62 3 120 "by cluster,freq" Benign 0.106 14 conservative 602069 10p12 neuropilin 1 2984 rs2228638 NRP1 8829 10 33515288 NM_003873 NP_003864 A/G V733I minus 3173338 902 AFFY Caucasian 22 0.09 0.25 0.15 76 3 0.18 0.02 62 3 120 "by cluster,freq" Benign 0.106 14 conservative 602069 10p12 neuropilin 1 2985 rs2228638 NRP1 8829 10 33515288 NM_003873 NP_003864 A/G V733I minus 3173338 904 AFFY CEPH 8 0.13 0.25 0.15 76 3 0.18 0.02 62 3 120 "by cluster,freq" Benign 0.106 14 conservative 602069 10p12 neuropilin 1 2986 rs2228667 CETP 1071 16 55574780 NM_000078 NP_000069 A/G V455M plus 3173371 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 118 0.03 0.03 0 118 1 98 by freq Intolerant 0.04 3.09 9 conservative 118470 16q21 "cholesteryl ester transfer protein, plasma" 2987 rs2228672 SELP 6403 1 166297923 NM_003005 NP_002996 G/T S619A minus 3173377 615 WIAF-CSNP WIAF-CSNP-MITOGPOP5 CORIELL Mixed 134 0.01 0.01 0 134 1 0.04 0 46 1 108 "by cluster,freq" Borderline 1.194 5 Borderline 0.18 3.08 21 moderately conservative 173610 1q22-q25 "selectin P (granule membrane protein 140kDa, antigen CD62)" 2988 rs2228949 ADCY8 114 8 132121524 NM_001115 NP_001106 A/G A80T minus 3175912 619 WICVAR MITOGPOP6 CORIELL Mixed 24 0.17 0.17 0 24 1 98 by freq moderately conservative 103070 8q24 adenylate cyclase 8 (brain) 2989 rs2228965 GJA1 2697 6 121810303 NM_000165 NP_000156 C/T T204M plus 3175929 619 WICVAR MITOGPOP6 CORIELL Mixed 26 0.23 0.23 0 26 1 98 by freq Possibly damaging 1.711 13 Potentially intolerant 0.06 2.8 64 moderately conservative 121014 6q21-q23.2 "gap junction protein, alpha 1, 43kDa (connexin 43)" 2990 rs2228991 REST 5978 4 57637828 NM_005612 NP_005603 A/G V626I plus 3175956 619 WICVAR MITOGPOP6 CORIELL Mixed 48 0.04 0.04 0 96 2 0.19 0.03 1556 3 123 "by cluster,freq" conservative 600571 4q12 RE1-silencing transcription factor 2991 rs2228991 REST 5978 4 57637828 NM_005612 NP_005603 A/G V626I plus 23968309 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 96 2 0.19 0.03 1556 3 123 "by cluster,freq" conservative 600571 4q12 RE1-silencing transcription factor 2992 rs2229032 ATR 545 3 143660842 NM_001184 NP_001175 A/G R2425Q minus 3176005 619 WICVAR MITOGPOP6 CORIELL Mixed 64 0.08 0.08 0 64 1 98 by freq Tolerant 0.32 2.87 35 conservative 601215 3q22-q24 ataxia telangiectasia and Rad3 related 2993 rs2229080 DCC 1630 18 48686600 NM_005215 NP_005206 C/G R201G plus 3176063 619 WICVAR MITOGPOP6 CORIELL Mixed 28 0.36 0.34 0.03 196 3 0.41 0.08 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.477 7 Tolerant 0.47 2.82 26 moderately radical 120470 18q21.3 deleted in colorectal carcinoma 2994 rs2229080 DCC 1630 18 48686600 NM_005215 NP_005206 C/G R201G plus 10904080 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.35 0.34 0.03 196 3 0.41 0.08 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.477 7 Tolerant 0.47 2.82 26 moderately radical 120470 18q21.3 deleted in colorectal carcinoma 2995 rs2229080 DCC 1630 18 48686600 NM_005215 NP_005206 C/G R201G plus 24087358 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.34 0.03 196 3 0.41 0.08 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.477 7 Tolerant 0.47 2.82 26 moderately radical 120470 18q21.3 deleted in colorectal carcinoma 2996 rs2229083 SMAD4 4089 18 46829105 NM_005359 NP_005350 G/T W101G plus 3176066 619 WICVAR MITOGPOP6 CORIELL Mixed 56 0.14 0.14 0 56 1 98 by freq Probably damaging 3.677 20 Intolerant 0 2.83 115 radical 600993 18q21.1 "SMAD, mothers against DPP homolog 4 (Drosophila)" 2997 rs2229086 FER 2241 5 108309808 NM_005246 NP_005237 C/G L439V plus 3176069 619 WICVAR MITOGPOP6 CORIELL Mixed 30 0.13 0.13 0 30 1 98 by freq Borderline 1.21 16 conservative 176942 5q21 fer (fps/fes related) tyrosine kinase (phosphoprotein NCP94) 2998 rs2229109 ABCB1 5243 7 86824460 NM_000927 NP_000918 A/G S400N minus 3176096 619 WICVAR MITOGPOP6 CORIELL Mixed 48 0.04 0.03 0.01 96 2 0.5 0 6 1 123 by freq Benign 0.04 39 Tolerant 0.45 2.88 30 conservative 171050 7q21.1 "ATP-binding cassette, sub-family B (MDR/TAP), member 1" 2999 rs2229109 ABCB1 5243 7 86824460 NM_000927 NP_000918 A/G S400N minus 24421031 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.03 0.01 96 2 0.5 0 6 1 123 by freq Benign 0.04 39 Tolerant 0.45 2.88 30 conservative 171050 7q21.1 "ATP-binding cassette, sub-family B (MDR/TAP), member 1" 3000 rs2229113 IL10RA 3587 11 117374880 NM_001558 NP_001549 A/G R351G plus 3176101 619 WICVAR MITOGPOP6 CORIELL Mixed 48 0.29 0.31 0.03 94 2 0.19 0.01 88 2 123 "by cluster,freq" moderately radical 146933 11q23 "interleukin 10 receptor, alpha" 3001 rs2229113 IL10RA 3587 11 117374880 NM_001558 NP_001549 A/G R351G plus 24565558 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.33 0.31 0.03 94 2 0.19 0.01 88 2 123 "by cluster,freq" moderately radical 146933 11q23 "interleukin 10 receptor, alpha" 3002 rs2229114 IL10RA 3587 11 117375088 NM_001558 NP_001549 C/T S420L plus 3176102 619 WICVAR MITOGPOP6 CORIELL Mixed 50 0.04 0.04 0 50 1 111 "by cluster,freq" moderately radical 146933 11q23 "interleukin 10 receptor, alpha" 3003 rs2229116 RYR3 6263 15 31692702 NM_001036 NP_001027 A/G I731V plus 3176104 619 WICVAR MITOGPOP6 CORIELL Mixed 32 0.31 0.25 0.03 200 3 0.19 0.01 1590 3 123 "HapMap,submitter,freq,cluster" conservative 180903 15q14-q15 ryanodine receptor 3 3004 rs2229116 RYR3 6263 15 31692702 NM_001036 NP_001027 A/G I731V plus 12343691 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.24 0.25 0.03 200 3 0.19 0.01 1590 3 123 "HapMap,submitter,freq,cluster" conservative 180903 15q14-q15 ryanodine receptor 3 3005 rs2229116 RYR3 6263 15 31692702 NM_001036 NP_001027 A/G I731V plus 24612827 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.25 0.03 200 3 0.19 0.01 1590 3 123 "HapMap,submitter,freq,cluster" conservative 180903 15q14-q15 ryanodine receptor 3 3006 rs2229126 ADRA1A 148 8 26683589 NM_000680 NP_000671 A/T E465D minus 3176114 619 WICVAR MITOGPOP6 CORIELL Mixed 42 0.1 0.06 0.06 90 2 0.08 0.08 94 2 123 "by cluster,freq" Benign 0.92 9 conservative 104221 8p21-p11.2 "adrenergic, alpha-1A-, receptor" 3007 rs2229126 ADRA1A 148 8 26683589 NM_000680 NP_000671 A/T E465D minus 24079631 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.06 0.06 90 2 0.08 0.08 94 2 123 "by cluster,freq" Benign 0.92 9 conservative 104221 8p21-p11.2 "adrenergic, alpha-1A-, receptor" 3008 rs2229137 PDHA2 5161 4 97119317 NM_005390 NP_005381 A/C M280L plus 3176126 619 WICVAR MITOGPOP6 CORIELL Mixed 60 0.03 0.03 0 60 1 98 by freq Probably damaging 2.001 31 Tolerant 1 2.75 62 conservative 179061 4q22-q23 pyruvate dehydrogenase (lipoamide) alpha 2 3009 rs2229228 PDE4C 5143 19 18190784 NM_000923 NP_000914 A/G R344Q minus 3176228 619 WICVAR MITOGPOP6 CORIELL Mixed 34 0.38 0.38 0 34 1 98 by freq Benign 0.573 73 Borderline 0.17 2.8 109 conservative 600128 19p13.11 "phosphodiesterase 4C, cAMP-specific (phosphodiesterase E1 dunce homolog, Drosophila)" 3010 rs2229278 LRP1 4035 12 55864491 NM_002332 NP_002323 G/T V2059L plus 3176282 619 WICVAR MITOGPOP6 CORIELL Mixed 56 0.18 0.18 0 56 1 98 by freq Borderline 0.11 2.87 22 conservative 107770 12q13-q14 low density lipoprotein-related protein 1 (alpha-2-macroglobulin receptor) 3011 rs2229304 HOXB3 3213 17 43984592 NM_002146 NP_002137 A/C P82T minus 3176311 619 WICVAR MITOGPOP6 CORIELL Mixed 24 0.38 0.38 0 24 1 119 "by doubleHit,freq,cluster" Benign 0.445 18 conservative 142966 17q21.3 homeo box B3 3012 rs2229309 NFATC4 4776 14 23908923 NM_004554 NP_004545 C/G G160A plus 3176316 619 WICVAR MITOGPOP6 CORIELL Mixed 42 0.36 0.36 0 42 1 121 "by cluster,freq" Tolerant 0.39 3.24 13 moderately conservative 602699 14q11.2 "nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4" 3013 rs2229319 MHC2TA 4261 16 10908823 NM_000246 NP_000237 C/G A658G plus 3176328 619 WICVAR MITOGPOP6 CORIELL Mixed 60 0.03 0.03 0 60 1 98 by freq Borderline 1.219 9 Tolerant 0.29 2.82 51 moderately conservative 600005 16p13 MHC class II transactivator 3014 rs2229331 HRG 3273 3 187878102 NM_000412 NP_000403 A/G G436R plus 3176341 619 WICVAR MITOGPOP6 CORIELL Mixed 32 0.06 0.06 0 32 1 98 by freq moderately radical 142640 3q27 histidine-rich glycoprotein 3015 rs2229357 INHBC 3626 12 56129978 NM_005538 NP_005529 A/G R322Q plus 3176367 619 WICVAR MITOGPOP6 CORIELL Mixed 62 0.11 0.11 0 62 1 111 "by doubleHit,freq,cluster" Potentially intolerant 0.09 2.76 33 conservative 601233 12q13.1 "inhibin, beta C" 3016 rs2229373 ZNF140 7699 12 132293370 NM_003440 NP_003431 C/T A386V plus 3176388 619 WICVAR MITOGPOP6 CORIELL Mixed 26 0.04 0.04 0 26 1 108 "HapMap,cluster" Benign 0.225 7 Intolerant 0.03 2.79 41 moderately conservative 604082 12q24.32-q24.33 zinc finger protein 140 (clone pHZ-39) 3017 rs2229424 FASN 2194 17 77635157 NM_004104 NP_004095 A/G R1694H minus 3176450 619 WICVAR MITOGPOP6 CORIELL Mixed 50 0.04 0.04 0 50 1 98 by freq Possibly damaging 1.687 9 Intolerant 0.04 2.78 17 conservative 600212 17q25 fatty acid synthase 3018 rs2229440 SREBF2 6721 22 40601325 NM_004599 NP_004590 A/G V623M plus 3176466 619 WICVAR MITOGPOP6 CORIELL Mixed 62 0.05 0.05 0 62 1 98 by freq Benign 0.952 8 Potentially intolerant 0.1 2.78 24 conservative 600481 22q13 sterol regulatory element binding transcription factor 2 3019 rs2229531 ACP5 54 19 11548195 NM_001611 NP_001602 A/G V200M minus 3176561 619 WICVAR MITOGPOP6 CORIELL Mixed 46 0.22 0.14 0.07 164 2 0.08 0 1470 1 100 "HapMap,freq,cluster" Benign 0.877 13 Potentially intolerant 0.07 2.76 16 conservative 171640 19p13.3-p13.2 "acid phosphatase 5, tartrate resistant" 3020 rs2229531 ACP5 54 19 11548195 NM_001611 NP_001602 A/G V200M minus 3176561 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.11 0.14 0.07 164 2 0.08 0 1470 1 100 "HapMap,freq,cluster" Benign 0.877 13 Potentially intolerant 0.07 2.76 16 conservative 171640 19p13.3-p13.2 "acid phosphatase 5, tartrate resistant" 3021 rs2229532 ACP5 54 19 11548132 NM_001611 NP_001602 A/G V221I minus 3176562 619 WICVAR MITOGPOP6 CORIELL Mixed 40 0.08 0.08 0 40 1 98 by freq Benign 0.05 13 Tolerant 0.76 2.76 16 conservative 171640 19p13.3-p13.2 "acid phosphatase 5, tartrate resistant" 3022 rs2229571 BARD1 580 2 215470970 NM_000465 NP_000456 C/G R378S minus 3176612 619 WICVAR MITOGPOP6 CORIELL Mixed 24 0.25 0.39 0.14 72 2 0.42 0.04 92 2 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.23 2.79 181 moderately radical 601593 2q34-q35 BRCA1 associated RING domain 1 3023 rs2229571 BARD1 580 2 215470970 NM_000465 NP_000456 C/G R378S minus 24350567 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.39 0.14 72 2 0.42 0.04 92 2 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.23 2.79 181 moderately radical 601593 2q34-q35 BRCA1 associated RING domain 1 3024 rs2229579 CNR2 1269 1 23946468 NM_001841 NP_001832 C/T H316Y minus 3176621 619 WICVAR MITOGPOP6 CORIELL Mixed 56 0.07 0.1 0.04 104 2 0.21 0 48 1 123 "by cluster,freq" Benign 0.225 5 Borderline 0.15 2.97 88 moderately conservative 605051 1p36.11 cannabinoid receptor 2 (macrophage) 3025 rs2229579 CNR2 1269 1 23946468 NM_001841 NP_001832 C/T H316Y minus 24133592 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.1 0.04 104 2 0.21 0 48 1 123 "by cluster,freq" Benign 0.225 5 Borderline 0.15 2.97 88 moderately conservative 605051 1p36.11 cannabinoid receptor 2 (macrophage) 3026 rs2229595 AOC3 8639 17 38257872 NM_003734 NP_003725 A/G R329Q plus 3176637 619 WICVAR MITOGPOP6 CORIELL Mixed 28 0.07 0.07 0 28 1 98 by freq Benign 0.416 15 Tolerant 0.61 2.82 26 conservative 603735 17q21 "amine oxidase, copper containing 3 (vascular adhesion protein 1)" 3027 rs2229617 MC1R 4157 16 88513477 NM_002386 NP_002377 A/G G104S plus 3176660 619 WICVAR MITOGPOP6 CORIELL Mixed 62 0.03 0.03 0 62 1 98 by freq Benign 0.833 210 Intolerant 0.02 2.8 286 moderately conservative 155555 16q24.3 melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor) 3028 rs2229629 HK2 3099 2 75028182 NM_000189 NP_000180 A/G R844K plus 3176672 619 WICVAR MITOGPOP6 CORIELL Mixed 60 0.25 0.02 0.07 1137 3 0.13 0.02 1284 2 123 "by doubleHit,submitter,freq,cluster" Potentially damaging 1.393 38 Tolerant 1 2.82 49 conservative 601125 2p13 hexokinase 2 3029 rs2229629 HK2 3099 2 75028182 NM_000189 NP_000180 A/G R844K plus 12587268 928 IBARROSO ELY UK (Ely region of East Anglia) 921 0.01 0.02 0.07 1137 3 0.13 0.02 1284 2 123 "by doubleHit,submitter,freq,cluster" Potentially damaging 1.393 38 Tolerant 1 2.82 49 conservative 601125 2p13 hexokinase 2 3030 rs2229629 HK2 3099 2 75028182 NM_000189 NP_000180 A/G R844K plus 28459845 549 KYUGEN CP CEPH (78) 156 0.02 0.02 0.07 1137 3 0.13 0.02 1284 2 123 "by doubleHit,submitter,freq,cluster" Potentially damaging 1.393 38 Tolerant 1 2.82 49 conservative 601125 2p13 hexokinase 2 3031 rs2229642 ITPR3 3710 6 33767450 NM_002224 NP_002215 C/G L2436V plus 3176685 619 WICVAR MITOGPOP6 CORIELL Mixed 58 0.05 0.28 0.19 198 3 0.17 0.04 1588 3 123 by freq Benign 0.851 25 conservative 147267 6p21 "inositol 1,4,5-triphosphate receptor, type 3" 3032 rs2229642 ITPR3 3710 6 33767450 NM_002224 NP_002215 C/G L2436V plus 12838343 1303 SEQUENOM CEPH CEPH (92) 92 0.33 0.28 0.19 198 3 0.17 0.04 1588 3 123 by freq Benign 0.851 25 conservative 147267 6p21 "inositol 1,4,5-triphosphate receptor, type 3" 3033 rs2229642 ITPR3 3710 6 33767450 NM_002224 NP_002215 C/G L2436V plus 24364141 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.28 0.19 198 3 0.17 0.04 1588 3 123 by freq Benign 0.851 25 conservative 147267 6p21 "inositol 1,4,5-triphosphate receptor, type 3" 3034 rs2229659 SORD 6652 15 43151909 NM_003104 NP_003095 A/C V297L minus 3176705 619 WICVAR MITOGPOP6 CORIELL Mixed 34 0.06 0.06 0 34 1 98 by freq Potentially damaging 1.301 25 Borderline 0.19 2.76 54 conservative 182500 15q15.3 sorbitol dehydrogenase 3035 rs2229692 PLCB2 5330 15 38368835 NM_004573 NP_004564 A/G E1091G minus 3176738 619 WICVAR MITOGPOP6 CORIELL Mixed 54 0.13 0.13 0 54 1 98 "by doubleHit,freq" Tolerant 0.5 2.79 27 moderately conservative 604114 15q15 "phospholipase C, beta 2" 3036 rs2229742 NRIP1 8204 21 15261043 NM_003489 NP_003480 C/G R448G minus 3176794 619 WICVAR MITOGPOP6 CORIELL Mixed 24 0.13 0.11 0.01 190 3 0.02 0 46 1 123 "HapMap,freq" moderately radical 602490 21q11.2 nuclear receptor interacting protein 1 3037 rs2229742 NRIP1 8204 21 15261043 NM_003489 NP_003480 C/G R448G minus 3176794 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.1 0.11 0.01 190 3 0.02 0 46 1 123 "HapMap,freq" moderately radical 602490 21q11.2 nuclear receptor interacting protein 1 3038 rs2229742 NRIP1 8204 21 15261043 NM_003489 NP_003480 C/G R448G minus 24720030 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.11 0.11 0.01 190 3 0.02 0 46 1 123 "HapMap,freq" moderately radical 602490 21q11.2 nuclear receptor interacting protein 1 3039 rs2229774 RARG 5916 12 51891812 NM_000966 NP_000957 C/T S427L minus 3176826 619 WICVAR MITOGPOP6 CORIELL Mixed 48 0.02 0.03 0.01 168 2 120 "HapMap,submitter,freq" Possibly damaging 1.67 43 moderately radical 180190 12q13 "retinoic acid receptor, gamma" 3040 rs2229774 RARG 5916 12 51891812 NM_000966 NP_000957 C/T S427L minus 3176826 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.04 0.03 0.01 168 2 120 "HapMap,submitter,freq" Possibly damaging 1.67 43 moderately radical 180190 12q13 "retinoic acid receptor, gamma" 3041 rs2229839 ACE 1636 17 58912765 NM_000789 NP_000780 C/T P351L plus 3176897 619 WICVAR MITOGPOP6 CORIELL Mixed 48 0.06 0.06 0 48 1 98 by freq Probably damaging 2.55 15 Intolerant 0 2.79 39 moderately conservative 106180 17q23 angiotensin I converting enzyme (peptidyl-dipeptidase A) 1 3042 rs2230048 IGF2R 3482 6 160459759 NM_000876 NP_000867 A/T T1395S plus 3177139 619 WICVAR MITOGPOP6 CORIELL Mixed 64 0.03 0.03 0 64 1 98 by freq Potentially damaging 1.423 17 Tolerant 0.46 2.96 32 moderately conservative 147280 6q26 insulin-like growth factor 2 receptor 3043 rs2230055 IFNW1 3467 9 21131287 NM_002177 NP_002168 A/C R95S minus 3177147 619 WICVAR MITOGPOP6 CORIELL Mixed 28 0.07 0.07 0 28 1 0.1 0 1498 1 116 "HapMap,freq,cluster" Benign 0.812 117 Tolerant 0.71 2.86 175 moderately radical 147553 9p22 "interferon, omega 1" 3044 rs2230086 TBL3 10607 16 1965603 NM_006453 NP_006444 A/G Q293R plus 3177184 619 WICVAR MITOGPOP6 CORIELL Mixed 36 0.06 0.06 0 36 1 123 by freq Potentially damaging 1.362 8 Tolerant 0.48 2.88 16 conservative 605915 16p13.3 transducin (beta)-like 3 3045 rs2230143 VIL2 7430 6 159158818 NM_003379 NP_003370 C/G A494P minus 3177248 619 WICVAR MITOGPOP6 CORIELL Mixed 52 0.06 0.06 0 52 1 0.09 0 46 1 123 "by cluster,freq" Borderline 1.23 38 Borderline 0.16 2.91 46 conservative 123900 6q25.2-q26 villin 2 (ezrin) 3046 rs2230179 ACADVL 37 17 7064076 NM_000018 NP_000009 C/T L17F plus 3177289 619 WICVAR MITOGPOP6 CORIELL Mixed 22 0.09 0.09 0 22 1 123 by freq conservative 201475 17p13-p11 "acyl-Coenzyme A dehydrogenase, very long chain" 3047 rs2230180 ACADVL 37 17 7068431 NM_000018 NP_000009 A/G E534K plus 3177290 619 WICVAR MITOGPOP6 CORIELL Mixed 54 0.04 0.04 0 54 1 98 by freq Benign 0.035 9 Tolerant 1 2.81 31 moderately conservative 201475 17p13-p11 "acyl-Coenzyme A dehydrogenase, very long chain" 3048 rs2230190 PDE4A 5141 19 10439058 NM_006202 NP_006193 C/T H569Y plus 3177302 619 WICVAR MITOGPOP6 CORIELL Mixed 56 0.02 0.02 0 56 1 98 HapMap Possibly damaging 1.885 12 moderately conservative 600126 19p13.2 "phosphodiesterase 4A, cAMP-specific (phosphodiesterase E2 dunce homolog, Drosophila)" 3049 rs2230199 C3 718 19 6669387 NM_000064 NP_000055 C/G R102G minus 3177312 619 WICVAR MITOGPOP6 CORIELL Mixed 40 0.15 0.15 0 40 1 98 by freq Benign 0.325 6 moderately radical 120700 19p13.3-p13.2 complement component 3 3050 rs2230210 C3 718 19 6629030 NM_000064 NP_000055 A/C S1619R minus 3177323 619 WICVAR MITOGPOP6 CORIELL Mixed 46 0.04 0.04 0 46 1 98 by freq Possibly damaging 1.773 9 Intolerant 0.04 2.83 19 moderately radical 120700 19p13.3-p13.2 complement component 3 3051 rs2230229 TNFRSF10A 8797 8 23105237 NM_003844 NP_003835 A/G R441K minus 3177342 619 WICVAR MITOGPOP6 CORIELL Mixed 58 0.03 0.03 0 58 1 121 "by cluster,freq" conservative 603611 8p21 "tumor necrosis factor receptor superfamily, member 10a" 3052 rs2230239 MCM3 4172 6 52237452 NM_002388 NP_002379 C/T R774W minus 3177353 619 WICVAR MITOGPOP6 CORIELL Mixed 56 0.02 0.01 0.01 226 2 100 "by cluster,freq" Possibly damaging 1.735 15 Intolerant 0.01 2.86 28 moderately radical 602693 6p12 MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) 3053 rs2230239 MCM3 4172 6 52237452 NM_002388 NP_002379 C/T R774W minus 3255150 506 NCBI NIHPDR NIHPDR 170 0.01 0.01 0.01 226 2 100 "by cluster,freq" Possibly damaging 1.735 15 Intolerant 0.01 2.86 28 moderately radical 602693 6p12 MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) 3054 rs2230240 MCM3 4172 6 52237443 NM_002388 NP_002379 A/G E777K minus 3177354 619 WICVAR MITOGPOP6 CORIELL Mixed 48 0.1 0.13 0.09 358 4 0.04 0.04 94 2 123 "by cluster,freq" Borderline 1.196 15 Tolerant 0.66 2.86 28 moderately conservative 602693 6p12 MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) 3055 rs2230240 MCM3 4172 6 52237443 NM_002388 NP_002379 A/G E777K minus 3177354 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.13 0.09 358 4 0.04 0.04 94 2 123 "by cluster,freq" Borderline 1.196 15 Tolerant 0.66 2.86 28 moderately conservative 602693 6p12 MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) 3056 rs2230240 MCM3 4172 6 52237443 NM_002388 NP_002379 A/G E777K minus 3255148 506 NCBI NIHPDR NIHPDR 170 0.17 0.13 0.09 358 4 0.04 0.04 94 2 123 "by cluster,freq" Borderline 1.196 15 Tolerant 0.66 2.86 28 moderately conservative 602693 6p12 MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) 3057 rs2230240 MCM3 4172 6 52237443 NM_002388 NP_002379 A/G E777K minus 24374408 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.13 0.09 358 4 0.04 0.04 94 2 123 "by cluster,freq" Borderline 1.196 15 Tolerant 0.66 2.86 28 moderately conservative 602693 6p12 MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) 3058 rs2230241 POLD1 5424 19 55596886 NM_002691 NP_002682 A/G R119H plus 3177355 619 WICVAR MITOGPOP6 CORIELL Mixed 34 0.26 0.26 0 34 1 98 "by doubleHit,freq" Benign 0.534 22 Tolerant 0.55 2.79 29 conservative 174761 19q13.3 "polymerase (DNA directed), delta 1, catalytic subunit 125kDa" 3059 rs2230243 POLD1 5424 19 55598191 NM_002691 NP_002682 C/T P347L plus 3177357 619 WICVAR MITOGPOP6 CORIELL Mixed 60 0.07 0.07 0 60 1 98 by freq Benign 0.728 30 Tolerant 0.23 2.78 31 moderately conservative 174761 19q13.3 "polymerase (DNA directed), delta 1, catalytic subunit 125kDa" 3060 rs2230294 GPI 2821 19 39576672 NM_000175 NP_000166 A/G R308H plus 3177413 619 WICVAR MITOGPOP6 CORIELL Mixed 36 0.06 0.06 0 36 1 98 by freq Benign 0.679 124 Tolerant 0.55 2.76 229 conservative 172400 19q13.1 glucose phosphate isomerase 3061 rs2230301 EPRS 2058 1 216586020 NM_004446 NP_004437 A/C D236E minus 3177420 619 WICVAR MITOGPOP6 CORIELL Mixed 58 0.34 0.34 0 58 1 121 "by cluster,freq" Benign 0.114 8 conservative 138295 1q41-q42 glutamyl-prolyl-tRNA synthetase 3062 rs2230339 GPR68 8111 14 90770990 NM_003485 NP_003476 A/G R63Q minus 3177467 619 WICVAR MITOGPOP6 CORIELL Mixed 42 0.05 0.05 0 42 1 98 "HapMap,freq" Intolerant 0.03 2.77 27 conservative 601404 14q31 G protein-coupled receptor 68 3063 rs2230399 ICAM3 3385 19 10305603 NM_002162 NP_002153 C/G S525T minus 3177529 619 WICVAR MITOGPOP6 CORIELL Mixed 50 0.26 0.17 0.13 98 2 0.3 0 46 1 123 "by cluster,freq" Tolerant 0.24 2.86 16 moderately conservative 146631 19p13.3-p13.2 intercellular adhesion molecule 3 3064 rs2230399 ICAM3 3385 19 10305603 NM_002162 NP_002153 C/G S525T minus 23756769 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.17 0.13 98 2 0.3 0 46 1 123 "by cluster,freq" Tolerant 0.24 2.86 16 moderately conservative 146631 19p13.3-p13.2 intercellular adhesion molecule 3 3065 rs2230433 ITGAL 3683 16 30425542 NM_002209 NP_002200 C/G R791T plus 3177564 619 WICVAR MITOGPOP6 CORIELL Mixed 18 0.06 0.19 0.09 114 3 0.23 0.19 94 2 123 "by submitter,freq,cluster" Possibly damaging 1.532 8 Tolerant 0.45 2.85 19 moderately conservative 153370 16p11.2 "integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)" 3066 rs2230433 ITGAL 3683 16 30425542 NM_002209 NP_002200 C/G R791T plus 4318997 650 MRG IBD-24P "German (24 European Caucasians with inflammatory bowel disease, 15 crohns disease, 9 ulcerative colitis)" 48 0.27 0.19 0.09 114 3 0.23 0.19 94 2 123 "by submitter,freq,cluster" Possibly damaging 1.532 8 Tolerant 0.45 2.85 19 moderately conservative 153370 16p11.2 "integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)" 3067 rs2230433 ITGAL 3683 16 30425542 NM_002209 NP_002200 C/G R791T plus 23385867 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.19 0.09 114 3 0.23 0.19 94 2 123 "by submitter,freq,cluster" Possibly damaging 1.532 8 Tolerant 0.45 2.85 19 moderately conservative 153370 16p11.2 "integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)" 3068 rs2230462 PIK3CB 5291 3 139892560 NM_006219 NP_006210 G/T Q672H minus 3177595 619 WICVAR MITOGPOP6 CORIELL Mixed 54 0.04 0.04 0 54 1 98 by freq Benign 0.882 11 Tolerant 1 2.81 29 conservative 602925 3q22.3 "phosphoinositide-3-kinase, catalytic, beta polypeptide" 3069 rs2230512 TTK 7272 6 80806273 NM_003318 NP_003309 A/G D758N plus 3177647 619 WICVAR MITOGPOP6 CORIELL Mixed 64 0.03 0.03 0 64 1 98 by freq Benign 0.031 7 Tolerant 0.49 2.79 349 conservative 604092 6q13-q21 TTK protein kinase 3070 rs2230516 MERTK 10461 2 112502265 NM_006343 NP_006334 C/T R865W plus 3177652 619 WICVAR MITOGPOP6 CORIELL Mixed 48 0.04 0.03 0.01 168 2 98 "HapMap,freq" Intolerant 0.02 3.09 26 moderately radical 604705 2q14.1 c-mer proto-oncogene tyrosine kinase 3071 rs2230516 MERTK 10461 2 112502265 NM_006343 NP_006334 C/T R865W plus 3177652 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.02 0.03 0.01 168 2 98 "HapMap,freq" Intolerant 0.02 3.09 26 moderately radical 604705 2q14.1 c-mer proto-oncogene tyrosine kinase 3072 rs2230517 MERTK 10461 2 112502280 NM_006343 NP_006334 A/G V870I plus 3177653 619 WICVAR MITOGPOP6 CORIELL Mixed 46 0.13 0.08 0.06 94 2 0.11 0 46 1 123 "by cluster,freq" Tolerant 0.55 2.75 39 conservative 604705 2q14.1 c-mer proto-oncogene tyrosine kinase 3073 rs2230517 MERTK 10461 2 112502280 NM_006343 NP_006334 A/G V870I plus 23254961 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.08 0.06 94 2 0.11 0 46 1 123 "by cluster,freq" Tolerant 0.55 2.75 39 conservative 604705 2q14.1 c-mer proto-oncogene tyrosine kinase 3074 rs2230523 LY64 4064 5 66515139 NM_005582 NP_005573 A/G T430A minus 3177659 619 WICVAR MITOGPOP6 CORIELL Mixed 64 0.02 0.02 0 64 1 0.11 0.05 154 4 123 "by submitter,freq,cluster" Intolerant 0.02 2.82 26 moderately conservative 602226 5q12 "lymphocyte antigen 64 homolog, radioprotective 105kDa (mouse)" 3075 rs2230524 LY64 4064 5 66514485 NM_005582 NP_005573 C/T F648L minus 3177660 619 WICVAR MITOGPOP6 CORIELL Mixed 48 0.02 0.07 0.11 76 3 0.15 0.06 196 5 123 "by submitter,freq,cluster" Tolerant 0.98 2.86 19 conservative 602226 5q12 "lymphocyte antigen 64 homolog, radioprotective 105kDa (mouse)" 3076 rs2230524 LY64 4064 5 66514485 NM_005582 NP_005573 C/T F648L minus 3177660 902 AFFY Caucasian 18 0.06 0.07 0.11 76 3 0.15 0.06 196 5 123 "by submitter,freq,cluster" Tolerant 0.98 2.86 19 conservative 602226 5q12 "lymphocyte antigen 64 homolog, radioprotective 105kDa (mouse)" 3077 rs2230524 LY64 4064 5 66514485 NM_005582 NP_005573 C/T F648L minus 3177660 904 AFFY CEPH 10 0.3 0.07 0.11 76 3 0.15 0.06 196 5 123 "by submitter,freq,cluster" Tolerant 0.98 2.86 19 conservative 602226 5q12 "lymphocyte antigen 64 homolog, radioprotective 105kDa (mouse)" 3078 rs2230590 MST1R 4486 3 49911106 NM_002447 NP_002438 A/G Q523R minus 3177736 619 WICVAR MITOGPOP6 CORIELL Mixed 16 0.5 0.46 0.02 136 2 116 "HapMap,doubleHit,freq,cluster" conservative 600168 3p21.3 macrophage stimulating 1 receptor (c-met-related tyrosine kinase) 3079 rs2230590 MST1R 4486 3 49911106 NM_002447 NP_002438 A/G Q523R minus 4074624 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.45 0.46 0.02 136 2 116 "HapMap,doubleHit,freq,cluster" conservative 600168 3p21.3 macrophage stimulating 1 receptor (c-met-related tyrosine kinase) 3080 rs2230592 MST1R 4486 3 49911612 NM_002447 NP_002438 A/G N440S minus 3177738 619 WICVAR MITOGPOP6 CORIELL Mixed 54 0.04 0.04 0 54 1 98 by freq Tolerant 0.56 2.76 17 conservative 600168 3p21.3 macrophage stimulating 1 receptor (c-met-related tyrosine kinase) 3081 rs2230593 MST1R 4486 3 49915082 NM_002447 NP_002438 A/G R322Q minus 3177739 619 WICVAR MITOGPOP6 CORIELL Mixed 50 0.04 0.04 0 50 1 98 by freq conservative 600168 3p21.3 macrophage stimulating 1 receptor (c-met-related tyrosine kinase) 3082 rs2230674 ATF1 466 12 49494389 NM_005171 NP_005162 C/G P191A plus 3177832 619 WICVAR MITOGPOP6 CORIELL Mixed 40 0.03 0.04 0.01 86 2 0.02 0 46 1 123 "by submitter,freq" Probably damaging 2.274 39 Borderline 0.18 3.09 66 conservative 123803 12q13 activating transcription factor 1 3083 rs2230674 ATF1 466 12 49494389 NM_005171 NP_005162 C/G P191A plus 24421603 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.04 0.04 0.01 86 2 0.02 0 46 1 123 "by submitter,freq" Probably damaging 2.274 39 Borderline 0.18 3.09 66 conservative 123803 12q13 activating transcription factor 1 3084 rs2230681 PSMD9 5715 12 120789532 NM_002813 NP_002804 C/T V17A plus 3177839 619 WICVAR MITOGPOP6 CORIELL Mixed 32 0.19 0.14 0.06 80 2 0.19 0.08 94 2 123 "by cluster,freq" Benign 0.073 5 moderately conservative 603146 12q24.31-q24.32 "proteasome (prosome, macropain) 26S subunit, non-ATPase, 9" 3085 rs2230681 PSMD9 5715 12 120789532 NM_002813 NP_002804 C/T V17A plus 23936226 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.14 0.06 80 2 0.19 0.08 94 2 123 "by cluster,freq" Benign 0.073 5 moderately conservative 603146 12q24.31-q24.32 "proteasome (prosome, macropain) 26S subunit, non-ATPase, 9" 3086 rs2230767 SYNJ1 8867 21 32925258 NM_003895 NP_003886 C/T P1547L minus 3177942 619 WICVAR MITOGPOP6 CORIELL Mixed 62 0.03 0.03 0 62 1 98 by freq Possibly damaging 1.562 7 moderately conservative 604297 21q22.2 synaptojanin 1 3087 rs2230848 F13A1 2162 6 6167325 NM_000129 NP_000120 A/T M351K minus 3178028 619 WICVAR MITOGPOP6 CORIELL Mixed 48 0.15 0.15 0 48 1 98 by freq Intolerant 0.01 2.78 18 moderately conservative 134570 6p25.3-p24.3 "coagulation factor XIII, A1 polypeptide" 3088 rs2230849 F2R 2149 5 76064365 NM_001992 NP_001983 A/T Y187N plus 3178029 619 WICVAR MITOGPOP6 CORIELL Mixed 42 0.07 0.07 0 42 1 98 by freq Probably damaging 2.616 8 Intolerant 0 2.79 25 moderately radical 187930 5q13 coagulation factor II (thrombin) receptor 3089 rs2230853 IFNA10 3446 9 21196972 NM_002171 NP_002162 C/G G42A minus 3178035 619 WICVAR MITOGPOP6 CORIELL Mixed 18 0.39 0.39 0 18 1 98 by freq Benign 0.227 181 Tolerant 0.87 2.85 167 moderately conservative 147577 9p22 "interferon, alpha 10" 3090 rs2230912 P2RX7 5027 12 120084916 NM_002562 NP_002553 A/G Q460R plus 3178096 619 WICVAR MITOGPOP6 CORIELL Mixed 50 0.16 0.19 0.04 218 3 0.02 0 46 1 123 "HapMap,submitter,freq" Benign 0.9 5 conservative 602566 12q24 "purinergic receptor P2X, ligand-gated ion channel, 7" 3091 rs2230912 P2RX7 5027 12 120084916 NM_002562 NP_002553 A/G Q460R plus 3178096 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.22 0.19 0.04 218 3 0.02 0 46 1 123 "HapMap,submitter,freq" Benign 0.9 5 conservative 602566 12q24 "purinergic receptor P2X, ligand-gated ion channel, 7" 3092 rs2230912 P2RX7 5027 12 120084916 NM_002562 NP_002553 A/G Q460R plus 24357605 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.19 0.04 218 3 0.02 0 46 1 123 "HapMap,submitter,freq" Benign 0.9 5 conservative 602566 12q24 "purinergic receptor P2X, ligand-gated ion channel, 7" 3093 rs2231142 ABCG2 9429 4 89409502 NM_004827 NP_004818 A/C Q141K minus 23885505 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.05 0.05 0 44 1 0.24 0.08 1976 4 123 "by cluster,freq" Potentially damaging 1.367 12 Tolerant 0.91 2.82 21 moderately conservative 603756 4q22 "ATP-binding cassette, sub-family G (WHITE), member 2" 3094 rs2231909 ATF7IP 55729 12 14469159 NM_018179 NP_060649 A/T N348I plus 24338980 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.38 0 48 1 0.2 0.16 94 2 123 "by doubleHit,submitter,freq" Borderline 0.17 2.93 15 moderately radical 12p13.2 activating transcription factor 7 interacting protein 3095 rs2232016 HRMT1L6 55170 1 107311960 NM_018137 NP_060607 C/T A135V plus 23850099 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 0.19 0.04 1554 3 123 "by submitter,freq,cluster" Potentially damaging 1.413 9 Borderline 0.19 2.83 55 moderately conservative 608274 1p13.3 protein arginine N-methyltransferase 6 3096 rs2232176 PLA2G3 50487 22 29860687 NM_015715 NP_056530 G/T S70A minus 23790588 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.17 0 48 1 0.14 0.15 90 2 123 "by doubleHit,freq,cluster" moderately conservative 22q11.2-q13.2 "phospholipase A2, group III" 3097 rs2232183 PLA2G3 50487 22 29857514 NM_015715 NP_056530 A/G R378Q minus 24703511 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.4 0 48 1 0.09 0 46 1 123 by freq conservative 22q11.2-q13.2 "phospholipase A2, group III" 3098 rs2232430 ZNF305 9753 6 28467165 NM_014724 NP_055539 A/G R294K minus 23916623 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.19 0 48 1 0.18 0.16 94 2 123 "by cluster,freq" Tolerant 0.31 2.77 61 conservative 6p22.2-p21.3 zinc finger protein 305 3099 rs2232434 ZNF305 9753 6 28466872 NM_014724 NP_055539 A/G N392D minus 24336040 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 0.04 0 94 2 123 by freq Intolerant 0.04 2.72 63 conservative 6p22.2-p21.3 zinc finger protein 305 3100 rs2232580 LBP 3929 20 36408359 NM_004139 NP_004130 C/T P9L plus 16215277 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.1 0.1 0 40 1 120 "by cluster,freq" moderately conservative 151990 20q11.23-q12 lipopolysaccharide binding protein 3101 rs2232607 LBP 3929 20 36426747 NM_004139 NP_004130 A/G D283G plus 7988345 848 IIPGA-WEISS-MARTINEZ E-1 CEPH 6 0.17 0.17 0 12 2 120 "by submitter,freq,cluster" Possibly damaging 1.886 5 Borderline 0.11 2.89 17 moderately conservative 151990 20q11.23-q12 lipopolysaccharide binding protein 3102 rs2232607 LBP 3929 20 36426747 NM_004139 NP_004130 A/G D283G plus 16215360 848 IIPGA-WEISS-MARTINEZ E-1 CEPH 6 0.17 0.17 0 12 2 120 "by submitter,freq,cluster" Possibly damaging 1.886 5 Borderline 0.11 2.89 17 moderately conservative 151990 20q11.23-q12 lipopolysaccharide binding protein 3103 rs2232613 LBP 3929 20 36431069 NM_004139 NP_004130 C/T P333L plus 7988355 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 36 0.14 0.12 0.03 76 2 0.06 0 96 2 120 "by cluster,freq" Probably damaging 2.55 5 Intolerant 0 2.89 17 moderately conservative 151990 20q11.23-q12 lipopolysaccharide binding protein 3104 rs2232613 LBP 3929 20 36431069 NM_004139 NP_004130 C/T P333L plus 16215376 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.1 0.12 0.03 76 2 0.06 0 96 2 120 "by cluster,freq" Probably damaging 2.55 5 Intolerant 0 2.89 17 moderately conservative 151990 20q11.23-q12 lipopolysaccharide binding protein 3105 rs2232618 LBP 3929 20 36435175 NM_004139 NP_004130 C/T F436L plus 7988369 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.03 0.05 0.02 198 3 0.23 0 96 2 120 "HapMap,doubleHit,freq,cluster" Borderline 1.242 5 Tolerant 0.57 2.89 17 conservative 151990 20q11.23-q12 lipopolysaccharide binding protein 3106 rs2232618 LBP 3929 20 36435175 NM_004139 NP_004130 C/T F436L plus 8387959 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.07 0.05 0.02 198 3 0.23 0 96 2 120 "HapMap,doubleHit,freq,cluster" Borderline 1.242 5 Tolerant 0.57 2.89 17 conservative 151990 20q11.23-q12 lipopolysaccharide binding protein 3107 rs2232618 LBP 3929 20 36435175 NM_004139 NP_004130 C/T F436L plus 16215395 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.03 0.05 0.02 198 3 0.23 0 96 2 120 "HapMap,doubleHit,freq,cluster" Borderline 1.242 5 Tolerant 0.57 2.89 17 conservative 151990 20q11.23-q12 lipopolysaccharide binding protein 3108 rs2232619 LBP 3929 20 36436003 NM_004139 NP_004130 A/G A445T plus 7988371 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.03 0.03 0 80 2 0.09 0.01 86 2 120 "by cluster,freq" Borderline 1.227 5 Tolerant 0.34 2.89 17 moderately conservative 151990 20q11.23-q12 lipopolysaccharide binding protein 3109 rs2232619 LBP 3929 20 36436003 NM_004139 NP_004130 A/G A445T plus 16215404 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.03 0.03 0 80 2 0.09 0.01 86 2 120 "by cluster,freq" Borderline 1.227 5 Tolerant 0.34 2.89 17 moderately conservative 151990 20q11.23-q12 lipopolysaccharide binding protein 3110 rs2232950 SCGB1D2 10647 11 61767439 NM_006551 NP_006542 C/T P53L plus 2075790 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.34 0.37 0.05 260 3 0.21 0.04 1566 3 123 "HapMap,doubleHit,freq,cluster" Tolerant 0.25 2.98 14 moderately conservative 11q13 "secretoglobin, family 1D, member 2" 3111 rs2232950 SCGB1D2 10647 11 61767439 NM_006551 NP_006542 C/T P53L plus 2075790 1303 SEQUENOM CEPH CEPH (92) 92 0.36 0.37 0.05 260 3 0.21 0.04 1566 3 123 "HapMap,doubleHit,freq,cluster" Tolerant 0.25 2.98 14 moderately conservative 11q13 "secretoglobin, family 1D, member 2" 3112 rs2232950 SCGB1D2 10647 11 61767439 NM_006551 NP_006542 C/T P53L plus 24668733 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.37 0.05 260 3 0.21 0.04 1566 3 123 "HapMap,doubleHit,freq,cluster" Tolerant 0.25 2.98 14 moderately conservative 11q13 "secretoglobin, family 1D, member 2" 3113 rs2233369 ABI3 51225 17 44648905 NM_016428 NP_057512 A/G R44Q plus 3180791 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.07 0.07 0.01 164 2 0.09 0.01 1524 2 123 "HapMap,submitter,freq,cluster" Benign 0.084 7 Tolerant 0.55 2.93 23 conservative 606363 17q21.3 "ABI gene family, member 3" 3114 rs2233369 ABI3 51225 17 44648905 NM_016428 NP_057512 A/G R44Q plus 24112458 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.07 0.01 164 2 0.09 0.01 1524 2 123 "HapMap,submitter,freq,cluster" Benign 0.084 7 Tolerant 0.55 2.93 23 conservative 606363 17q21.3 "ABI gene family, member 3" 3115 rs2233531 NUBP1 4682 16 10745414 NM_002484 NP_002475 C/G P39A plus 3562799 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.1 0.1 0 120 1 0.09 0 1476 1 100 "HapMap,freq,cluster" Borderline 0.17 2.87 34 conservative 600280 16p13.2 "nucleotide binding protein 1 (MinD homolog, E. coli)" 3116 rs2233919 SMUG1 23583 12 52863985 NM_014311 NP_055126 C/T Q3X minus 4318944 506 NCBI NIHPDR NIHPDR 574 0.01 0.01 0 740 2 103 "by cluster,freq" Probably damaging Intolerant radical 607753 12q13.11-q13.3 single-strand selective monofunctional uracil DNA glycosylase 3117 rs2233919 SMUG1 23583 12 52863985 NM_014311 NP_055126 C/T Q3X minus 4384657 693 EGP_SNPS PDR90 NIHPDR 166 0.01 0.01 0 740 2 103 "by cluster,freq" Probably damaging Intolerant radical 607753 12q13.11-q13.3 single-strand selective monofunctional uracil DNA glycosylase 3118 rs2233920 SMUG1 23583 12 52863948 NM_014311 NP_055126 G/T G15V minus 4384658 693 EGP_SNPS PDR90 NIHPDR 164 0.02 0.02 0 164 1 103 "by cluster,freq" Possibly damaging 1.542 5 moderately radical 607753 12q13.11-q13.3 single-strand selective monofunctional uracil DNA glycosylase 3119 rs2234163 TNFRSF14 8764 1 2525414 NM_003820 NP_003811 A/G A117T minus 16359065 693 EGP_SNPS PDR90 NIHPDR 162 0.02 0.02 0 162 1 120 "by cluster,freq" Tolerant 1 2.77 52 moderately conservative 602746 1p36.3-p36.2 "tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)" 3120 rs2234167 TNFRSF14 8764 1 2522390 NM_003820 NP_003811 A/G V241I minus 16359082 693 EGP_SNPS PDR90 NIHPDR 176 0.14 0.12 0.03 296 2 0.03 0 1492 1 120 "HapMap,freq,cluster" Tolerant 0.47 3.06 9 conservative 602746 1p36.3-p36.2 "tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)" 3121 rs2234167 TNFRSF14 8764 1 2522390 NM_003820 NP_003811 A/G V241I minus 16359082 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.1 0.12 0.03 296 2 0.03 0 1492 1 120 "HapMap,freq,cluster" Tolerant 0.47 3.06 9 conservative 602746 1p36.3-p36.2 "tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)" 3122 rs2234237 TREM1 54210 6 41358444 NM_018643 NP_061113 A/T T25S minus 23952381 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.23 0.04 90 2 123 "by submitter,freq,cluster" Tolerant 0.74 3.04 10 moderately conservative 605085 6p21.1 triggering receptor expressed on myeloid cells 1 3123 rs2234500 VAX2 25806 2 71071877 NM_012476 NP_036608 C/G P254R plus 23876044 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 0.17 0.04 1020 3 123 "by cluster,freq" Probably damaging 2.325 5 Intolerant 0.05 3.17 15 moderately radical 604295 2p13 ventral anterior homeobox 2 3124 rs2234671 IL8RA 3577 2 218854614 NM_000634 NP_000625 C/G S276T minus 4325280 649 FHCRC POPU1 USA (20) 40 0.1 0.12 0.03 98 2 0.11 0.05 322 4 120 "by submitter,freq,cluster" Possibly damaging 1.6 22 Tolerant 1 2.85 36 moderately conservative 146929 2q35 "interleukin 8 receptor, alpha" 3125 rs2234671 IL8RA 3577 2 218854614 NM_000634 NP_000625 C/G S276T minus 12675495 775 SNP500CANCER CAUC1 Caucasian (31) 58 0.14 0.12 0.03 98 2 0.11 0.05 322 4 120 "by submitter,freq,cluster" Possibly damaging 1.6 22 Tolerant 1 2.85 36 moderately conservative 146929 2q35 "interleukin 8 receptor, alpha" 3126 rs2234922 EPHX1 2052 1 222333141 NM_000120 NP_000111 A/G H139R plus 5586491 775 SNP500CANCER CAUC1 Caucasian (31) 56 0.21 0.21 0 56 1 0.17 0.03 1832 5 120 "by cluster,freq" Benign 0.232 14 Tolerant 0.79 2.81 24 conservative 132810 1q42.1 "epoxide hydrolase 1, microsomal (xenobiotic)" 3127 rs2234942 CCNH 902 5 86744285 NM_001239 NP_001230 G/T R28L minus 2667788 506 NCBI NIHPDR NIHPDR 186 0.01 0.01 0 360 2 110 "by cluster,freq" Borderline 0.17 2.85 13 moderately radical 601953 5q13.3-q14 cyclin H 3128 rs2234942 CCNH 902 5 86744285 NM_001239 NP_001230 G/T R28L minus 4329079 693 EGP_SNPS PDR90 NIHPDR 174 0.01 0.01 0 360 2 110 "by cluster,freq" Borderline 0.17 2.85 13 moderately radical 601953 5q13.3-q14 cyclin H 3129 rs2234949 MPG 4350 16 75771 NM_002434 NP_002425 G/T A298S plus 4388617 693 EGP_SNPS PDR90 NIHPDR 180 0.01 0.01 0 180 1 106 "by cluster,freq" Benign 0.675 6 moderately conservative 156565 16p13.3 N-methylpurine-DNA glycosylase 3130 rs2234951 GSTA2 2939 6 52725697 NM_000846 NP_000837 C/T P110S minus 869780 506 NCBI NIHPDR NIHPDR 92 0.02 0.02 0 92 1 100 "by cluster,freq" Probably damaging 2.257 63 Intolerant 0.05 2.84 66 moderately conservative 138360 6p12.1 glutathione S-transferase A2 3131 rs2234997 ATM 472 11 107611653 NM_000051 NP_000042 A/T D126E plus 4479878 506 NCBI NIHPDR NIHPDR 164 0.07 0.07 0.01 328 2 0.08 0.05 534 5 123 "HapMap,freq,cluster" Borderline 1.231 5 conservative 607585 11q22-q23 "ataxia telangiectasia mutated (includes complementation groups A, C and D)" 3132 rs2234997 ATM 472 11 107611653 NM_000051 NP_000042 A/T D126E plus 6904800 693 EGP_SNPS PDR90 NIHPDR 164 0.06 0.07 0.01 328 2 0.08 0.05 534 5 123 "HapMap,freq,cluster" Borderline 1.231 5 conservative 607585 11q22-q23 "ataxia telangiectasia mutated (includes complementation groups A, C and D)" 3133 rs2235000 ATM 472 11 107626943 NM_000051 NP_000042 A/G G514D plus 4479886 506 NCBI NIHPDR NIHPDR 178 0.01 0.01 0 358 2 0.03 0.04 240 2 123 "by cluster,freq" Possibly damaging 1.806 5 moderately conservative 607585 11q22-q23 "ataxia telangiectasia mutated (includes complementation groups A, C and D)" 3134 rs2235000 ATM 472 11 107626943 NM_000051 NP_000042 A/G G514D plus 6904852 693 EGP_SNPS PDR90 NIHPDR 180 0.01 0.01 0 358 2 0.03 0.04 240 2 123 "by cluster,freq" Possibly damaging 1.806 5 moderately conservative 607585 11q22-q23 "ataxia telangiectasia mutated (includes complementation groups A, C and D)" 3135 rs2235542 LAMB3 3914 1 206196210 NM_000228 NP_000219 C/T N181D plus 24155097 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.02 0.02 0 46 1 0.24 0.06 1576 3 123 "by cluster,freq" Potentially damaging 1.342 5 Tolerant 0.21 2.79 77 conservative 150310 1q32 "laminin, beta 3" 3136 rs2235967 ZFYVE26 23503 14 67319252 NM_015346 NP_056161 C/T C1457Y plus 21180237 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.39 0.39 0.01 166 2 0.03 0 1528 2 123 "HapMap,submitter,freq,cluster" radical 14q24.1 "zinc finger, FYVE domain containing 26" 3137 rs2235967 ZFYVE26 23503 14 67319252 NM_015346 NP_056161 C/T C1457Y plus 24707354 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.39 0.01 166 2 0.03 0 1528 2 123 "HapMap,submitter,freq,cluster" radical 14q24.1 "zinc finger, FYVE domain containing 26" 3138 rs2236005 MYO18B 84700 22 24747534 NM_032608 NP_115997 A/G Q2347R plus 23557096 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.19 0.19 0 42 1 0.21 0.01 1558 3 123 "by doubleHit,submitter,freq,cluster" conservative 607295 22q11.2-q12.1 myosin XVIIIB 3139 rs2236225 MTHFD1 4522 14 63978598 NM_005956 NP_005947 C/T R653Q minus 24601855 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.4 0 48 1 0.23 0.01 94 2 123 "by doubleHit,submitter,freq,cluster" Potentially damaging 1.4 43 conservative 172460 14q24 "methylenetetrahydrofolate dehydrogenase (NADP+ dependent), methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase" 3140 rs2236264 LGMN 5641 14 92268833 NM_005606 NP_005597 A/G V18I minus 8829966 870 WTB-CW MS UK (MRC MS cohort) 44 0.11 0.11 0.03 304 4 0.19 0.01 1582 3 123 "HapMap,submitter,freq,cluster" Benign 0.889 11 Borderline 0.18 2.88 36 conservative 602620 14q32.1 legumain 3141 rs2236264 LGMN 5641 14 92268833 NM_005606 NP_005597 A/G V18I minus 8829966 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.11 0.11 0.03 304 4 0.19 0.01 1582 3 123 "HapMap,submitter,freq,cluster" Benign 0.889 11 Borderline 0.18 2.88 36 conservative 602620 14q32.1 legumain 3142 rs2236264 LGMN 5641 14 92268833 NM_005606 NP_005597 A/G V18I minus 8829966 1303 SEQUENOM CEPH CEPH (92) 92 0.08 0.11 0.03 304 4 0.19 0.01 1582 3 123 "HapMap,submitter,freq,cluster" Benign 0.889 11 Borderline 0.18 2.88 36 conservative 602620 14q32.1 legumain 3143 rs2236264 LGMN 5641 14 92268833 NM_005606 NP_005597 A/G V18I minus 24128671 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.11 0.03 304 4 0.19 0.01 1582 3 123 "HapMap,submitter,freq,cluster" Benign 0.889 11 Borderline 0.18 2.88 36 conservative 602620 14q32.1 legumain 3144 rs2236338 GZMB 3002 14 24170122 NM_004131 NP_004122 A/G Y247H plus 3190690 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.19 0.2 0.01 166 2 0.21 0.02 1596 3 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.715 9 moderately conservative 123910 14q11.2 "granzyme B (granzyme 2, cytotoxic T-lymphocyte-associated serine esterase 1)" 3145 rs2236338 GZMB 3002 14 24170122 NM_004131 NP_004122 A/G Y247H plus 23799424 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.2 0.01 166 2 0.21 0.02 1596 3 123 "HapMap,submitter,freq,cluster" Possibly damaging 1.715 9 moderately conservative 123910 14q11.2 "granzyme B (granzyme 2, cytotoxic T-lymphocyte-associated serine esterase 1)" 3146 rs2236405 PTCH 5727 9 95291127 NM_000264 NP_000255 A/T T1195S plus 4479835 506 NCBI NIHPDR NIHPDR 78 0.04 0.04 0 78 1 0.12 0 1492 1 106 "by cluster,freq" Potentially damaging 1.255 7 Tolerant 0.29 3.02 21 moderately conservative 601309 9q22.3 patched homolog (Drosophila) 3147 rs2236493 RAGE 5891 14 101765446 NM_014226 NP_055041 C/T Q398R plus 12301161 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.2 0.21 0.03 168 2 0.25 0.3 94 2 123 "HapMap,doubleHit,freq,cluster" conservative 605762 14q32 renal tumor antigen 3148 rs2236493 RAGE 5891 14 101765446 NM_014226 NP_055041 C/T Q398R plus 23803529 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.21 0.03 168 2 0.25 0.3 94 2 123 "HapMap,doubleHit,freq,cluster" conservative 605762 14q32 renal tumor antigen 3149 rs2237051 EGF 1950 4 111258802 NM_001963 NP_001954 A/G M708I plus 8819735 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.39 0.43 0.03 282 3 0.31 0.06 1932 7 123 "by doubleHit,submitter,freq,cluster" Borderline 1.161 10 conservative 131530 4q25 epidermal growth factor (beta-urogastrone) 3150 rs2237051 EGF 1950 4 111258802 NM_001963 NP_001954 A/G M708I plus 16340339 693 EGP_SNPS PDR90 NIHPDR 172 0.45 0.43 0.03 282 3 0.31 0.06 1932 7 123 "by doubleHit,submitter,freq,cluster" Borderline 1.161 10 conservative 131530 4q25 epidermal growth factor (beta-urogastrone) 3151 rs2237051 EGF 1950 4 111258802 NM_001963 NP_001954 A/G M708I plus 24325863 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.43 0.03 282 3 0.31 0.06 1932 7 123 "by doubleHit,submitter,freq,cluster" Borderline 1.161 10 conservative 131530 4q25 epidermal growth factor (beta-urogastrone) 3152 rs2238472 ABCC6 368 16 16159100 NM_001171 NP_001162 A/G R1268Q minus 24522768 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.3 0.3 0 46 1 0.12 0.07 94 2 123 "by doubleHit,submitter,freq,cluster" Borderline 0.15 2.78 35 conservative 603234 16p13.1 "ATP-binding cassette, sub-family C (CFTR/MRP), member 6" 3153 rs2239359 FANCA 2175 16 88376981 NM_000135 NP_000126 C/T G501S plus 12675397 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.45 0.38 0.05 226 3 0.18 0.08 1944 7 123 "HapMap,doubleHit,freq,cluster" moderately conservative 607139 16q24.3 "Fanconi anemia, complementation group A" 3154 rs2239359 FANCA 2175 16 88376981 NM_000135 NP_000126 C/T G501S plus 16702260 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.36 0.38 0.05 226 3 0.18 0.08 1944 7 123 "HapMap,doubleHit,freq,cluster" moderately conservative 607139 16q24.3 "Fanconi anemia, complementation group A" 3155 rs2239359 FANCA 2175 16 88376981 NM_000135 NP_000126 C/T G501S plus 24590236 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.38 0.05 226 3 0.18 0.08 1944 7 123 "HapMap,doubleHit,freq,cluster" moderately conservative 607139 16q24.3 "Fanconi anemia, complementation group A" 3156 rs2239730 ZNF215 7762 11 6933751 NM_013250 NP_037382 C/G V323L minus 4045936 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.22 0.22 0.01 164 2 0.16 0.06 1012 3 123 "HapMap,submitter,freq,cluster" conservative 605016 11p15.4 zinc finger protein 215 3157 rs2239730 ZNF215 7762 11 6933751 NM_013250 NP_037382 C/G V323L minus 23538306 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.22 0.01 164 2 0.16 0.06 1012 3 123 "HapMap,submitter,freq,cluster" conservative 605016 11p15.4 zinc finger protein 215 3158 rs2240026 PPP1R9A 55607 7 94548071 XM_371933 XP_371933 A/G S1057N plus 24194081 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.47 0.11 1004 3 123 "by doubleHit,submitter,freq,cluster" conservative 602468 7q21.3 "protein phosphatase 1, regulatory (inhibitor) subunit 9A" 3159 rs2240154 GRIN3B 116444 19 954172 XM_290850 XP_290850 C/T T157M plus 3195690 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.16 0.16 0 120 1 0.43 0 1452 1 98 "HapMap,freq" Intolerant 0.03 2.84 31 moderately conservative 606651 19p13.3 "glutamate receptor, ionotropic, N-methyl-D-aspartate 3B" 3160 rs2240308 AXIN2 8313 17 60985053 NM_004655 NP_004646 A/G P50S plus 17582346 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.47 0.47 0 118 1 121 "HapMap,doubleHit,freq,cluster" Probably damaging 2.008 6 moderately conservative 604025 17q23-q24 "axin 2 (conductin, axil)" 3161 rs2240345 SEC14L3 266629 22 29181927 NM_174975 NP_777635 A/C D335E plus 8002153 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.42 0.42 0 168 2 0.09 0.02 1590 3 123 "HapMap,freq,cluster" Potentially damaging 1.319 16 Tolerant 1 2.87 25 conservative 22q12.2 SEC14-like 3 (S. cerevisiae) 3162 rs2240345 SEC14L3 266629 22 29181927 NM_174975 NP_777635 A/C D335E plus 24587563 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.42 0 168 2 0.09 0.02 1590 3 123 "HapMap,freq,cluster" Potentially damaging 1.319 16 Tolerant 1 2.87 25 conservative 22q12.2 SEC14-like 3 (S. cerevisiae) 3163 rs2241002 CD5 921 11 60643489 NM_014207 NP_055022 C/T P224L plus 12159051 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.19 0.19 0 118 1 0.04 0 1470 1 116 "HapMap,freq,cluster" Probably damaging 2.169 6 Intolerant 0 2.79 56 moderately conservative 153340 11q13 CD5 antigen (p56-62) 3164 rs2241057 CYP26B1 56603 2 72273615 NM_019885 NP_063938 C/T L264S minus 9997893 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.16 0.16 0 120 1 116 "HapMap,freq,cluster" Potentially damaging 1.351 5 Tolerant 0.88 2.9 23 moderately radical 605207 2p13.2 "cytochrome P450, family 26, subfamily B, polypeptide 1" 3165 rs2241384 ILT7 23547 19 59541754 NM_012276 NP_036408 C/T P27L minus 3197318 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.19 0.16 0.07 168 2 0.16 0 1594 3 123 "HapMap,freq,cluster" Probably damaging 2.724 65 Intolerant 0.02 2.9 54 moderately conservative 607517 19q13.4 "leukocyte immunoglobulin-like receptor, subfamily A (without TM domain), member 4" 3166 rs2241384 ILT7 23547 19 59541754 NM_012276 NP_036408 C/T P27L minus 23778078 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.16 0.07 168 2 0.16 0 1594 3 123 "HapMap,freq,cluster" Probably damaging 2.724 65 Intolerant 0.02 2.9 54 moderately conservative 607517 19q13.4 "leukocyte immunoglobulin-like receptor, subfamily A (without TM domain), member 4" 3167 rs2241586 ZNF610 162963 19 57560834 NM_173530 NP_775801 A/C A131S minus 24204177 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.09 0.09 0 46 1 0.36 0.05 1386 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.964 7 moderately conservative 19q13.41 zinc finger protein 610 3168 rs2241797 TGFBRAP1 9392 2 105344479 NM_004257 NP_004248 C/T H725R plus 23212515 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.25 0 48 1 0.23 0.05 1565 3 123 "by doubleHit,submitter,freq,cluster" conservative 606237 2q12.2 "transforming growth factor, beta receptor associated protein 1" 3169 rs2241883 FABP1 2168 2 88263328 NM_001443 NP_001434 C/T T94A plus 24160905 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.27 0 48 1 0.24 0.02 1580 3 123 "by cluster,freq" Potentially damaging 1.315 17 Tolerant 0.29 2.8 37 moderately conservative 134650 2p11 "fatty acid binding protein 1, liver" 3170 rs2242089 PYCRL 65263 8 144760289 NM_023078 NP_075566 A/G V105M minus 3198258 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.35 0.35 0 120 1 0.33 0 1486 1 98 "HapMap,freq" Borderline 1.143 7 Intolerant 0.01 2.82 37 conservative 8q24.3 pyrroline-5-carboxylate reductase-like 3171 rs2242093 ZC3HDC3 23144 8 144694717 NM_015117 NP_055932 A/G I6M minus 3198263 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.13 0.13 0 120 1 98 "HapMap,freq" conservative 8q24.3 zinc finger CCCH type domain containing 3 3172 rs2243072 F2RL1 2150 5 76150825 NM_005242 NP_005233 C/T S21F plus 3199535 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.04 0.04 0 94 2 123 by freq radical 600933 5q13 coagulation factor II (thrombin) receptor-like 1 3173 rs2243072 F2RL1 2150 5 76150825 NM_005242 NP_005233 C/T S21F plus 24676218 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 94 2 123 by freq radical 600933 5q13 coagulation factor II (thrombin) receptor-like 1 3174 rs2243639 SFTPD 6441 10 81691702 NM_003019 NP_003010 C/T T180A plus 8819860 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.45 0.45 0.01 110 2 0.2 0.11 440 6 123 "by doubleHit,freq,cluster" Potentially damaging 1.413 11 moderately conservative 178635 10q22.2-q23.1 "surfactant, pulmonary-associated protein D" 3175 rs2243639 SFTPD 6441 10 81691702 NM_003019 NP_003010 C/T T180A plus 24410034 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.45 0.01 110 2 0.2 0.11 440 6 123 "by doubleHit,freq,cluster" Potentially damaging 1.413 11 moderately conservative 178635 10q22.2-q23.1 "surfactant, pulmonary-associated protein D" 3176 rs2244008 LAMA2 3908 6 129854746 NM_000426 NP_000417 A/G T2636A plus 23966262 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.15 0.01 1576 3 123 "by cluster,freq" Tolerant 0.65 2.77 12 moderately conservative 156225 6q22-q23 "laminin, alpha 2 (merosin, congenital muscular dystrophy)" 3177 rs2245803 MMP20 9313 11 102001208 NM_004771 NP_004762 A/C K18T minus 16334128 902 AFFY Caucasian 24 0.46 0.33 0.06 196 3 0.15 0.06 1558 4 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.87 2.76 47 moderately conservative 604629 11q22.3 matrix metalloproteinase 20 (enamelysin) 3178 rs2245803 MMP20 9313 11 102001208 NM_004771 NP_004762 A/C K18T minus 16334128 904 AFFY CEPH 12 0.33 0.33 0.06 196 3 0.15 0.06 1558 4 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.87 2.76 47 moderately conservative 604629 11q22.3 matrix metalloproteinase 20 (enamelysin) 3179 rs2245803 MMP20 9313 11 102001208 NM_004771 NP_004762 A/C K18T minus 28446749 693 EGP_SNPS PDR90 NIHPDR 160 0.31 0.33 0.06 196 3 0.15 0.06 1558 4 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.87 2.76 47 moderately conservative 604629 11q22.3 matrix metalloproteinase 20 (enamelysin) 3180 rs2249060 PCNT2 5116 21 46597605 NM_006031 NP_006022 C/T T539I plus 4020280 634 PERLEGEN NCBI|NIHPDR NIHPDR 18 0.11 0.19 0.05 184 3 0.24 0.03 1588 3 123 "HapMap,freq,cluster" moderately conservative 605925 21q22.3 pericentrin 2 (kendrin) 3181 rs2249060 PCNT2 5116 21 46597605 NM_006031 NP_006022 C/T T539I plus 14449669 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.18 0.19 0.05 184 3 0.24 0.03 1588 3 123 "HapMap,freq,cluster" moderately conservative 605925 21q22.3 pericentrin 2 (kendrin) 3182 rs2249060 PCNT2 5116 21 46597605 NM_006031 NP_006022 C/T T539I plus 24532927 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.19 0.05 184 3 0.24 0.03 1588 3 123 "HapMap,freq,cluster" moderately conservative 605925 21q22.3 pericentrin 2 (kendrin) 3183 rs2249542 FLJ10581 55178 17 632502 NM_018146 NP_060616 A/G G45E plus 3883094 1303 SEQUENOM CEPH CEPH (92) 92 0.39 0.37 0.04 140 2 0.13 0.01 1200 3 123 "by submitter,freq,cluster" moderately conservative 17p13.3 putative RNA methyltransferase 3184 rs2249542 FLJ10581 55178 17 632502 NM_018146 NP_060616 A/G G45E plus 24579134 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.37 0.04 140 2 0.13 0.01 1200 3 123 "by submitter,freq,cluster" moderately conservative 17p13.3 putative RNA methyltransferase 3185 rs2250242 AKNA 80709 9 114183527 NM_030767 NP_110394 A/G S1303P plus 3945346 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.44 0.44 0 120 1 0.39 0 1498 1 121 "HapMap,doubleHit,freq,cluster" Benign 0.739 7 moderately conservative 605729 9q32 AT-hook transcription factor 3186 rs2250889 MMP9 4318 20 44075813 NM_004994 NP_004985 C/G R574P plus 5112479 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.09 0.1 0.04 98 3 0.3 0.05 1628 4 123 "by submitter,freq,cluster" Possibly damaging 1.754 8 moderately radical 120361 20q11.2-q13.1 "matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)" 3187 rs2250889 MMP9 4318 20 44075813 NM_004994 NP_004985 C/G R574P plus 16338515 1120 WIPGA POP-WIPGA-12-05-2003 CORIELL Mixed 4 0.25 0.1 0.04 98 3 0.3 0.05 1628 4 123 "by submitter,freq,cluster" Possibly damaging 1.754 8 moderately radical 120361 20q11.2-q13.1 "matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)" 3188 rs2250889 MMP9 4318 20 44075813 NM_004994 NP_004985 C/G R574P plus 24084492 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0.04 98 3 0.3 0.05 1628 4 123 "by submitter,freq,cluster" Possibly damaging 1.754 8 moderately radical 120361 20q11.2-q13.1 "matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)" 3189 rs2255336 KLRK1 22914 12 10423593 NM_007360 NP_031386 A/G T72A minus 3859325 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.16 0.16 0.01 166 2 0.25 0.22 94 2 123 "HapMap,doubleHit,freq,cluster" Borderline 1.183 5 moderately conservative 12p13.2-p12.3 "killer cell lectin-like receptor subfamily K, member 1" 3190 rs2255336 KLRK1 22914 12 10423593 NM_007360 NP_031386 A/G T72A minus 23787285 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.16 0.01 166 2 0.25 0.22 94 2 123 "HapMap,doubleHit,freq,cluster" Borderline 1.183 5 moderately conservative 12p13.2-p12.3 "killer cell lectin-like receptor subfamily K, member 1" 3191 rs2255703 PLXND1 23129 3 130775954 NM_015103 NP_055918 C/T M870V plus 23910228 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.28 0.28 0 46 1 0.37 0.02 1582 3 123 "by doubleHit,freq,cluster" Borderline 1.07 5 Tolerant 0.6 2.8 19 conservative 604282 3q21.3 plexin D1 3192 rs2256871 CYP2C9 1559 10 96698964 NM_000771 NP_000762 C/T H251R minus 12588508 693 EGP_SNPS PDR90 NIHPDR 176 0.01 0.01 0 292 2 120 "HapMap,doubleHit,freq,cluster" Probably damaging 3.13 153 Intolerant 0.02 2.79 165 conservative 601130 10q24 "cytochrome P450, family 2, subfamily C, polypeptide 9" 3193 rs2256871 CYP2C9 1559 10 96698964 NM_000771 NP_000762 C/T H251R minus 12588508 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.01 0.01 0 292 2 120 "HapMap,doubleHit,freq,cluster" Probably damaging 3.13 153 Intolerant 0.02 2.79 165 conservative 601130 10q24 "cytochrome P450, family 2, subfamily C, polypeptide 9" 3194 rs2257167 IFNAR1 3454 21 33637569 NM_000629 NP_000620 C/G V168L plus 4013264 634 PERLEGEN NCBI|NIHPDR NIHPDR 18 0.11 0.1 0.05 184 3 0.26 0.26 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.07 6 Tolerant 0.86 2.8 18 conservative 107450 21q22.11 "interferon (alpha, beta and omega) receptor 1" 3195 rs2257167 IFNAR1 3454 21 33637569 NM_000629 NP_000620 C/G V168L plus 14438710 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.13 0.1 0.05 184 3 0.26 0.26 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.07 6 Tolerant 0.86 2.8 18 conservative 107450 21q22.11 "interferon (alpha, beta and omega) receptor 1" 3196 rs2257167 IFNAR1 3454 21 33637569 NM_000629 NP_000620 C/G V168L plus 24116232 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.1 0.05 184 3 0.26 0.26 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Borderline 1.07 6 Tolerant 0.86 2.8 18 conservative 107450 21q22.11 "interferon (alpha, beta and omega) receptor 1" 3197 rs2257401 CYP3A7 1551 7 98951336 NM_000765 NP_000756 C/G R409T plus 3868318 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.07 0.07 0 120 1 0.26 0 1486 1 121 "HapMap,doubleHit,freq,cluster" Potentially damaging 1.409 67 moderately conservative 605340 7q21-q22.1 "cytochrome P450, family 3, subfamily A, polypeptide 7" 3198 rs2258689 MAPT 4137 17 41423219 NM_016835 NP_058519 C/T H441Y plus 3412711 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.18 0.21 0.06 168 2 0.44 0.06 1570 3 123 "HapMap,submitter,freq,cluster" Tolerant 0.63 2.79 46 moderately conservative 157140 17q21.1 microtubule-associated protein tau 3199 rs2258689 MAPT 4137 17 41423219 NM_016835 NP_058519 C/T H441Y plus 24573522 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.21 0.06 168 2 0.44 0.06 1570 3 123 "HapMap,submitter,freq,cluster" Tolerant 0.63 2.79 46 moderately conservative 157140 17q21.1 microtubule-associated protein tau 3200 rs2266607 MPG 4350 16 69595 NM_002434 NP_002425 C/T Y71H plus 4388569 693 EGP_SNPS PDR90 NIHPDR 178 0.01 0.01 0 178 1 106 "by cluster,freq" Potentially damaging 1.411 5 moderately conservative 156565 16p13.3 N-methylpurine-DNA glycosylase 3201 rs2266631 GSTA2 2939 6 52724434 NM_000846 NP_000837 C/T V149A minus 869775 506 NCBI NIHPDR NIHPDR 94 0.18 0.18 0 94 1 100 by freq Possibly damaging 1.949 63 Intolerant 0 2.85 65 moderately conservative 138360 6p12.1 glutathione S-transferase A2 3202 rs2266633 GSTT1 2952 22 22701483 NM_000853 NP_000844 A/G D141N minus 869783 506 NCBI NIHPDR NIHPDR 80 0.03 0.03 0 80 1 100 by freq Benign 0.382 18 Tolerant 0.76 2.8 23 conservative 600436 22q11.23 glutathione S-transferase theta 1 3203 rs2266637 GSTT1 2952 22 22701399 NM_000853 NP_000844 A/G V169I minus 869788 506 NCBI NIHPDR NIHPDR 80 0.04 0.04 0 80 1 100 by freq Benign 0.923 18 Borderline 0.15 2.79 22 conservative 600436 22q11.23 glutathione S-transferase theta 1 3204 rs2266690 CCNH 902 5 86731030 NM_001239 NP_001230 C/T V270A minus 2667785 506 NCBI NIHPDR NIHPDR 184 0.13 0.13 0.05 540 4 0.1 0.04 1438 5 120 "HapMap,freq,cluster" Intolerant 0.05 2.85 13 moderately conservative 601953 5q13.3-q14 cyclin H 3205 rs2266690 CCNH 902 5 86731030 NM_001239 NP_001230 C/T V270A minus 4329127 693 EGP_SNPS PDR90 NIHPDR 178 0.08 0.13 0.05 540 4 0.1 0.04 1438 5 120 "HapMap,freq,cluster" Intolerant 0.05 2.85 13 moderately conservative 601953 5q13.3-q14 cyclin H 3206 rs2266690 CCNH 902 5 86731030 NM_001239 NP_001230 C/T V270A minus 4329127 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.2 0.13 0.05 540 4 0.1 0.04 1438 5 120 "HapMap,freq,cluster" Intolerant 0.05 2.85 13 moderately conservative 601953 5q13.3-q14 cyclin H 3207 rs2266690 CCNH 902 5 86731030 NM_001239 NP_001230 C/T V270A minus 5586332 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.12 0.13 0.05 540 4 0.1 0.04 1438 5 120 "HapMap,freq,cluster" Intolerant 0.05 2.85 13 moderately conservative 601953 5q13.3-q14 cyclin H 3208 rs2266691 CCNH 902 5 86739661 NM_001239 NP_001230 A/G K138R minus 2667786 506 NCBI NIHPDR NIHPDR 166 0.02 0.02 0.01 320 2 110 "by cluster,freq" Tolerant 0.3 3.05 12 conservative 601953 5q13.3-q14 cyclin H 3209 rs2266691 CCNH 902 5 86739661 NM_001239 NP_001230 A/G K138R minus 4329092 693 EGP_SNPS PDR90 NIHPDR 154 0.03 0.02 0.01 320 2 110 "by cluster,freq" Tolerant 0.3 3.05 12 conservative 601953 5q13.3-q14 cyclin H 3210 rs2267161 GAL3ST1 9514 22 29277849 NM_004861 NP_004852 C/T V29M plus 11007280 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.38 0.38 0 120 1 0.34 0 1310 1 120 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.225 5 conservative 602300 22q12.2 galactose-3-O-sulfotransferase 1 3211 rs2269429 TNXB 7148 6 32137161 NM_019105 NP_061978 A/G G2555S minus 3203509 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.07 0.07 0.01 168 2 0.11 0.01 1592 3 123 "HapMap,freq" Possibly damaging 1.722 5 Tolerant 0.4 3.07 13 moderately conservative 600985 6p21.3 tenascin XB 3212 rs2269429 TNXB 7148 6 32137161 NM_019105 NP_061978 A/G G2555S minus 23714772 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.07 0.01 168 2 0.11 0.01 1592 3 123 "HapMap,freq" Possibly damaging 1.722 5 Tolerant 0.4 3.07 13 moderately conservative 600985 6p21.3 tenascin XB 3213 rs2269529 MYH9 4627 22 35008854 NM_002473 NP_002464 C/T I1626V plus 16923656 1303 SEQUENOM CEPH CEPH (92) 92 0.39 0.39 0 92 1 121 "HapMap,doubleHit,cluster" Benign 0.48 53 Borderline 0.13 2.8 120 conservative 160775 22q13.1 "myosin, heavy polypeptide 9, non-muscle" 3214 rs2269961 SEC14L3 266629 22 29185384 NM_174975 NP_777635 C/T R214H plus 3204235 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.28 0.29 0.02 168 2 0.24 0.02 94 2 123 "HapMap,submitter,freq" Possibly damaging 1.765 16 Intolerant 0.04 2.82 30 conservative 22q12.2 SEC14-like 3 (S. cerevisiae) 3215 rs2269961 SEC14L3 266629 22 29185384 NM_174975 NP_777635 C/T R214H plus 24587577 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.29 0.02 168 2 0.24 0.02 94 2 123 "HapMap,submitter,freq" Possibly damaging 1.765 16 Intolerant 0.04 2.82 30 conservative 22q12.2 SEC14-like 3 (S. cerevisiae) 3216 rs2270493 ZNF597 146434 16 3430880 NM_152457 NP_689670 A/T T30S plus 3204940 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.03 0.03 0 118 1 0.04 0 1478 1 100 "HapMap,freq" Tolerant 0.42 2.78 27 moderately conservative 16p13.3 zinc finger protein 597 3217 rs2270915 NPR3 4883 5 32822146 NM_000908 NP_000899 A/G N521D plus 3205516 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.14 0.12 0.04 168 2 0.22 0.02 1584 3 123 "HapMap,submitter,freq,cluster" Benign 0.371 10 Tolerant 0.21 2.78 24 conservative 108962 5p14-p13 natriuretic peptide receptor C/guanylate cyclase C (atrionatriuretic peptide receptor C) 3218 rs2270915 NPR3 4883 5 32822146 NM_000908 NP_000899 A/G N521D plus 24011877 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.12 0.04 168 2 0.22 0.02 1584 3 123 "HapMap,submitter,freq,cluster" Benign 0.371 10 Tolerant 0.21 2.78 24 conservative 108962 5p14-p13 natriuretic peptide receptor C/guanylate cyclase C (atrionatriuretic peptide receptor C) 3219 rs2270941 DHDH 27294 19 54130175 NM_014475 NP_055290 C/T S66N minus 6903783 775 SNP500CANCER CAUC1 Caucasian (31) 56 0.3 0.25 0.04 224 3 0.44 0.07 1821 7 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.299 9 Tolerant 1 2.78 23 conservative 606377 19q13.3 dihydrodiol dehydrogenase (dimeric) 3220 rs2270941 DHDH 27294 19 54130175 NM_014475 NP_055290 C/T S66N minus 6903783 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.22 0.25 0.04 224 3 0.44 0.07 1821 7 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.299 9 Tolerant 1 2.78 23 conservative 606377 19q13.3 dihydrodiol dehydrogenase (dimeric) 3221 rs2270941 DHDH 27294 19 54130175 NM_014475 NP_055290 C/T S66N minus 24225624 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.25 0.04 224 3 0.44 0.07 1821 7 123 "HapMap,doubleHit,submitter,freq,cluster" Potentially damaging 1.299 9 Tolerant 1 2.78 23 conservative 606377 19q13.3 dihydrodiol dehydrogenase (dimeric) 3222 rs2270968 MCCC1 56922 3 184237911 NM_020166 NP_064551 A/C H464P minus 23334685 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.32 0.32 0 44 1 0.26 0.02 1576 3 123 "by cluster,freq" Potentially damaging 1.372 13 moderately conservative 210200 3q27 methylcrotonoyl-Coenzyme A carboxylase 1 (alpha) 3223 rs2271023 CDH16 1014 16 65505631 NM_004062 NP_004053 A/G H257Y plus 3205660 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.03 0.03 0 118 1 0.17 0 1486 1 100 "HapMap,freq" Possibly damaging 1.803 5 Tolerant 0.43 2.78 32 moderately conservative 603118 16q22.1 "cadherin 16, KSP-cadherin" 3224 rs2271433 ZFP29 54993 15 82950775 NM_017894 NP_060364 G/T V140F plus 6689596 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.13 0.13 0 118 1 0.03 0 1502 1 121 "HapMap,doubleHit,submitter,freq,cluster" conservative 15q25.2 zinc finger protein 29 3225 rs2271462 CUBN 8029 10 17022067 NM_001081 NP_001072 C/T G1840S plus 23891909 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.16 0.01 1588 3 123 "by cluster,freq" Tolerant 0.49 2.76 8 moderately conservative 602997 10p12.31 cubilin (intrinsic factor-cobalamin receptor) 3226 rs2271725 ITGA11 22801 15 66396701 NM_012211 NP_036343 A/C Q891K minus 23411162 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 0.23 0.02 1390 3 123 "by submitter,freq,cluster" Benign 0.175 6 Tolerant 1 2.76 16 moderately conservative 604789 15q22.3-q23 "integrin, alpha 11" 3227 rs2271733 RAX 30062 18 55091287 NM_013435 NP_038463 A/C D44E minus 3206631 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.29 0.29 0 120 1 0.25 0 1504 1 100 "HapMap,freq" Benign 0.145 11 Tolerant 0.79 3.05 17 conservative 601881 18q21.32 retina and anterior neural fold homeobox 3228 rs2271815 DEPC-1 221120 11 43879672 NM_139178 NP_631917 C/T R164C plus 3206735 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.01 0.01 0 116 1 0.01 0 1494 1 100 HapMap Borderline 0.16 2.79 40 radical 11p11.2 prostate cancer antigen-1 3229 rs2271900 DEPDC6 64798 8 121082951 NM_022783 NP_073620 A/G N204S plus 3206836 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.26 0.26 0 118 1 100 "HapMap,freq" conservative 8q24.12 DEP domain containing 6 3230 rs2272095 MKRN1 23608 7 139612035 NM_013446 NP_038474 C/G V243L minus 13434944 885 TSC-CSHL HapMap-CEPH-30-trios 112 0.18 0.18 0 112 1 0.16 0 1078 1 120 "HapMap,freq,cluster" Potentially damaging 1.341 15 conservative 607754 7q34 "makorin, ring finger protein, 1" 3231 rs2272296 SOAT2 8435 12 51796200 NM_003578 NP_003569 C/T T254I plus 23959293 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.12 0.12 0 42 1 0.42 0.03 1574 3 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.69 2.77 27 moderately conservative 601311 12q13.13 sterol O-acyltransferase 2 3232 rs2272641 ENTPD4 9583 8 23350706 NM_004901 NP_004892 A/G K354E minus 24040489 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.28 0.04 1588 3 123 "by submitter,freq,cluster" Benign 0.821 13 Tolerant 0.81 3.08 18 moderately conservative 607577 8p21.2 lysosomal apyrase-like 1 3233 rs2272837 MOV10L1 54456 22 48885083 NM_018995 NP_061868 A/G Q820R plus 24214808 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.17 0 48 1 0.29 0.04 94 2 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.98 2.97 233 conservative 605794 22q13.33 "Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)" 3234 rs2272843 MOV10L1 54456 22 48901923 NM_018995 NP_061868 A/C A1179E plus 24214831 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 0.14 0.03 1590 3 123 "by doubleHit,freq,cluster" Tolerant 1 3.07 106 moderately radical 605794 22q13.33 "Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)" 3235 rs2272996 VNN1 8876 6 133056964 NM_004666 NP_004657 C/T N131S plus 24027495 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.27 0 48 1 0.33 0.1 94 2 123 "by doubleHit,freq,cluster" Possibly damaging 1.838 17 Tolerant 0.52 2.76 18 conservative 603570 6q23-q24 vanin 1 3236 rs2273137 NOL5A 10528 20 2583212 NM_006392 NP_006383 C/T I121V minus 3208482 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.11 0.11 0 118 1 0.22 0 1502 1 100 "HapMap,freq" Borderline 1.103 21 Borderline 0.19 2.82 71 conservative 20p13 nucleolar protein 5A (56kDa with KKE/D repeat) 3237 rs2273621 FHL5 9457 6 97165274 NM_020482 NP_065228 A/G R204G plus 23369274 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.33 0 48 1 0.36 0.13 94 2 123 "by doubleHit,freq,cluster" Probably damaging 2.133 17 Potentially intolerant 0.06 2.82 55 moderately radical 605126 6q16.1-q16.3 four and a half LIM domains 5 3238 rs2273697 ABCC2 1244 10 101553805 NM_000392 NP_000383 A/G V417I plus 23596946 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.14 0.03 2068 4 123 "by doubleHit,submitter,freq,cluster" Benign 0.115 13 Tolerant 0.34 2.79 51 conservative 601107 10q24 "ATP-binding cassette, sub-family C (CFTR/MRP), member 2" 3239 rs2274271 DLG7 9787 14 54725445 NM_014750 NP_055565 A/G G69E minus 3210003 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.09 0.08 0.02 168 2 0.24 0.02 1584 3 123 "HapMap,freq,cluster" moderately conservative 14q22.2 "discs, large homolog 7 (Drosophila)" 3240 rs2274271 DLG7 9787 14 54725445 NM_014750 NP_055565 A/G G69E minus 24118910 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.08 0.02 168 2 0.24 0.02 1584 3 123 "HapMap,freq,cluster" moderately conservative 14q22.2 "discs, large homolog 7 (Drosophila)" 3241 rs2274327 CA6 765 1 8943672 NM_001215 NP_001206 C/T T55M plus 24241367 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.33 0 48 1 0.26 0.02 1594 3 123 by freq Benign 0.052 8 Potentially intolerant 0.07 2.75 20 moderately conservative 114780 1p36.2 carbonic anhydrase VI 3242 rs2274333 CA6 765 1 8951470 NM_001215 NP_001206 A/G S90G plus 23840429 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.31 0 48 1 0.42 0.08 1566 3 123 "by doubleHit,freq,cluster" Potentially damaging 1.404 8 moderately conservative 114780 1p36.2 carbonic anhydrase VI 3243 rs2274407 ABCC4 10257 13 94657036 NM_005845 NP_005836 A/C K304N plus 8819642 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.06 0.04 0.03 110 2 0.14 0.03 992 7 123 "by cluster,freq" Borderline 1.08 6 Intolerant 0.02 2.82 36 moderately conservative 605250 13q32 "ATP-binding cassette, sub-family C (CFTR/MRP), member 4" 3244 rs2274407 ABCC4 10257 13 94657036 NM_005845 NP_005836 A/C K304N plus 23810886 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.04 0.03 110 2 0.14 0.03 992 7 123 "by cluster,freq" Borderline 1.08 6 Intolerant 0.02 2.82 36 moderately conservative 605250 13q32 "ATP-binding cassette, sub-family C (CFTR/MRP), member 4" 3245 rs2274419 MUSK 4593 9 110617677 NM_005592 NP_005583 C/T M413I minus 3210188 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.13 0.13 0 118 1 0.23 0 1278 1 100 "HapMap,freq" Benign 0.9 5 Tolerant 0.63 2.82 26 conservative 601296 9q31.3-q32 "muscle, skeletal, receptor tyrosine kinase" 3246 rs2274531 GPA33 10223 1 163774420 NM_005814 NP_005805 A/G D20N minus 23847640 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 0.14 0.04 1538 3 123 "by submitter,freq,cluster" Tolerant 0.48 2.81 22 conservative 602171 1q23.3 glycoprotein A33 (transmembrane) 3247 rs2274616 ITGA10 8515 1 143025126 NM_003637 NP_003628 C/T R725Q minus 23836092 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.15 0.02 1592 3 123 "by doubleHit,freq,cluster" Tolerant 0.22 2.75 18 conservative 604042 1q21 "integrin, alpha 10" 3248 rs2274736 PTPN21 11099 14 88008405 NM_007039 NP_008970 C/T V936A minus 10722750 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.31 0.33 0.04 168 2 0.33 0.04 802 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.086 10 moderately conservative 603271 14q31.3 "protein tyrosine phosphatase, non-receptor type 21" 3249 rs2274736 PTPN21 11099 14 88008405 NM_007039 NP_008970 C/T V936A minus 23800588 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.33 0.04 168 2 0.33 0.04 802 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.086 10 moderately conservative 603271 14q31.3 "protein tyrosine phosphatase, non-receptor type 21" 3250 rs2274750 TNC 3371 9 114882825 NM_002160 NP_002151 A/G A1781T minus 3210625 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.03 0.03 0.01 168 2 0.11 0.02 1582 3 123 "HapMap,submitter,freq,cluster" Intolerant 0.02 2.78 24 moderately conservative 187380 9q33 tenascin C (hexabrachion) 3251 rs2274750 TNC 3371 9 114882825 NM_002160 NP_002151 A/G A1781T minus 24058009 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.03 0.01 168 2 0.11 0.02 1582 3 123 "HapMap,submitter,freq,cluster" Intolerant 0.02 2.78 24 moderately conservative 187380 9q33 tenascin C (hexabrachion) 3252 rs2274756 MMP9 4318 20 44076518 NM_004994 NP_004985 A/G R668Q plus 5112482 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 44 0.14 0.13 0.01 92 2 0.17 0.02 1636 4 123 "by cluster,freq" Benign 0.361 8 Tolerant 0.93 2.81 39 conservative 120361 20q11.2-q13.1 "matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)" 3253 rs2274756 MMP9 4318 20 44076518 NM_004994 NP_004985 A/G R668Q plus 23574610 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0.01 92 2 0.17 0.02 1636 4 123 "by cluster,freq" Benign 0.361 8 Tolerant 0.93 2.81 39 conservative 120361 20q11.2-q13.1 "matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)" 3254 rs2274802 USP16 10600 21 29330541 NM_006447 NP_006438 A/T Q141H plus 16908412 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.16 0 92 1 0.12 0 1490 1 120 "by submitter,freq,cluster" Tolerant 0.32 2.82 15 conservative 604735 21q22.11 ubiquitin specific protease 16 3255 rs2274924 TRPM6 140803 9 74606201 NM_017662 NP_060132 A/G K1584E minus 3210873 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.15 0.14 0.03 168 2 0.48 0 90 2 123 "HapMap,freq,cluster" moderately conservative 607009 9q21.13 "transient receptor potential cation channel, subfamily M, member 6" 3256 rs2274924 TRPM6 140803 9 74606201 NM_017662 NP_060132 A/G K1584E minus 24030235 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.14 0.03 168 2 0.48 0 90 2 123 "HapMap,freq,cluster" moderately conservative 607009 9q21.13 "transient receptor potential cation channel, subfamily M, member 6" 3257 rs2274976 MTHFR 4524 1 11785193 NM_005957 NP_005948 A/G R594Q minus 23838280 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.04 0.04 0 46 1 0.1 0.02 1580 3 123 "by submitter,freq,cluster" Potentially damaging 1.432 5 conservative 607093 1p36.3 "5,10-methylenetetrahydrofolate reductase (NADPH)" 3258 rs2275140 LAMC3 10319 9 130977603 NM_006059 NP_006050 A/G S1082G plus 24093189 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.31 0.02 1590 3 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.39 2.86 16 moderately conservative 604349 9q31-q34 "laminin, gamma 3" 3259 rs2275249 CHD1L 9557 1 143984136 NM_004284 NP_004275 C/G S743C plus 23836488 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.24 0.05 1588 3 123 "by cluster,freq" Possibly damaging 1.548 6 moderately radical 1q12 chromodomain helicase DNA binding protein 1-like 3260 rs2275272 PYCS 5832 10 97378152 NM_002860 NP_002851 A/G T299I plus 3211318 902 AFFY Caucasian 24 0.08 0.1 0.07 84 3 0.04 0.01 1650 5 123 by freq Possibly damaging 1.628 9 moderately conservative 138250 10q24.3 pyrroline-5-carboxylate synthetase (glutamate gamma-semialdehyde synthetase) 3261 rs2275272 PYCS 5832 10 97378152 NM_002860 NP_002851 A/G T299I plus 3211318 904 AFFY CEPH 12 0.25 0.1 0.07 84 3 0.04 0.01 1650 5 123 by freq Possibly damaging 1.628 9 moderately conservative 138250 10q24.3 pyrroline-5-carboxylate synthetase (glutamate gamma-semialdehyde synthetase) 3262 rs2275272 PYCS 5832 10 97378152 NM_002860 NP_002851 A/G T299I plus 24557807 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.1 0.07 84 3 0.04 0.01 1650 5 123 by freq Possibly damaging 1.628 9 moderately conservative 138250 10q24.3 pyrroline-5-carboxylate synthetase (glutamate gamma-semialdehyde synthetase) 3263 rs2275307 SIPA1L2 57568 1 228881656 NM_020808 NP_065859 A/G T1098A minus 23893630 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.17 0 48 1 0.48 0.03 1554 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.993 15 moderately conservative 1q42.2 signal-induced proliferation-associated 1 like 2 3264 rs2275363 RAP1GA1 5909 1 21685861 NM_002885 NP_002876 A/G A107T minus 23845014 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.39 0.39 0 46 1 0.44 0.02 1590 3 123 "by doubleHit,freq,cluster" Benign 0.201 9 moderately conservative 600278 1p36.1-p35 "RAP1, GTPase activating protein 1" 3265 rs2275554 AK7 122481 14 95940857 NM_152327 NP_689540 A/G R102Q plus 6779500 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.28 0.28 0 120 1 0.21 0 1470 1 120 "HapMap,doubleHit,freq,cluster" Benign 0.403 5 conservative 14q32.31 adenylate kinase 7 3266 rs2275586 MMS19L 64210 10 99230748 NM_022362 NP_071757 C/G A68G plus 23584279 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.07 0.04 1522 2 123 "by doubleHit,submitter,freq,cluster" Possibly damaging 1.581 5 moderately conservative 10q24-q25 "MMS19-like (MET18 homolog, S. cerevisiae)" 3267 rs2275603 FREB 84824 1 158413438 NM_032738 NP_116127 A/G S186G plus 23158520 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.19 0 48 1 0.49 0.03 1584 3 123 "by doubleHit,freq,cluster" Tolerant 0.83 2.75 49 moderately conservative 606891 1q23.1 Fc receptor homolog expressed in B cells 3268 rs2275697 CNTN2 6900 1 201759394 NM_005076 NP_005067 C/T A145T minus 24159641 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.19 0 48 1 0.48 0.08 1586 3 123 "by doubleHit,freq,cluster" Benign 0.038 7 Borderline 0.11 2.86 34 moderately conservative 190197 1q32.1 contactin 2 (axonal) 3269 rs2275848 NINJ1 4814 9 92966875 NM_004148 NP_004139 G/T A110D plus 6540754 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.15 0.11 0.07 212 2 120 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.677 5 moderately radical 602062 9q22 ninjurin 1 3270 rs2275848 NINJ1 4814 9 92966875 NM_004148 NP_004139 G/T A110D plus 6540754 1303 SEQUENOM CEPH CEPH (92) 92 0.05 0.11 0.07 212 2 120 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.677 5 moderately radical 602062 9q22 ninjurin 1 3271 rs2275984 GGTLA1 2687 22 22947202 NM_004121 NP_004112 C/T K330R plus 12526265 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.28 0.28 0 120 1 0.2 0 1502 1 121 "HapMap,doubleHit,freq,cluster" conservative 137168 22q11.23 gamma-glutamyltransferase-like activity 1 3272 rs2275992 ZFP91 80829 11 58135000 NM_053023 NP_444251 A/G S207G plus 16126805 1303 SEQUENOM CEPH CEPH (92) 92 0.34 0.32 0.05 140 2 0.19 0.02 1546 3 123 "by doubleHit,freq,cluster" Benign 0.9 5 Tolerant 0.37 2.82 162 moderately conservative 11q12 zinc finger protein 91 homolog (mouse) 3273 rs2275992 ZFP91 80829 11 58135000 NM_053023 NP_444251 A/G S207G plus 24560494 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.32 0.05 140 2 0.19 0.02 1546 3 123 "by doubleHit,freq,cluster" Benign 0.9 5 Tolerant 0.37 2.82 162 moderately conservative 11q12 zinc finger protein 91 homolog (mouse) 3274 rs2276038 P2RX3 5024 11 56894000 NM_002559 NP_002550 A/G A383V minus 24574003 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.33 0 48 1 0.37 0.08 1590 3 123 "by submitter,freq,cluster" Tolerant 1 3.24 17 moderately conservative 600843 11q12 "purinergic receptor P2X, ligand-gated ion channel, 3" 3275 rs2276054 LOH11CR2A 4013 11 123512182 NM_014622 NP_055437 A/C S499I minus 3212369 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.08 0.08 0 120 1 0.05 0 1482 1 100 "HapMap,freq" Benign 0.514 9 Tolerant 1 2.87 21 moderately radical 602929 11q23 "loss of heterozygosity, 11, chromosomal region 2, gene A" 3276 rs2276211 ZNF236 7776 18 72709768 NM_007345 NP_031371 A/G S166L minus 3212601 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.03 0.03 0 120 1 0.04 0 1504 1 100 "HapMap,freq" Intolerant 0 2.84 38 moderately radical 604760 18q22-q23 zinc finger protein 236 3277 rs2276360 NADSYN1 55191 11 70847195 NM_018161 NP_060631 C/G V74L plus 12160450 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.27 0.24 0.08 168 2 0.33 0.03 1584 3 123 "HapMap,doubleHit,freq,cluster" Potentially damaging 1.255 25 Tolerant 1 2.8 27 conservative 608285 11q13.2 NAD synthetase 1 3278 rs2276360 NADSYN1 55191 11 70847195 NM_018161 NP_060631 C/G V74L plus 24176611 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.24 0.08 168 2 0.33 0.03 1584 3 123 "HapMap,doubleHit,freq,cluster" Potentially damaging 1.255 25 Tolerant 1 2.8 27 conservative 608285 11q13.2 NAD synthetase 1 3279 rs2276774 SEMA5B 54437 3 124129518 NM_018987 NP_061860 C/T I220T minus 23268530 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 0.05 0.05 1594 3 123 "by submitter,freq,cluster" Benign 0.301 8 Tolerant 0.66 2.85 185 moderately conservative 3q21.1 "sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B" 3280 rs2277119 CYP39A1 51302 6 46717864 NM_016593 NP_057677 A/G R103H minus 24622412 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.29 0 48 1 0.19 0 1562 3 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.29 2.75 19 conservative 605994 6p21.1-p11.2 "cytochrome P450, family 39, subfamily A, polypeptide 1" 3281 rs2277339 PRIM1 5557 12 55432336 NM_000946 NP_000937 G/T D5A plus 3214152 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.11 0.09 0.04 166 2 0.21 0.01 1564 3 123 "HapMap,freq,cluster" Probably damaging 2.111 6 moderately radical 176635 12q13 "primase, polypeptide 1, 49kDa" 3282 rs2277339 PRIM1 5557 12 55432336 NM_000946 NP_000937 G/T D5A plus 23924102 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.09 0.04 166 2 0.21 0.01 1564 3 123 "HapMap,freq,cluster" Probably damaging 2.111 6 moderately radical 176635 12q13 "primase, polypeptide 1, 49kDa" 3283 rs2277531 ELL3 80237 15 41856361 NM_025165 NP_079441 C/G Q11E plus 3214415 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.06 0.09 0.04 274 2 0.26 0.02 1696 2 123 "HapMap,freq,cluster" conservative 15q15.1 elongation factor RNA polymerase II-like 3 3284 rs2277531 ELL3 80237 15 41856361 NM_025165 NP_079441 C/G Q11E plus 28461617 549 KYUGEN CP CEPH (78) 156 0.12 0.09 0.04 274 2 0.26 0.02 1696 2 123 "HapMap,freq,cluster" conservative 15q15.1 elongation factor RNA polymerase II-like 3 3285 rs2277680 CXCL16 58191 17 4585312 NM_022059 NP_071342 A/G A200V plus 24213399 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.35 0 48 1 0.34 0.08 94 2 123 "by doubleHit,freq,cluster" moderately conservative 605398 17p13 chemokine (C-X-C motif) ligand 16 3286 rs2277838 P2RXL1 9127 22 19702204 NM_005446 NP_005437 A/G R232H plus 24702936 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.21 0 48 1 0.02 0 1454 1 123 by freq Intolerant 0.03 2.78 64 conservative 608077 22q11.21 "purinergic receptor P2X-like 1, orphan receptor" 3287 rs2278008 AMACR 23600 5 34025275 NM_014324 NP_055139 C/T E277K plus 12675252 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.32 0.28 0.06 320 4 0.19 0.07 1896 7 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.262 13 Tolerant 0.71 2.81 40 moderately conservative 604489 5p13.2-q11.1 alpha-methylacyl-CoA racemase 3288 rs2278008 AMACR 23600 5 34025275 NM_014324 NP_055139 C/T E277K plus 12675252 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.24 0.28 0.06 320 4 0.19 0.07 1896 7 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.262 13 Tolerant 0.71 2.81 40 moderately conservative 604489 5p13.2-q11.1 alpha-methylacyl-CoA racemase 3289 rs2278008 AMACR 23600 5 34025275 NM_014324 NP_055139 C/T E277K plus 12675252 1303 SEQUENOM CEPH CEPH (92) 92 0.35 0.28 0.06 320 4 0.19 0.07 1896 7 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.262 13 Tolerant 0.71 2.81 40 moderately conservative 604489 5p13.2-q11.1 alpha-methylacyl-CoA racemase 3290 rs2278008 AMACR 23600 5 34025275 NM_014324 NP_055139 C/T E277K plus 23457404 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.28 0.06 320 4 0.19 0.07 1896 7 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.262 13 Tolerant 0.71 2.81 40 moderately conservative 604489 5p13.2-q11.1 alpha-methylacyl-CoA racemase 3291 rs2278106 EPHA7 2045 6 94176940 NM_004440 NP_004431 A/G P278S plus 3215180 902 AFFY Caucasian 20 0.05 0.05 0 20 1 0.14 0.01 1560 3 100 by freq Borderline 1.197 89 Intolerant 0.05 2.81 84 moderately conservative 602190 6q16.1 EphA7 3292 rs2278176 PVT1 5820 8 129020987 XM_372058 XP_372058 C/T H125Y plus 13436201 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.31 0.31 0 120 1 119 "HapMap,freq,cluster" moderately conservative 165140 8q24 "Pvt1 oncogene homolog, MYC activator (mouse)" 3293 rs2278370 FAT2 2196 5 150910379 NM_001447 NP_001438 C/T G1515S plus 3215557 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.06 0.06 0 120 1 0.17 0 1488 1 120 "HapMap,doubleHit,freq,cluster" Tolerant 0.32 2.82 16 moderately conservative 604269 5q32-q33 FAT tumor suppressor homolog 2 (Drosophila) 3294 rs2278371 FAT2 2196 5 150910538 NM_001447 NP_001438 C/T V1462M plus 24198513 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.17 0 48 1 0.22 0.03 1570 3 123 "by submitter,freq,cluster" Borderline 0.13 2.82 16 conservative 604269 5q32-q33 FAT tumor suppressor homolog 2 (Drosophila) 3295 rs2278415 ZNF350 59348 19 57160015 NM_021632 NP_067645 A/T R501S plus 5586998 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.23 0.22 0.02 108 2 0.22 0.03 2032 8 123 "by submitter,freq,cluster" Borderline 0.18 2.81 34 moderately radical 605422 19q13.41 zinc finger protein 350 3296 rs2278415 ZNF350 59348 19 57160015 NM_021632 NP_067645 A/T R501S plus 24203888 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.2 0.22 0.02 108 2 0.22 0.03 2032 8 123 "by submitter,freq,cluster" Borderline 0.18 2.81 34 moderately radical 605422 19q13.41 zinc finger protein 350 3297 rs2278420 ZNF350 59348 19 57163684 NM_021632 NP_067645 A/G L66P plus 5586996 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.27 0.25 0.03 108 2 0.24 0.05 2056 8 123 "by doubleHit,submitter,freq,cluster" Benign 0.502 5 Tolerant 0.82 2.76 37 moderately conservative 605422 19q13.41 zinc finger protein 350 3298 rs2278420 ZNF350 59348 19 57163684 NM_021632 NP_067645 A/G L66P plus 23776840 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.22 0.25 0.03 108 2 0.24 0.05 2056 8 123 "by doubleHit,submitter,freq,cluster" Benign 0.502 5 Tolerant 0.82 2.76 37 moderately conservative 605422 19q13.41 zinc finger protein 350 3299 rs2278428 NCR1 9437 19 60109866 NM_004829 NP_004820 A/C K82Q plus 24200495 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.39 0.04 1350 2 123 by freq Potentially damaging 1.26 13 Tolerant 0.36 2.87 39 moderately conservative 604530 19q13.42 natural cytotoxicity triggering receptor 1 3300 rs2278586 OXER1 165140 2 42901752 NM_148962 NP_683765 C/G L407V plus 23871598 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.23 0 48 1 0.32 0.02 1558 3 123 "by doubleHit,submitter,freq,cluster" Tolerant 1 2.91 27 conservative 2p22.1 oxoeicosanoid (OXE) receptor 1 3301 rs2278831 SIGLEC5 8778 19 56822931 NM_003830 NP_003821 A/G F322S plus 3216216 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.06 0.06 0 118 1 100 "HapMap,freq" Tolerant 1 2.82 27 radical 604200 19q13.3 sialic acid binding Ig-like lectin 5 3302 rs2278868 SCAP1 8631 17 43617170 NM_003726 NP_003717 C/T G161S plus 10852511 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.33 0.34 0.03 168 2 0.22 0.03 1596 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 604969 17q21.32 src family associated phosphoprotein 1 3303 rs2278868 SCAP1 8631 17 43617170 NM_003726 NP_003717 C/T G161S plus 24579848 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.34 0.03 168 2 0.22 0.03 1596 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 604969 17q21.32 src family associated phosphoprotein 1 3304 rs2279112 NOV 4856 8 120498205 NM_002514 NP_002505 A/G R42Q plus 23386113 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.22 0.22 0 46 1 0.21 0.22 86 2 123 "by doubleHit,freq,cluster" Tolerant 0.93 2.99 41 conservative 164958 8q24.1 nephroblastoma overexpressed gene 3305 rs2279587 ITGA1 3672 5 52250338 NM_181501 NP_852478 C/T V670I minus 23982908 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.06 0.03 94 2 123 "by submitter,freq,cluster" Tolerant 0.48 2.76 17 conservative 192968 5q11.2 "integrin, alpha 1" 3306 rs2280026 MBTPS1 8720 16 82645527 NM_201268 NP_957720 A/G Q634R minus 3217931 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.04 0.04 0 118 1 0.25 0 1480 1 120 "HapMap,freq,cluster" conservative 603355 16q24 "membrane-bound transcription factor protease, site 1" 3307 rs2281891 CYP2C18 1562 10 96483048 NM_000772 NP_000763 A/G T385M minus 24092193 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.27 0.03 1558 3 123 "by submitter,freq,cluster" Benign 0.832 162 Intolerant 0 2.79 164 moderately conservative 601131 10q24 "cytochrome P450, family 2, subfamily C, polypeptide 18" 3308 rs2281939 SORBS1 10580 10 97164342 NM_015385 NP_056200 A/G T205A minus 23589374 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.12 0.15 90 2 123 "by cluster,freq" Potentially damaging 1.486 5 moderately conservative 605264 10q23.3-q24.1 sorbin and SH3 domain containing 1 3309 rs2282076 ZFP37 7539 9 112898504 NM_003408 NP_003399 A/T V7D minus 3220843 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.42 0.4 0.04 166 2 0.39 0.03 1554 3 123 "HapMap,doubleHit,submitter,freq,cluster" radical 602951 9q32 zinc finger protein 37 homolog (mouse) 3310 rs2282076 ZFP37 7539 9 112898504 NM_003408 NP_003399 A/T V7D minus 24049399 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.35 0.4 0.04 166 2 0.39 0.03 1554 3 123 "HapMap,doubleHit,submitter,freq,cluster" radical 602951 9q32 zinc finger protein 37 homolog (mouse) 3311 rs2282537 POU2F3 25833 11 119693181 NM_014352 NP_055167 C/T R390K minus 3221563 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.12 0.12 0 120 1 0.18 0 1488 1 100 "HapMap,freq" Benign 0.675 8 conservative 607394 11q23.3 "POU domain, class 2, transcription factor 3" 3312 rs2285487 XPMC2H 57109 9 133307036 NM_020385 NP_065118 C/T T283A plus 23650917 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.02 0.02 0 42 1 0.05 0 44 1 123 "by cluster,freq" Potentially damaging 1.486 5 Tolerant 0.65 2.78 37 moderately conservative 602930 9q34.3 XPMC2 prevents mitotic catastrophe 2 homolog (Xenopus laevis) 3313 rs2286007 PRKWNK1 65125 12 841552 NM_018979 NP_061852 C/T T665I plus 3226322 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.06 0.05 0.01 190 3 0.07 0.02 1636 5 123 "HapMap,freq,cluster" Potentially intolerant 0.07 3.02 22 moderately conservative 605232 12p13.3 "protein kinase, lysine deficient 1" 3314 rs2286007 PRKWNK1 65125 12 841552 NM_018979 NP_061852 C/T T665I plus 3226322 902 AFFY Caucasian 24 0.04 0.05 0.01 190 3 0.07 0.02 1636 5 123 "HapMap,freq,cluster" Potentially intolerant 0.07 3.02 22 moderately conservative 605232 12p13.3 "protein kinase, lysine deficient 1" 3315 rs2286007 PRKWNK1 65125 12 841552 NM_018979 NP_061852 C/T T665I plus 24137264 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.04 0.05 0.01 190 3 0.07 0.02 1636 5 123 "HapMap,freq,cluster" Potentially intolerant 0.07 3.02 22 moderately conservative 605232 12p13.3 "protein kinase, lysine deficient 1" 3316 rs2286963 ACADL 33 2 210885556 NM_001608 NP_001599 G/T K333Q plus 3227594 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.38 0.35 0.06 168 2 0.17 0 94 2 123 "HapMap,submitter,freq" Potentially damaging 1.272 10 Tolerant 0.3 2.78 36 moderately conservative 201460 2q34-q35 "acyl-Coenzyme A dehydrogenase, long chain" 3317 rs2286963 ACADL 33 2 210885556 NM_001608 NP_001599 G/T K333Q plus 24303063 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.35 0.06 168 2 0.17 0 94 2 123 "HapMap,submitter,freq" Potentially damaging 1.272 10 Tolerant 0.3 2.78 36 moderately conservative 201460 2q34-q35 "acyl-Coenzyme A dehydrogenase, long chain" 3318 rs2287622 ABCB11 8647 2 169655835 NM_003742 NP_003733 C/T V444A minus 5326526 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.42 0.42 0 118 1 0.33 0.09 1962 2 121 "HapMap,doubleHit,freq,cluster" Benign 0.351 10 Borderline 0.11 2.86 31 moderately conservative 603201 2q24 "ATP-binding cassette, sub-family B (MDR/TAP), member 11" 3319 rs2287679 GPATC1 55094 19 38292604 NM_018025 NP_060495 C/T L476P plus 12472236 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.18 0.18 0 120 1 0.43 0 1108 1 120 "HapMap,doubleHit,freq,cluster" Tolerant 0.3 2.83 12 moderately conservative 19q13.12 G patch domain containing 1 3320 rs2287749 ADAM19 8728 5 156851428 NM_033274 NP_150377 C/T G660D plus 3228663 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.19 0.18 0.01 208 3 0.02 0.01 1606 4 123 "HapMap,submitter,freq,cluster" Tolerant 0.31 2.8 22 moderately conservative 603640 5q32-q33 a disintegrin and metalloproteinase domain 19 (meltrin beta) 3321 rs2287749 ADAM19 8728 5 156851428 NM_033274 NP_150377 C/T G660D plus 15357331 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.18 0.18 0.01 208 3 0.02 0.01 1606 4 123 "HapMap,submitter,freq,cluster" Tolerant 0.31 2.8 22 moderately conservative 603640 5q32-q33 a disintegrin and metalloproteinase domain 19 (meltrin beta) 3322 rs2287749 ADAM19 8728 5 156851428 NM_033274 NP_150377 C/T G660D plus 24476331 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.18 0.01 208 3 0.02 0.01 1606 4 123 "HapMap,submitter,freq,cluster" Tolerant 0.31 2.8 22 moderately conservative 603640 5q32-q33 a disintegrin and metalloproteinase domain 19 (meltrin beta) 3323 rs2287798 AQP8 343 16 25147306 NM_001169 NP_001160 C/G A260P minus 24004952 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.3 0.3 0 46 1 0.49 0.03 1340 3 123 "by cluster,freq" conservative 603750 16p12 aquaporin 8 3324 rs2287926 CSPG2 1462 5 82851164 NM_004385 NP_004376 A/G G428D plus 3228889 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.08 0.08 0 120 1 0.16 0 1448 1 100 "HapMap,freq" Tolerant 0.24 2.78 18 moderately conservative 118661 5q14.3 chondroitin sulfate proteoglycan 2 (versican) 3325 rs2287939 AMACR 23600 5 34034640 NM_014324 NP_055139 C/T L201S minus 12675256 775 SNP500CANCER CAUC1 Caucasian (31) 58 0.35 0.35 0 58 1 0.3 0.11 334 4 121 "by doubleHit,freq,cluster" Benign 0.296 14 Tolerant 0.7 2.81 40 moderately radical 604489 5p13.2-q11.1 alpha-methylacyl-CoA racemase 3326 rs2288466 CDH9 1007 5 27024085 NM_016279 NP_057363 A/G A38V plus 24361876 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.44 0 48 1 0.24 0.05 94 2 123 "by doubleHit,submitter,freq,cluster" Borderline 1.001 23 Tolerant 0.29 3.15 36 moderately conservative 5p14 "cadherin 9, type 2 (T1-cadherin)" 3327 rs2288467 CDH9 1007 5 27024181 NM_016279 NP_057363 C/T Y6C plus 24361890 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.44 0 48 1 0.31 0.14 94 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.818 19 radical 5p14 "cadherin 9, type 2 (T1-cadherin)" 3328 rs2288675 ANP32C 23520 4 165476257 NM_012403 NP_036535 A/G R71K minus 24660475 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.46 0 48 1 0.13 0.01 1562 3 123 "by submitter,freq" Possibly damaging 1.555 43 Tolerant 0.37 2.81 51 conservative 606877 4q32.3 "acidic (leucine-rich) nuclear phosphoprotein 32 family, member C" 3329 rs2288868 ZNF577 84765 19 57068319 NM_032679 NP_116068 C/T K239E plus 12457682 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.38 0.38 0 120 1 0.31 0 1488 1 119 "HapMap,doubleHit,freq,cluster" moderately conservative 19q13.41 zinc finger protein 577 3330 rs2289043 UNC5C 8633 4 96463500 NM_003728 NP_003719 C/T M721T minus 23919947 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.33 0 48 1 0.37 0.03 1186 3 123 "by doubleHit,submitter,freq,cluster" Probably damaging 2.259 16 moderately conservative 603610 4q21-q23 unc-5 homolog C (C. elegans) 3331 rs2289520 SERPINB5 5268 18 59311300 NM_002639 NP_002630 C/G V187L plus 23499116 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.25 0.05 1586 3 123 by freq conservative 154790 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 5" 3332 rs2289664 CDH2 1000 18 23786302 NM_001792 NP_001783 C/T N845S plus 3231241 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.02 0.02 0 120 1 0.02 0 1484 1 100 "HapMap,freq" Possibly damaging 1.593 15 Tolerant 0.45 2.83 40 conservative 114020 18q11.2 "cadherin 2, type 1, N-cadherin (neuronal)" 3333 rs2290480 PLD1 5337 3 172887180 NM_002662 NP_002653 A/C A622S plus 3232391 902 AFFY Caucasian 20 0.15 0.15 0 20 1 0.13 0.01 1560 4 100 by freq Benign 0.395 11 Tolerant 0.73 2.92 17 moderately conservative 602382 3q26 "phospholipase D1, phophatidylcholine-specific" 3334 rs2291087 ITGB5 3693 3 125998188 NM_002213 NP_002204 C/T N477S plus 23673373 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.02 0 46 1 123 "by doubleHit,freq,cluster" Benign 0.307 37 Tolerant 0.78 2.79 61 conservative 147561 3q21.2 "integrin, beta 5" 3335 rs2291090 ITGB5 3693 3 125998336 NM_002213 NP_002204 A/C L428V plus 23673375 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.02 0 46 1 123 "by submitter,freq,cluster" Borderline 1.201 37 Tolerant 1 2.79 61 conservative 147561 3q21.2 "integrin, beta 5" 3336 rs2291569 FLNC 2318 7 128082685 NM_001458 NP_001449 A/G R1547Q plus 24447614 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.14 0.03 1564 3 123 by freq Possibly damaging 1.529 20 Tolerant 0.21 2.91 26 conservative 102565 7q32-q35 "filamin C, gamma (actin binding protein 280)" 3337 rs2291725 GIP 2695 17 44394131 NM_004123 NP_004114 C/T S103G plus 24541002 1371 PERLEGEN AFD_EUR_PANEL European American (24) 20 0.5 0.5 0 20 1 0.27 0.02 1552 3 123 by freq moderately conservative 137240 17q21.3-q22 gastric inhibitory polypeptide 3338 rs2291739 TIMELESS 8914 12 55100920 NM_003920 NP_003911 C/T P1018L minus 19232977 1303 SEQUENOM CEPH CEPH (92) 92 0.39 0.36 0.06 138 2 0.43 0.03 1592 3 123 "by submitter,freq,cluster" Intolerant 0.03 2.89 14 moderately conservative 603887 12q12-q13 timeless homolog (Drosophila) 3339 rs2291739 TIMELESS 8914 12 55100920 NM_003920 NP_003911 C/T P1018L minus 23448306 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.3 0.36 0.06 138 2 0.43 0.03 1592 3 123 "by submitter,freq,cluster" Intolerant 0.03 2.89 14 moderately conservative 603887 12q12-q13 timeless homolog (Drosophila) 3340 rs2292245 PTPRG 5793 3 62164229 NM_002841 NP_002832 A/G G574S plus 3234845 885 TSC-CSHL HapMap-CEPH-30-trios 108 0.14 0.14 0.01 156 2 0.23 0.02 1544 3 123 "HapMap,submitter,freq,cluster" Potentially damaging 1.396 6 moderately conservative 176886 3p21-p14 "protein tyrosine phosphatase, receptor type, G" 3341 rs2292245 PTPRG 5793 3 62164229 NM_002841 NP_002832 A/G G574S plus 23872438 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.14 0.01 156 2 0.23 0.02 1544 3 123 "HapMap,submitter,freq,cluster" Potentially damaging 1.396 6 moderately conservative 176886 3p21-p14 "protein tyrosine phosphatase, receptor type, G" 3342 rs2292596 AHRR 57491 5 475955 NM_020731 NP_065782 C/G P185A minus 7986195 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.33 0.38 0.05 174 2 0.36 0.06 1832 5 121 "HapMap,freq,cluster" Tolerant 0.54 2.98 62 conservative 606517 5p15.3 aryl-hydrocarbon receptor repressor 3343 rs2292596 AHRR 57491 5 475955 NM_020731 NP_065782 C/G P185A minus 7986195 885 TSC-CSHL HapMap-CEPH-30-trios 114 0.41 0.38 0.05 174 2 0.36 0.06 1832 5 121 "HapMap,freq,cluster" Tolerant 0.54 2.98 62 conservative 606517 5p15.3 aryl-hydrocarbon receptor repressor 3344 rs2292954 SPG7 6687 16 88140624 NM_003119 NP_003110 C/T T503A minus 24695014 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.19 0 48 1 0.11 0.02 1598 3 123 "by cluster,freq" Benign 0.062 9 Tolerant 0.25 2.74 65 moderately conservative 602783 16q24.3 "spastic paraplegia 7, paraplegin (pure and complicated autosomal recessive)" 3345 rs2293180 KSR 8844 17 22933943 XM_290793 XP_290793 C/T A337V plus 6618407 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.14 0.14 0 120 1 0.27 0 1470 1 111 "HapMap,freq,cluster" moderately conservative 601132 17q11.2 kinase suppressor of ras 3346 rs2293275 LHCGR 3973 2 48833026 NM_000233 NP_000224 A/G N312S minus 24637400 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.35 0 48 1 0.07 0.03 1568 3 123 "by submitter,freq,cluster" Benign 0.234 39 conservative 152790 2p21 luteinizing hormone/choriogonadotropin receptor 3347 rs2293869 RP1 6101 8 55701948 NM_006269 NP_006260 A/T N985Y plus 3237063 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.45 0.45 0.02 150 3 0.12 0.04 1532 3 100 "HapMap,freq" Probably damaging 2.374 6 moderately radical 603937 8q11-q13 retinitis pigmentosa 1 (autosomal dominant) 3348 rs2293869 RP1 6101 8 55701948 NM_006269 NP_006260 A/T N985Y plus 3237063 902 AFFY Caucasian 24 0.42 0.45 0.02 150 3 0.12 0.04 1532 3 100 "HapMap,freq" Probably damaging 2.374 6 moderately radical 603937 8q11-q13 retinitis pigmentosa 1 (autosomal dominant) 3349 rs2293869 RP1 6101 8 55701948 NM_006269 NP_006260 A/T N985Y plus 3237063 904 AFFY CEPH 6 0.5 0.45 0.02 150 3 0.12 0.04 1532 3 100 "HapMap,freq" Probably damaging 2.374 6 moderately radical 603937 8q11-q13 retinitis pigmentosa 1 (autosomal dominant) 3350 rs2293925 TOP1MT 116447 8 144463743 NM_052963 NP_443195 A/G R525W plus 22709157 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.45 0.29 0.2 252 3 0.29 0.05 1548 2 123 "HapMap,freq,cluster" Possibly damaging 1.693 33 Intolerant 0 2.79 52 moderately radical 606387 8q24.3 mitochondrial topoisomerase I 3351 rs2293925 TOP1MT 116447 8 144463743 NM_052963 NP_443195 A/G R525W plus 22709157 1303 SEQUENOM CEPH CEPH (92) 92 0.2 0.29 0.2 252 3 0.29 0.05 1548 2 123 "HapMap,freq,cluster" Possibly damaging 1.693 33 Intolerant 0 2.79 52 moderately radical 606387 8q24.3 mitochondrial topoisomerase I 3352 rs2293925 TOP1MT 116447 8 144463743 NM_052963 NP_443195 A/G R525W plus 23372055 1371 PERLEGEN AFD_EUR_PANEL European American (24) 40 0.03 0.29 0.2 252 3 0.29 0.05 1548 2 123 "HapMap,freq,cluster" Possibly damaging 1.693 33 Intolerant 0 2.79 52 moderately radical 606387 8q24.3 mitochondrial topoisomerase I 3353 rs2294008 PSCA 8000 8 143758933 NM_005672 NP_005663 C/T T1M plus 11959612 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.42 0.43 0.03 168 2 0.36 0.01 1588 3 123 "HapMap,doubleHit,freq,cluster" moderately conservative 602470 8q24.2 prostate stem cell antigen 3354 rs2294008 PSCA 8000 8 143758933 NM_005672 NP_005663 C/T T1M plus 24395070 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.43 0.03 168 2 0.36 0.01 1588 3 123 "HapMap,doubleHit,freq,cluster" moderately conservative 602470 8q24.2 prostate stem cell antigen 3355 rs2294013 ANXA13 312 8 124779910 NM_004306 NP_004297 A/G R86H minus 3237284 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.26 0.3 0.09 168 2 0.15 0.01 1582 3 123 "HapMap,submitter,freq" Possibly damaging 1.665 17 Intolerant 0.04 2.81 131 conservative 602573 8q24.1-q24.2 annexin A13 3356 rs2294013 ANXA13 312 8 124779910 NM_004306 NP_004297 A/G R86H minus 24528510 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.3 0.09 168 2 0.15 0.01 1582 3 123 "HapMap,submitter,freq" Possibly damaging 1.665 17 Intolerant 0.04 2.81 131 conservative 602573 8q24.1-q24.2 annexin A13 3357 rs2294015 ANXA13 312 8 124766048 NM_004306 NP_004297 A/G V272I minus 11925585 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.47 0.44 0.08 168 2 0.31 0.25 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.506 17 Tolerant 0.75 2.81 131 conservative 602573 8q24.1-q24.2 annexin A13 3358 rs2294015 ANXA13 312 8 124766048 NM_004306 NP_004297 A/G V272I minus 24070475 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.44 0.08 168 2 0.31 0.25 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.506 17 Tolerant 0.75 2.81 131 conservative 602573 8q24.1-q24.2 annexin A13 3359 rs2294451 CHTF18 63922 16 787744 NM_022092 NP_071375 C/T P928L plus 6901119 1303 SEQUENOM CEPH CEPH (92) 92 0.13 0.13 0 92 1 0.3 0 1464 1 123 "by doubleHit,freq,cluster" Probably damaging 2.724 6 moderately conservative 16p13.3 "CTF18, chromosome transmission fidelity factor 18 homolog (S. cerevisiae)" 3360 rs2294689 TTRAP 51567 6 24761252 NM_016614 NP_057698 C/G Q249E minus 4403022 649 FHCRC POPU1 USA (20) 40 0.15 0.12 0.04 88 2 0.44 0.06 1574 3 123 "by submitter,freq,cluster" Borderline 0.19 2.84 9 conservative 605764 6p22.3-p22.1 TRAF and TNF receptor associated protein 3361 rs2294689 TTRAP 51567 6 24761252 NM_016614 NP_057698 C/G Q249E minus 24166776 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.12 0.04 88 2 0.44 0.06 1574 3 123 "by submitter,freq,cluster" Borderline 0.19 2.84 9 conservative 605764 6p22.3-p22.1 TRAF and TNF receptor associated protein 3362 rs2294757 VNN1 8876 6 133076791 NM_004666 NP_004657 A/G T26I plus 24477573 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.43 0.43 0 46 1 0.38 0.06 1590 3 123 "by doubleHit,submitter,freq,cluster" Possibly damaging 1.849 16 moderately conservative 603570 6q23-q24 vanin 1 3363 rs2295000 DATF1 11083 20 61007383 NM_080797 NP_542987 A/G S535L plus 24538413 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.19 0 48 1 0.33 0.08 842 3 123 "by cluster,freq" moderately radical 604140 20q13.33 death associated transcription factor 1 3364 rs2295615 CD48 962 1 157467831 NM_001778 NP_001769 C/G E102Q plus 11387295 902 AFFY Caucasian 24 0.17 0.21 0.11 84 3 0.08 0.01 1656 5 123 "by cluster,freq" Intolerant 0.03 2.79 21 conservative 109530 1q21.3-q22 CD48 antigen (B-cell membrane protein) 3365 rs2295615 CD48 962 1 157467831 NM_001778 NP_001769 C/G E102Q plus 11387295 904 AFFY CEPH 12 0.42 0.21 0.11 84 3 0.08 0.01 1656 5 123 "by cluster,freq" Intolerant 0.03 2.79 21 conservative 109530 1q21.3-q22 CD48 antigen (B-cell membrane protein) 3366 rs2295615 CD48 962 1 157467831 NM_001778 NP_001769 C/G E102Q plus 24633582 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.21 0.11 84 3 0.08 0.01 1656 5 123 "by cluster,freq" Intolerant 0.03 2.79 21 conservative 109530 1q21.3-q22 CD48 antigen (B-cell membrane protein) 3367 rs2295769 SERPINB6 5269 6 2900801 NM_004568 NP_004559 C/T M90V plus 3239646 1303 SEQUENOM CEPH CEPH (92) 91 0.35 0.39 0.07 139 2 0.27 0.05 1572 3 123 "by submitter,freq,cluster" Benign 0.431 38 Tolerant 1 2.82 62 conservative 173321 6p25 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 6" 3368 rs2295769 SERPINB6 5269 6 2900801 NM_004568 NP_004559 C/T M90V plus 24423703 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.39 0.07 139 2 0.27 0.05 1572 3 123 "by submitter,freq,cluster" Benign 0.431 38 Tolerant 1 2.82 62 conservative 173321 6p25 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 6" 3369 rs2295778 HIF1AN 55662 10 102285826 NM_017902 NP_060372 C/G P41A plus 8819751 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.26 0.25 0.02 110 2 0.22 0.05 1904 7 123 "by submitter,freq,cluster" Possibly damaging 1.679 6 conservative 606615 10q24 "hypoxia-inducible factor 1, alpha subunit inhibitor" 3370 rs2295778 HIF1AN 55662 10 102285826 NM_017902 NP_060372 C/G P41A plus 24036640 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.25 0.02 110 2 0.22 0.05 1904 7 123 "by submitter,freq,cluster" Possibly damaging 1.679 6 conservative 606615 10q24 "hypoxia-inducible factor 1, alpha subunit inhibitor" 3371 rs2296556 FRMPD1 22844 9 37697441 NM_014907 NP_055722 C/T A44T minus 24090638 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.42 0.09 1586 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 9p13.1 FERM and PDZ domain containing 1 3372 rs2296961 PDLIM1 9124 10 97013620 NM_020992 NP_066272 C/T N175S plus 16490192 1303 SEQUENOM CEPH CEPH (92) 92 0.31 0.31 0 92 1 0.05 0 1476 1 121 "by doubleHit,freq,cluster" Benign 0.228 14 Tolerant 0.52 2.8 35 conservative 605900 10q22-q26.3 PDZ and LIM domain 1 (elfin) 3373 rs2297019 MEP1A 4224 6 46911061 NM_005588 NP_005579 C/T M634V minus 23434119 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.25 0 48 1 0.28 0.05 840 3 123 "by doubleHit,submitter,freq,cluster" Benign 0.9 6 conservative 600388 6p12-p11 "meprin A, alpha (PABA peptide hydrolase)" 3374 rs2297236 ZC3HAV1 56829 7 138197292 NM_020119 NP_064504 C/G Q701E plus 24478699 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.44 0 48 1 0.27 0.15 90 2 123 by freq Tolerant 1 3 26 conservative 607312 7q34 "zinc finger CCCH type, antiviral 1" 3375 rs2297603 COL15A1 1306 9 98857820 NM_001855 NP_001846 A/C G504V minus 3242125 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.13 0.12 0.02 168 2 0.14 0.01 1544 2 123 "HapMap,freq,cluster" Intolerant 0.01 2.88 64 moderately radical 120325 9q21-q22 "collagen, type XV, alpha 1" 3376 rs2297603 COL15A1 1306 9 98857820 NM_001855 NP_001846 A/C G504V minus 24169527 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.12 0.02 168 2 0.14 0.01 1544 2 123 "HapMap,freq,cluster" Intolerant 0.01 2.88 64 moderately radical 120325 9q21-q22 "collagen, type XV, alpha 1" 3377 rs2297809 CYP4B1 1580 1 46994792 NM_000779 NP_000770 A/G R375C minus 23843621 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.21 0.01 92 2 123 "by cluster,freq" Probably damaging 2.792 45 Intolerant 0 2.8 89 radical 124075 1p34-p12 "cytochrome P450, family 4, subfamily B, polypeptide 1" 3378 rs2297810 CYP4B1 1580 1 46992879 NM_000779 NP_000770 C/T M331I minus 23160478 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.32 0.03 1576 3 123 "by doubleHit,submitter,freq,cluster" Possibly damaging 1.862 45 Intolerant 0.01 2.8 89 conservative 124075 1p34-p12 "cytochrome P450, family 4, subfamily B, polypeptide 1" 3379 rs2297950 CHIT1 1118 1 199925843 NM_003465 NP_003456 C/T G102S plus 24256571 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.4 0 48 1 0.29 0.01 1398 3 123 "by doubleHit,submitter,freq,cluster" Possibly damaging 1.917 22 Intolerant 0 2.8 59 moderately conservative 600031 1q31-q32 chitinase 1 (chitotriosidase) 3380 rs2297970 AIM1 202 6 107106515 XM_166300 XP_166300 A/G C2018Y plus 24361060 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.25 0 48 1 0.08 0.01 838 3 123 by freq radical 601797 6q21 absent in melanoma 1 3381 rs2297980 TINAG 27283 6 54281372 NM_014464 NP_055279 C/T Q22R minus 23339795 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.01 0.02 1538 2 123 "by cluster,freq" Benign 0.098 5 conservative 606749 6p11.2-p12 tubulointerstitial nephritis antigen 3382 rs2298033 ITGA8 8516 10 15689716 XM_167711 XP_167711 C/T S707F minus 12675949 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.02 0.02 0 140 3 0.11 0.03 1666 5 123 "by cluster,freq" radical 604063 10p13 "integrin, alpha 8" 3383 rs2298033 ITGA8 8516 10 15689716 XM_167711 XP_167711 C/T S707F minus 16361674 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.02 0.02 0 140 3 0.11 0.03 1666 5 123 "by cluster,freq" radical 604063 10p13 "integrin, alpha 8" 3384 rs2298033 ITGA8 8516 10 15689716 XM_167711 XP_167711 C/T S707F minus 24075001 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 140 3 0.11 0.03 1666 5 123 "by cluster,freq" radical 604063 10p13 "integrin, alpha 8" 3385 rs2298553 MS4A12 54860 11 60021578 NM_017716 NP_060186 C/T Q71X plus 24103616 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.42 0 48 1 0.42 0.01 816 3 123 "by doubleHit,freq,cluster" Probably damaging Intolerant radical 606550 11q12 "membrane-spanning 4-domains, subfamily A, member 12" 3386 rs2298668 PRCP 5547 11 82241942 NM_005040 NP_005031 A/C E112D minus 16180875 885 TSC-CSHL HapMap-CEPH-30-trios 112 0.07 0.09 0.05 160 2 0.1 0.01 1566 3 123 "HapMap,freq,cluster" Potentially damaging 1.245 8 Borderline 0.15 2.85 25 conservative 176785 11q14 prolylcarboxypeptidase (angiotensinase C) 3387 rs2298668 PRCP 5547 11 82241942 NM_005040 NP_005031 A/C E112D minus 24572807 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.09 0.05 160 2 0.1 0.01 1566 3 123 "HapMap,freq,cluster" Potentially damaging 1.245 8 Borderline 0.15 2.85 25 conservative 176785 11q14 prolylcarboxypeptidase (angiotensinase C) 3388 rs2298813 SORL1 6653 11 120898894 NM_003105 NP_003096 A/G A528T plus 3243868 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.05 0.05 0.01 162 2 0.15 0.02 1560 3 123 "HapMap,freq,cluster" moderately conservative 602005 11q23.2-q24.2 "sortilin-related receptor, L(DLR class) A repeats-containing" 3389 rs2298813 SORL1 6653 11 120898894 NM_003105 NP_003096 A/G A528T plus 24149631 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.04 0.05 0.01 162 2 0.15 0.02 1560 3 123 "HapMap,freq,cluster" moderately conservative 602005 11q23.2-q24.2 "sortilin-related receptor, L(DLR class) A repeats-containing" 3390 rs2301246 CTRL 1506 16 66521704 NM_001907 NP_001898 A/G H173R minus 3247158 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.15 0.17 0.04 168 2 0.15 0.06 1580 3 123 "HapMap,freq,cluster" Benign 0.038 35 Tolerant 0.54 2.78 66 conservative 118888 16q22.1 chymotrypsin-like 3391 rs2301246 CTRL 1506 16 66521704 NM_001907 NP_001898 A/G H173R minus 23759013 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.17 0.04 168 2 0.15 0.06 1580 3 123 "HapMap,freq,cluster" Benign 0.038 35 Tolerant 0.54 2.78 66 conservative 118888 16q22.1 chymotrypsin-like 3392 rs2301721 HOXA7 3204 7 26969353 NM_006896 NP_008827 C/T A18T plus 17152392 885 TSC-CSHL HapMap-CEPH-30-trios 104 0.14 0.14 0 104 1 0.17 0 1492 1 121 "HapMap,doubleHit,freq,cluster" Benign 0.456 16 Tolerant 0.46 2.89 26 moderately conservative 142950 7p15-p14 homeo box A7 3393 rs2301870 LPO 4025 17 53687326 NM_006151 NP_006142 C/T V421M minus 9806412 693 EGP_SNPS PDR90 NIHPDR 178 0.11 0.09 0.03 298 2 0.08 0 1502 1 117 "HapMap,freq,cluster" Benign 0.385 20 Tolerant 0.3 2.77 33 conservative 150205 17q23.1 lactoperoxidase 3394 rs2301870 LPO 4025 17 53687326 NM_006151 NP_006142 C/T V421M minus 9806412 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.06 0.09 0.03 298 2 0.08 0 1502 1 117 "HapMap,freq,cluster" Benign 0.385 20 Tolerant 0.3 2.77 33 conservative 150205 17q23.1 lactoperoxidase 3395 rs2301963 DLGAP2 9228 8 1501416 NM_004745 NP_004736 A/C P384Q plus 24689867 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.44 0 48 1 0.48 0.04 1586 3 123 "by submitter,freq,cluster" Potentially damaging 1.41 8 moderately conservative 605438 8p23 "discs, large (Drosophila) homolog-associated protein 2" 3396 rs2302311 EPX 8288 17 53635446 NM_000502 NP_000493 A/T N572Y plus 3248554 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.01 0.01 0 120 1 0.03 0 1492 1 100 HapMap Probably damaging 2.317 20 Intolerant 0 2.8 33 moderately radical 131399 17q23.1 eosinophil peroxidase 3397 rs2302464 BST1 683 4 15385521 NM_004334 NP_004325 C/T R145Q minus 3248741 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.02 0.02 0 120 1 0.25 0 736 1 100 "HapMap,freq" Tolerant 0.33 2.95 13 conservative 600387 4p15 bone marrow stromal cell antigen 1 3398 rs2302465 BST1 683 4 15385461 NM_004334 NP_004325 C/T R125H minus 3248742 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.15 0.14 0.01 164 2 0.04 0 1480 1 123 "HapMap,freq" Borderline 0.12 2.79 14 conservative 600387 4p15 bone marrow stromal cell antigen 1 3399 rs2302465 BST1 683 4 15385461 NM_004334 NP_004325 C/T R125H minus 24347796 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.14 0.01 164 2 0.04 0 1480 1 123 "HapMap,freq" Borderline 0.12 2.79 14 conservative 600387 4p15 bone marrow stromal cell antigen 1 3400 rs2302515 APOBEC1 339 12 7696503 NM_001644 NP_001635 C/G M80I plus 12183575 1303 SEQUENOM CEPH CEPH (92) 92 0.13 0.13 0 92 1 121 "by doubleHit,freq,cluster" Potentially damaging 1.416 8 conservative 600130 12p13.1 "apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1" 3401 rs2302524 PLAUR 5329 19 48848312 NM_002659 NP_002650 C/T K220R plus 5607643 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.09 0.12 0.04 214 3 0.11 0.02 1642 4 123 "HapMap,freq,cluster" Benign 0.912 12 conservative 173391 19q13 "plasminogen activator, urokinase receptor" 3402 rs2302524 PLAUR 5329 19 48848312 NM_002659 NP_002650 C/T K220R plus 5607643 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.15 0.12 0.04 214 3 0.11 0.02 1642 4 123 "HapMap,freq,cluster" Benign 0.912 12 conservative 173391 19q13 "plasminogen activator, urokinase receptor" 3403 rs2302524 PLAUR 5329 19 48848312 NM_002659 NP_002650 C/T K220R plus 23608921 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.12 0.04 214 3 0.11 0.02 1642 4 123 "HapMap,freq,cluster" Benign 0.912 12 conservative 173391 19q13 "plasminogen activator, urokinase receptor" 3404 rs2302685 LRP6 4040 12 12193165 NM_002336 NP_002327 C/T V1062I plus 6570189 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.18 0.18 0 120 1 121 "HapMap,doubleHit,freq,cluster" Benign 0.96 13 conservative 603507 12p11-p13 low density lipoprotein receptor-related protein 6 3405 rs2302757 CUL4A 8451 13 112957340 NM_003589 NP_003580 A/G K544R plus 13253050 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.27 0.28 0.03 166 2 0.32 0.05 1580 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.216 31 Tolerant 0.31 2.85 40 conservative 603137 13q34 cullin 4A 3406 rs2302757 CUL4A 8451 13 112957340 NM_003589 NP_003580 A/G K544R plus 24180220 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.28 0.03 166 2 0.32 0.05 1580 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.216 31 Tolerant 0.31 2.85 40 conservative 603137 13q34 cullin 4A 3407 rs2303255 QPRT 23475 16 29613945 NM_014298 NP_055113 A/G A158V minus 3249780 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.21 0.2 0.01 168 2 0.06 0 1576 3 123 "HapMap,freq,cluster" Tolerant 0.44 2.81 13 moderately conservative 606248 16p12.1 quinolinate phosphoribosyltransferase (nicotinate-nucleotide pyrophosphorylase (carboxylating)) 3408 rs2303255 QPRT 23475 16 29613945 NM_014298 NP_055113 A/G A158V minus 24683303 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.2 0.01 168 2 0.06 0 1576 3 123 "HapMap,freq,cluster" Tolerant 0.44 2.81 13 moderately conservative 606248 16p12.1 quinolinate phosphoribosyltransferase (nicotinate-nucleotide pyrophosphorylase (carboxylating)) 3409 rs2303436 DLAT 1737 11 111401534 NM_001931 NP_001922 A/G A43V minus 3250013 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.24 0.29 0.08 212 2 0.46 0 740 1 120 "HapMap,doubleHit,freq,cluster" Benign 0.173 7 moderately conservative 608770 11q23.1 dihydrolipoamide S-acetyltransferase (E2 component of pyruvate dehydrogenase complex) 3410 rs2303436 DLAT 1737 11 111401534 NM_001931 NP_001922 A/G A43V minus 15806006 1303 SEQUENOM CEPH CEPH (92) 92 0.35 0.29 0.08 212 2 0.46 0 740 1 120 "HapMap,doubleHit,freq,cluster" Benign 0.173 7 moderately conservative 608770 11q23.1 dihydrolipoamide S-acetyltransferase (E2 component of pyruvate dehydrogenase complex) 3411 rs2303578 EIF3S1 8669 15 42636990 NM_003758 NP_003749 A/G A141T plus 3250207 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.03 0.03 0 118 1 0.07 0 734 1 100 "HapMap,freq" Benign 0.232 6 Tolerant 0.79 2.82 19 moderately conservative 603910 15q15.1 "eukaryotic translation initiation factor 3, subunit 1 alpha, 35kDa" 3412 rs2303743 LIFR 3977 5 38529631 NM_002310 NP_002301 C/T I633M plus 16338635 1120 WIPGA POP-WIPGA-12-05-2003 CORIELL Mixed 64 0.02 0.02 0 64 1 0.04 0 1502 1 120 "HapMap,cluster" Potentially intolerant 0.08 2.8 20 conservative 151443 5p13-p12 leukemia inhibitory factor receptor 3413 rs2303909 EFG1 85476 3 159849602 NM_024996 NP_079272 C/T V215I minus 10054264 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.39 0.38 0.03 168 2 0.23 0.06 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.124 31 Tolerant 0.9 2.73 250 conservative 606639 3q25.1-q26.2 mitochondrial elongation factor G1 3414 rs2303909 EFG1 85476 3 159849602 NM_024996 NP_079272 C/T V215I minus 24260627 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.38 0.03 168 2 0.23 0.06 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.124 31 Tolerant 0.9 2.73 250 conservative 606639 3q25.1-q26.2 mitochondrial elongation factor G1 3415 rs2303914 TAF1B 9014 2 9934284 NM_005680 NP_005671 G/T A6S plus 23706084 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.46 0 48 1 0.26 0.04 1568 3 123 "by doubleHit,freq,cluster" moderately conservative 604904 2p25 "TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa" 3416 rs2303982 SEMA5B 54437 3 124113013 NM_018987 NP_061860 G/T T1034P plus 10022137 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.13 0.13 0 120 1 0.28 0 1500 1 119 "HapMap,doubleHit,freq,cluster" conservative 3q21.1 "sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B" 3417 rs2304024 FAT2 2196 5 150889006 NM_001447 NP_001438 C/T R3318W minus 3250802 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.23 0.26 0.06 168 2 0.17 0.03 1540 2 123 "HapMap,freq" Borderline 0.12 2.82 16 moderately radical 604269 5q32-q33 FAT tumor suppressor homolog 2 (Drosophila) 3418 rs2304024 FAT2 2196 5 150889006 NM_001447 NP_001438 C/T R3318W minus 24339307 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.26 0.06 168 2 0.17 0.03 1540 2 123 "HapMap,freq" Borderline 0.12 2.82 16 moderately radical 604269 5q32-q33 FAT tumor suppressor homolog 2 (Drosophila) 3419 rs2304029 FAT2 2196 5 150871965 NM_001447 NP_001438 C/G Q3953H plus 24686699 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 0.03 0 1532 2 123 "by submitter,freq" Potentially intolerant 0.07 2.97 10 conservative 604269 5q32-q33 FAT tumor suppressor homolog 2 (Drosophila) 3420 rs2304053 FAT2 2196 5 150923162 NM_001447 NP_001438 A/G P1164L plus 14655829 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.48 0.48 0.01 142 2 0.27 0.02 1556 3 123 "HapMap,freq,cluster" Intolerant 0.01 2.82 16 moderately conservative 604269 5q32-q33 FAT tumor suppressor homolog 2 (Drosophila) 3421 rs2304053 FAT2 2196 5 150923162 NM_001447 NP_001438 A/G P1164L plus 24686747 1371 PERLEGEN AFD_EUR_PANEL European American (24) 22 0.5 0.48 0.01 142 2 0.27 0.02 1556 3 123 "HapMap,freq,cluster" Intolerant 0.01 2.82 16 moderately conservative 604269 5q32-q33 FAT tumor suppressor homolog 2 (Drosophila) 3422 rs2304167 GP6 51206 19 60218893 NM_016363 NP_057447 C/T A249T plus 3250985 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.19 0.18 0.03 164 2 0.2 0.05 1004 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 605546 19q13.4 glycoprotein VI (platelet) 3423 rs2304167 GP6 51206 19 60218893 NM_016363 NP_057447 C/T A249T plus 23778690 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.15 0.18 0.03 164 2 0.2 0.05 1004 3 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 605546 19q13.4 glycoprotein VI (platelet) 3424 rs2304237 ICAM3 3385 19 10307568 NM_002162 NP_002153 C/T D143G plus 14709927 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.2 0.22 0.04 166 2 0.15 0.03 1570 3 123 "HapMap,doubleHit,freq,cluster" moderately conservative 146631 19p13.3-p13.2 intercellular adhesion molecule 3 3425 rs2304237 ICAM3 3385 19 10307568 NM_002162 NP_002153 C/T D143G plus 23756777 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.22 0.04 166 2 0.15 0.03 1570 3 123 "HapMap,doubleHit,freq,cluster" moderately conservative 146631 19p13.3-p13.2 intercellular adhesion molecule 3 3426 rs2304255 TYK2 7297 19 10336649 NM_003331 NP_003322 C/T G363S plus 20399254 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.04 0.04 0 46 1 121 "by cluster,freq" Borderline 1.192 6 Tolerant 0.68 3.07 14 moderately conservative 176941 19p13.2 tyrosine kinase 2 3427 rs2304256 TYK2 7297 19 10336652 NM_003331 NP_003322 A/C V362F plus 20399148 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.3 0.3 0 46 1 0.1 0 48 1 121 "by cluster,freq" Possibly damaging 1.799 5 Potentially intolerant 0.07 3.07 14 conservative 176941 19p13.2 tyrosine kinase 2 3428 rs2304402 GREB1 9687 2 11724922 NM_014668 NP_055483 A/G D1687N plus 24267443 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.45 0.45 0 44 1 0.35 0.02 1582 3 123 "by doubleHit,freq,cluster" conservative 2p25.1 GREB1 protein 3429 rs2304445 FLJ10060 55065 17 4877622 NM_017986 NP_060456 A/G V296M minus 3251354 885 TSC-CSHL HapMap-CEPH-30-trios 112 0.15 0.15 0 112 1 0.44 0 1430 1 100 "HapMap,freq" Potentially damaging 1.289 11 Tolerant 0.36 2.81 23 conservative 607883 17p13.3 putative G-protein coupled receptor GPCR42 3430 rs2304789 CPNE3 8895 8 87636309 NM_003909 NP_003900 A/G T412M minus 11954602 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.27 0.27 0 120 1 120 "HapMap,doubleHit,freq,cluster" Benign 0.181 50 Borderline 0.11 2.88 39 moderately conservative 604207 8q21.2 copine III 3431 rs2304821 PTPRB 5787 12 69249886 NM_002837 NP_002828 A/G T939M plus 3251835 902 AFFY Caucasian 22 0.14 0.1 0.02 178 2 0.03 0.01 1714 3 123 "by cluster,freq" Borderline 1.139 6 Borderline 0.17 2.92 19 moderately conservative 176882 12q15-q21 "protein tyrosine phosphatase, receptor type, B" 3432 rs2304821 PTPRB 5787 12 69249886 NM_002837 NP_002828 A/G T939M plus 28458984 549 KYUGEN CP CEPH (78) 156 0.1 0.1 0.02 178 2 0.03 0.01 1714 3 123 "by cluster,freq" Borderline 1.139 6 Borderline 0.17 2.92 19 moderately conservative 176882 12q15-q21 "protein tyrosine phosphatase, receptor type, B" 3433 rs2304824 BG1 23205 15 76253182 NM_015162 NP_055977 A/G M633V minus 16152534 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.48 0.48 0 168 2 0.3 0.03 1596 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.923 6 Tolerant 1 2.78 24 conservative 15q23-q24 lipidosin 3434 rs2304824 BG1 23205 15 76253182 NM_015162 NP_055977 A/G M633V minus 24677665 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.48 0 168 2 0.3 0.03 1596 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.923 6 Tolerant 1 2.78 24 conservative 15q23-q24 lipidosin 3435 rs2304933 MS4A6E 245802 11 59859083 NM_139249 NP_640342 A/C V47F minus 3251979 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.28 0.26 0.04 168 2 0.33 0.02 1596 3 123 "HapMap,doubleHit,freq,cluster" conservative 608402 11q12.2 "membrane-spanning 4-domains, subfamily A, member 6E" 3436 rs2304933 MS4A6E 245802 11 59859083 NM_139249 NP_640342 A/C V47F minus 24102692 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.26 0.04 168 2 0.33 0.02 1596 3 123 "HapMap,doubleHit,freq,cluster" conservative 608402 11q12.2 "membrane-spanning 4-domains, subfamily A, member 6E" 3437 rs2304934 MS4A6E 245802 11 59858972 NM_139249 NP_640342 C/T T10A minus 24102685 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.21 0 48 1 0.28 0.02 94 2 123 "by doubleHit,freq,cluster" moderately conservative 608402 11q12.2 "membrane-spanning 4-domains, subfamily A, member 6E" 3438 rs2304935 MS4A6E 245802 11 59858960 NM_139249 NP_640342 C/T I6V minus 24102679 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.21 0 48 1 0.27 0.03 92 2 123 "by doubleHit,freq,cluster" conservative 608402 11q12.2 "membrane-spanning 4-domains, subfamily A, member 6E" 3439 rs2305165 R3HDM 23518 2 136243306 NM_015361 NP_056176 G/T Q632P minus 3252289 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.09 0.09 0.01 162 2 0.16 0.02 1550 3 123 "HapMap,submitter,freq,cluster" Potentially damaging 1.35 5 Intolerant 0.03 3.14 31 moderately conservative 2q21.3 R3H domain (binds single-stranded nucleic acids) containing 3440 rs2305165 R3HDM 23518 2 136243306 NM_015361 NP_056176 G/T Q632P minus 23874507 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.1 0.09 0.01 162 2 0.16 0.02 1550 3 123 "HapMap,submitter,freq,cluster" Potentially damaging 1.35 5 Intolerant 0.03 3.14 31 moderately conservative 2q21.3 R3H domain (binds single-stranded nucleic acids) containing 3441 rs2305397 TIP120B 23066 3 12832493 XM_371617 XP_371617 A/G P383L minus 24304631 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.46 0 48 1 0.18 0.05 1556 3 123 "by doubleHit,submitter,freq,cluster" Possibly damaging 1.673 15 Borderline 0.13 2.83 33 moderately conservative 3p25.2 TBP-interacting protein 3442 rs2305398 TIP120B 23066 3 12831856 XM_371617 XP_371617 C/T Q315R minus 24304622 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.4 0 48 1 0.28 0.04 1588 3 123 "by doubleHit,freq,cluster" Potentially damaging 1.357 15 Tolerant 1 2.94 29 conservative 3p25.2 TBP-interacting protein 3443 rs2305734 RARS 5917 5 167865736 NM_002887 NP_002878 A/T F397Y plus 24671425 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 0.11 0.02 1586 3 123 by freq Potentially damaging 1.346 12 Tolerant 1 2.77 38 conservative 107820 5q35.1 arginyl-tRNA synthetase 3444 rs2305799 ACP5 54 19 11548351 NM_001611 NP_001602 C/T V148M plus 3253130 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.11 0.11 0 118 1 0.08 0 1490 1 100 "HapMap,freq" Borderline 1.084 13 Potentially intolerant 0.07 2.91 15 conservative 171640 19p13.3-p13.2 "acid phosphatase 5, tartrate resistant" 3445 rs2305948 KDR 3791 4 55820486 NM_002253 NP_002244 C/T V297I plus 23368144 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 0.12 0.04 1596 3 123 "by submitter,freq,cluster" Benign 0.62 8 Intolerant 0.02 2.89 28 conservative 191306 4q11-q12 kinase insert domain receptor (a type III receptor tyrosine kinase) 3446 rs2306022 ITGA11 22801 15 66415217 NM_012211 NP_036343 A/G V433M minus 24427582 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.03 0.01 94 2 123 by freq Borderline 1.07 6 Intolerant 0.05 2.76 16 conservative 604789 15q22.3-q23 "integrin, alpha 11" 3447 rs2306024 ITGA11 22801 15 66415103 NM_012211 NP_036343 A/C M471L minus 23411427 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.02 0.02 0 46 1 0.05 0.04 1578 3 123 "by cluster,freq" Benign 0.677 6 Tolerant 1 2.76 16 conservative 604789 15q22.3-q23 "integrin, alpha 11" 3448 rs2306029 LRP4 4038 11 46849684 XM_035037 XP_035037 C/T S1524G plus 16000644 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.37 0.38 0.03 164 2 0.26 0.02 1578 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.027 5 Intolerant 0.05 2.85 27 moderately conservative 604270 11p11.2-p12 low density lipoprotein receptor-related protein 4 3449 rs2306029 LRP4 4038 11 46849684 XM_035037 XP_035037 C/T S1524G plus 24697440 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.38 0.03 164 2 0.26 0.02 1578 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.027 5 Intolerant 0.05 2.85 27 moderately conservative 604270 11p11.2-p12 low density lipoprotein receptor-related protein 4 3450 rs2306033 LRP4 4038 11 46854022 XM_035037 XP_035037 A/G A1173V plus 24207556 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 0.38 0.08 1590 3 123 "by submitter,freq,cluster" Benign 0.091 5 Tolerant 0.79 2.85 27 moderately conservative 604270 11p11.2-p12 low density lipoprotein receptor-related protein 4 3451 rs2306265 GRID1 2894 10 87474362 XM_043613 XP_043613 C/T V529I plus 24076759 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.02 0.02 0 46 1 0.06 0 1530 2 123 "by cluster,freq" conservative 10q22 "glutamate receptor, ionotropic, delta 1" 3452 rs2306536 CHFR 55743 12 132034012 NM_018223 NP_060693 C/T V539M plus 3254097 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.14 0.18 0.07 210 2 0.05 0 750 1 120 "HapMap,doubleHit,freq,cluster" Benign 0.758 8 conservative 605209 12q24.33 checkpoint with forkhead and ring finger domains 3453 rs2306536 CHFR 55743 12 132034012 NM_018223 NP_060693 C/T V539M plus 19253387 1303 SEQUENOM CEPH CEPH (92) 92 0.24 0.18 0.07 210 2 0.05 0 750 1 120 "HapMap,doubleHit,freq,cluster" Benign 0.758 8 conservative 605209 12q24.33 checkpoint with forkhead and ring finger domains 3454 rs2306541 CHFR 55743 12 132038592 NM_018223 NP_060693 A/G A456V plus 3254103 885 TSC-CSHL HapMap-CEPH-30-trios 112 0.32 0.32 0 112 1 0.16 0 1498 1 121 "HapMap,freq,cluster" Benign 0.173 8 moderately conservative 605209 12q24.33 checkpoint with forkhead and ring finger domains 3455 rs2306942 LAMA2 3908 6 129677493 NM_000426 NP_000417 C/T V1138M minus 23964998 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.16 0.01 1582 3 123 "by doubleHit,submitter,freq,cluster" Potentially intolerant 0.1 2.75 12 conservative 156225 6q22-q23 "laminin, alpha 2 (merosin, congenital muscular dystrophy)" 3456 rs2306985 MTP 4547 4 100873200 NM_000253 NP_000244 C/G H297Q plus 11684928 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.34 0.37 0.06 168 2 0.31 0.04 844 3 123 "HapMap,submitter,freq,cluster" Potentially damaging 1.462 9 Tolerant 0.56 2.78 15 conservative 157147 4q24 "microsomal triglyceride transfer protein (large polypeptide, 88kDa)" 3457 rs2306985 MTP 4547 4 100873200 NM_000253 NP_000244 C/G H297Q plus 24366024 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.37 0.06 168 2 0.31 0.04 844 3 123 "HapMap,submitter,freq,cluster" Potentially damaging 1.462 9 Tolerant 0.56 2.78 15 conservative 157147 4q24 "microsomal triglyceride transfer protein (large polypeptide, 88kDa)" 3458 rs2307145 IL12RB2 3595 1 67545548 NM_001559 NP_001550 C/G Q426H plus 3254918 506 NCBI NIHPDR NIHPDR 80 0.05 0.05 0 80 1 0.05 0 44 1 123 "by submitter,freq,cluster" Tolerant 0.23 2.82 14 conservative 601642 1p31.3-p31.2 "interleukin 12 receptor, beta 2" 3459 rs2307153 IL12RB2 3595 1 67545664 NM_001559 NP_001550 A/G G465D plus 3254927 506 NCBI NIHPDR NIHPDR 82 0.01 0.01 0.01 124 2 123 by freq Tolerant 0.32 2.89 13 moderately conservative 601642 1p31.3-p31.2 "interleukin 12 receptor, beta 2" 3460 rs2307153 IL12RB2 3595 1 67545664 NM_001559 NP_001550 A/G G465D plus 28446336 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 42 0.02 0.01 0.01 124 2 123 by freq Tolerant 0.32 2.89 13 moderately conservative 601642 1p31.3-p31.2 "interleukin 12 receptor, beta 2" 3461 rs2307191 XRCC1 7515 19 48749608 NM_006297 NP_006288 C/T P161L minus 4473973 693 EGP_SNPS PDR90 NIHPDR 168 0.01 0.01 0 168 1 106 "by cluster,freq" Probably damaging 2.19 6 moderately conservative 194360 19q13.2 X-ray repair complementing defective repair in Chinese hamster cells 1 3462 rs2307198 PLA2G4A 5321 1 183678569 NM_024420 NP_077734 A/G R651K plus 3254982 506 NCBI NIHPDR NIHPDR 84 0.02 0.03 0.02 310 3 123 "by cluster,freq" Borderline 1.047 6 conservative 600522 1q25 "phospholipase A2, group IVA (cytosolic, calcium-dependent)" 3463 rs2307198 PLA2G4A 5321 1 183678569 NM_024420 NP_077734 A/G R651K plus 20418623 693 EGP_SNPS PDR90 NIHPDR 178 0.02 0.03 0.02 310 3 123 "by cluster,freq" Borderline 1.047 6 conservative 600522 1q25 "phospholipase A2, group IVA (cytosolic, calcium-dependent)" 3464 rs2307198 PLA2G4A 5321 1 183678569 NM_024420 NP_077734 A/G R651K plus 24267026 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.03 0.02 310 3 123 "by cluster,freq" Borderline 1.047 6 conservative 600522 1q25 "phospholipase A2, group IVA (cytosolic, calcium-dependent)" 3465 rs2307227 CES1 1066 16 54412862 NM_001266 NP_001257 A/C D203E minus 3255029 506 NCBI NIHPDR NIHPDR 82 0.04 0.04 0 82 1 100 by freq Benign 0.244 51 Tolerant 0.8 2.79 59 conservative 114835 16q13-q22.1 carboxylesterase 1 (monocyte/macrophage serine esterase 1) 3466 rs2307240 CES1 1066 16 54420213 NM_001266 NP_001257 A/G S75N minus 3255044 506 NCBI NIHPDR NIHPDR 78 0.05 0.05 0 78 1 120 "by cluster,freq" Benign 0.087 50 Tolerant 0.42 2.78 56 conservative 114835 16q13-q22.1 carboxylesterase 1 (monocyte/macrophage serine esterase 1) 3467 rs2307254 HUS1 3364 7 47789593 NM_004507 NP_004498 A/C Q147K minus 3255063 506 NCBI NIHPDR NIHPDR 854 0.03 0.03 0.01 1012 2 0.15 0 48 1 123 "by cluster,freq" Benign 0.047 11 Tolerant 0.94 2.81 15 moderately conservative 603760 7p13-p12 HUS1 checkpoint homolog (S. pombe) 3468 rs2307254 HUS1 3364 7 47789593 NM_004507 NP_004498 A/C Q147K minus 4390130 693 EGP_SNPS PDR90 NIHPDR 158 0.02 0.03 0.01 1012 2 0.15 0 48 1 123 "by cluster,freq" Benign 0.047 11 Tolerant 0.94 2.81 15 moderately conservative 603760 7p13-p12 HUS1 checkpoint homolog (S. pombe) 3469 rs2307289 MBD4 8930 3 130638161 NM_003925 NP_003916 C/T S342P minus 3255105 506 NCBI NIHPDR NIHPDR 802 0.05 0.05 0.01 982 2 0.07 0.06 92 2 123 "by cluster,freq" moderately conservative 603574 3q21-q22 methyl-CpG binding domain protein 4 3470 rs2307289 MBD4 8930 3 130638161 NM_003925 NP_003916 C/T S342P minus 4385590 693 EGP_SNPS PDR90 NIHPDR 180 0.06 0.05 0.01 982 2 0.07 0.06 92 2 123 "by cluster,freq" moderately conservative 603574 3q21-q22 methyl-CpG binding domain protein 4 3471 rs2307293 MBD4 8930 3 130633083 NM_003925 NP_003916 C/G D568H minus 4385623 693 EGP_SNPS PDR90 NIHPDR 168 0.01 0.01 0 168 1 104 "by cluster,freq" moderately conservative 603574 3q21-q22 methyl-CpG binding domain protein 4 3472 rs2307306 GMNN 51053 6 24889714 NM_015895 NP_056979 C/T R54W plus 3255129 506 NCBI NIHPDR NIHPDR 162 0.06 0.06 0 162 1 0.14 0.17 94 2 123 "by cluster,freq" Probably damaging 3.757 6 moderately radical 602842 6p22.1 "geminin, DNA replication inhibitor" 3473 rs2307307 GMNN 51053 6 24889698 NM_015895 NP_056979 C/G L48F plus 3255130 506 NCBI NIHPDR NIHPDR 162 0.06 0.06 0 162 1 0.14 0.17 94 2 123 "by cluster,freq" Borderline 1.083 6 conservative 602842 6p22.1 "geminin, DNA replication inhibitor" 3474 rs2307313 MCM2 4171 3 128820733 NM_004526 NP_004517 A/G A727T plus 3255138 506 NCBI NIHPDR NIHPDR 150 0.01 0.01 0 150 1 100 by freq Potentially damaging 1.398 15 Intolerant 0.01 2.84 31 moderately conservative 116945 3q21 "MCM2 minichromosome maintenance deficient 2, mitotin (S. cerevisiae)" 3475 rs2307334 MCM5 4174 22 34124073 NM_006739 NP_006730 C/G S136T plus 3255163 506 NCBI NIHPDR NIHPDR 172 0.01 0.01 0 346 2 111 "by cluster,freq" Potentially damaging 1.325 15 Tolerant 0.54 2.82 31 moderately conservative 602696 22q13.1 "MCM5 minichromosome maintenance deficient 5, cell division cycle 46 (S. cerevisiae)" 3476 rs2307334 MCM5 4174 22 34124073 NM_006739 NP_006730 C/G S136T plus 6310448 693 EGP_SNPS PDR90 NIHPDR 174 0.01 0.01 0 346 2 111 "by cluster,freq" Potentially damaging 1.325 15 Tolerant 0.54 2.82 31 moderately conservative 602696 22q13.1 "MCM5 minichromosome maintenance deficient 5, cell division cycle 46 (S. cerevisiae)" 3477 rs2307340 MCM5 4174 22 34127215 NM_006739 NP_006730 C/G T180S plus 3255175 506 NCBI NIHPDR NIHPDR 166 0.03 0.07 0.05 476 4 123 "by cluster,freq" Benign 0.258 15 Tolerant 0.89 2.83 30 moderately conservative 602696 22q13.1 "MCM5 minichromosome maintenance deficient 5, cell division cycle 46 (S. cerevisiae)" 3478 rs2307340 MCM5 4174 22 34127215 NM_006739 NP_006730 C/G T180S plus 6310463 693 EGP_SNPS PDR90 NIHPDR 170 0.05 0.07 0.05 476 4 123 "by cluster,freq" Benign 0.258 15 Tolerant 0.89 2.83 30 moderately conservative 602696 22q13.1 "MCM5 minichromosome maintenance deficient 5, cell division cycle 46 (S. cerevisiae)" 3479 rs2307340 MCM5 4174 22 34127215 NM_006739 NP_006730 C/G T180S plus 6310463 1303 SEQUENOM CEPH CEPH (92) 92 0.12 0.07 0.05 476 4 123 "by cluster,freq" Benign 0.258 15 Tolerant 0.89 2.83 30 moderately conservative 602696 22q13.1 "MCM5 minichromosome maintenance deficient 5, cell division cycle 46 (S. cerevisiae)" 3480 rs2307340 MCM5 4174 22 34127215 NM_006739 NP_006730 C/G T180S plus 24596968 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.07 0.05 476 4 123 "by cluster,freq" Benign 0.258 15 Tolerant 0.89 2.83 30 moderately conservative 602696 22q13.1 "MCM5 minichromosome maintenance deficient 5, cell division cycle 46 (S. cerevisiae)" 3481 rs2307361 ORC2L 4999 2 201639794 NM_006190 NP_006181 A/T M106K minus 3255204 506 NCBI NIHPDR NIHPDR 176 0.01 0.01 0 352 2 123 "HapMap,freq,cluster" Probably damaging 2.505 6 Intolerant 0 3.13 9 moderately conservative 601182 2q33 "origin recognition complex, subunit 2-like (yeast)" 3482 rs2307361 ORC2L 4999 2 201639794 NM_006190 NP_006181 A/T M106K minus 28447653 693 EGP_SNPS PDR90 NIHPDR 176 0.01 0.01 0 352 2 123 "HapMap,freq,cluster" Probably damaging 2.505 6 Intolerant 0 3.13 9 moderately conservative 601182 2q33 "origin recognition complex, subunit 2-like (yeast)" 3483 rs2307440 POLG 5428 15 87662822 NM_002693 NP_002684 C/T R1146C minus 3255287 506 NCBI NIHPDR NIHPDR 164 0.01 0.01 0 290 2 106 "by cluster,freq" Probably damaging 2.257 6 Intolerant 0.02 2.86 20 radical 174763 15q25 "polymerase (DNA directed), gamma" 3484 rs2307440 POLG 5428 15 87662822 NM_002693 NP_002684 C/T R1146C minus 4388373 693 EGP_SNPS PDR90 NIHPDR 126 0.01 0.01 0 290 2 106 "by cluster,freq" Probably damaging 2.257 6 Intolerant 0.02 2.86 20 radical 174763 15q25 "polymerase (DNA directed), gamma" 3485 rs2307441 POLG 5428 15 87662830 NM_002693 NP_002684 A/G E1143G minus 3255288 506 NCBI NIHPDR NIHPDR 164 0.04 0.04 0.01 422 4 123 "by cluster,freq" Potentially damaging 1.37 6 Potentially intolerant 0.06 2.86 20 moderately conservative 174763 15q25 "polymerase (DNA directed), gamma" 3486 rs2307441 POLG 5428 15 87662830 NM_002693 NP_002684 A/G E1143G minus 4388372 693 EGP_SNPS PDR90 NIHPDR 118 0.03 0.04 0.01 422 4 123 "by cluster,freq" Potentially damaging 1.37 6 Potentially intolerant 0.06 2.86 20 moderately conservative 174763 15q25 "polymerase (DNA directed), gamma" 3487 rs2307441 POLG 5428 15 87662830 NM_002693 NP_002684 A/G E1143G minus 4388372 1303 SEQUENOM CEPH CEPH (92) 92 0.05 0.04 0.01 422 4 123 "by cluster,freq" Potentially damaging 1.37 6 Potentially intolerant 0.06 2.86 20 moderately conservative 174763 15q25 "polymerase (DNA directed), gamma" 3488 rs2307441 POLG 5428 15 87662830 NM_002693 NP_002684 A/G E1143G minus 24511266 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.04 0.01 422 4 123 "by cluster,freq" Potentially damaging 1.37 6 Potentially intolerant 0.06 2.86 20 moderately conservative 174763 15q25 "polymerase (DNA directed), gamma" 3489 rs2307442 POLG 5428 15 87662834 NM_002693 NP_002684 C/T R1142W minus 3255289 506 NCBI NIHPDR NIHPDR 164 0.01 0.01 0 294 2 106 "by cluster,freq" Possibly damaging 1.833 6 Intolerant 0.01 2.86 20 moderately radical 174763 15q25 "polymerase (DNA directed), gamma" 3490 rs2307442 POLG 5428 15 87662834 NM_002693 NP_002684 C/T R1142W minus 4388371 693 EGP_SNPS PDR90 NIHPDR 130 0.01 0.01 0 294 2 106 "by cluster,freq" Possibly damaging 1.833 6 Intolerant 0.01 2.86 20 moderately radical 174763 15q25 "polymerase (DNA directed), gamma" 3491 rs2307447 POLG 5428 15 87670923 NM_002693 NP_002684 C/T R546C minus 3255294 506 NCBI NIHPDR NIHPDR 176 0.01 0.01 0 344 2 106 "by cluster,freq" Benign 0.925 6 radical 174763 15q25 "polymerase (DNA directed), gamma" 3492 rs2307447 POLG 5428 15 87670923 NM_002693 NP_002684 C/T R546C minus 4388328 693 EGP_SNPS PDR90 NIHPDR 168 0.01 0.01 0 344 2 106 "by cluster,freq" Benign 0.925 6 radical 174763 15q25 "polymerase (DNA directed), gamma" 3493 rs2307450 POLG 5428 15 87668428 NM_002693 NP_002684 A/G E662K minus 3255297 506 NCBI NIHPDR NIHPDR 176 0.03 0.03 0.01 312 2 106 "by cluster,freq" Borderline 1.138 6 moderately conservative 174763 15q25 "polymerase (DNA directed), gamma" 3494 rs2307450 POLG 5428 15 87668428 NM_002693 NP_002684 A/G E662K minus 4388341 693 EGP_SNPS PDR90 NIHPDR 136 0.04 0.03 0.01 312 2 106 "by cluster,freq" Borderline 1.138 6 moderately conservative 174763 15q25 "polymerase (DNA directed), gamma" 3495 rs2307456 POLH 5429 6 43673546 NM_006502 NP_006493 G/T G209V plus 3255304 506 NCBI NIHPDR NIHPDR 174 0.01 0.01 0 336 2 119 "by cluster,freq" Possibly damaging 1.729 6 Borderline 0.11 2.76 15 moderately radical 603968 6p21.1 "polymerase (DNA directed), eta" 3496 rs2307456 POLH 5429 6 43673546 NM_006502 NP_006493 G/T G209V plus 12709504 693 EGP_SNPS PDR90 NIHPDR 162 0.01 0.01 0 336 2 119 "by cluster,freq" Possibly damaging 1.729 6 Borderline 0.11 2.76 15 moderately radical 603968 6p21.1 "polymerase (DNA directed), eta" 3497 rs2307491 ERCC5 2073 13 102312432 NM_000123 NP_000114 C/G S311C plus 3255341 506 NCBI NIHPDR NIHPDR 86 0.01 0.01 0 262 2 110 "by cluster,freq" Possibly damaging 1.503 7 Intolerant 0.04 2.9 8 moderately radical 133530 13q22 "excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))" 3498 rs2307491 ERCC5 2073 13 102312432 NM_000123 NP_000114 C/G S311C plus 5605244 693 EGP_SNPS PDR90 NIHPDR 176 0.01 0.01 0 262 2 110 "by cluster,freq" Possibly damaging 1.503 7 Intolerant 0.04 2.9 8 moderately radical 133530 13q22 "excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))" 3499 rs2308313 MPG 4350 16 73093 NM_002434 NP_002425 C/T R120C plus 24467287 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.02 0.02 0 44 1 0.02 0 46 1 123 "by cluster,freq" Probably damaging 2.257 11 Borderline 0.16 2.81 77 radical 156565 16p13.3 N-methylpurine-DNA glycosylase 3500 rs2308317 MLH1 4292 3 37028554 NM_000249 NP_000240 A/G V213M plus 3256180 506 NCBI NIHPDR NIHPDR 76 0.01 0.01 0 252 2 0.03 0.03 250 2 113 "by cluster,freq" Benign 0.971 8 Borderline 0.13 2.83 15 conservative 120436 3p21.3 "mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)" 3501 rs2308317 MLH1 4292 3 37028554 NM_000249 NP_000240 A/G V213M plus 6312968 693 EGP_SNPS PDR90 NIHPDR 176 0.01 0.01 0 252 2 0.03 0.03 250 2 113 "by cluster,freq" Benign 0.971 8 Borderline 0.13 2.83 15 conservative 120436 3p21.3 "mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)" 3502 rs2308321 MGMT 4255 10 131455054 NM_002412 NP_002403 A/G I143V plus 3256184 506 NCBI NIHPDR NIHPDR 802 0.05 0.06 0.03 1004 4 0.04 0.02 344 4 123 "by cluster,freq" Benign 0.96 7 Tolerant 0.58 2.76 30 conservative 156569 10q26 O-6-methylguanine-DNA methyltransferase 3503 rs2308321 MGMT 4255 10 131455054 NM_002412 NP_002403 A/G I143V plus 5586754 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.13 0.06 0.03 1004 4 0.04 0.02 344 4 123 "by cluster,freq" Benign 0.96 7 Tolerant 0.58 2.76 30 conservative 156569 10q26 O-6-methylguanine-DNA methyltransferase 3504 rs2308321 MGMT 4255 10 131455054 NM_002412 NP_002403 A/G I143V plus 5586754 1303 SEQUENOM CEPH CEPH (92) 92 0.1 0.06 0.03 1004 4 0.04 0.02 344 4 123 "by cluster,freq" Benign 0.96 7 Tolerant 0.58 2.76 30 conservative 156569 10q26 O-6-methylguanine-DNA methyltransferase 3505 rs2308321 MGMT 4255 10 131455054 NM_002412 NP_002403 A/G I143V plus 24537951 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.06 0.03 1004 4 0.04 0.02 344 4 123 "by cluster,freq" Benign 0.96 7 Tolerant 0.58 2.76 30 conservative 156569 10q26 O-6-methylguanine-DNA methyltransferase 3506 rs2308327 MGMT 4255 10 131455160 NM_002412 NP_002403 A/G K178R plus 3256191 506 NCBI NIHPDR NIHPDR 812 0.05 0.07 0.06 966 3 0.05 0.01 250 2 113 "by cluster,freq" conservative 156569 10q26 O-6-methylguanine-DNA methyltransferase 3507 rs2308327 MGMT 4255 10 131455160 NM_002412 NP_002403 A/G K178R plus 5586756 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.13 0.07 0.06 966 3 0.05 0.01 250 2 113 "by cluster,freq" conservative 156569 10q26 O-6-methylguanine-DNA methyltransferase 3508 rs2308327 MGMT 4255 10 131455160 NM_002412 NP_002403 A/G K178R plus 5586756 1303 SEQUENOM CEPH CEPH (92) 92 0.21 0.07 0.06 966 3 0.05 0.01 250 2 113 "by cluster,freq" conservative 156569 10q26 O-6-methylguanine-DNA methyltransferase 3509 rs2308949 CASP9 842 1 15578804 NM_001229 NP_001220 A/G G176R minus 3256834 506 NCBI NIHPDR NIHPDR 844 0.01 0.01 0 844 1 118 "by cluster,freq" Possibly damaging 1.846 10 Intolerant 0.02 2.83 21 moderately radical 602234 1p36.3-p36.1 "caspase 9, apoptosis-related cysteine protease" 3510 rs2308950 CASP9 842 1 15578812 NM_001229 NP_001220 A/G R173H minus 3256835 506 NCBI NIHPDR NIHPDR 844 0.01 0.01 0.01 1078 3 0.01 0.01 250 2 118 "by cluster,freq" Possibly damaging 1.567 10 Potentially intolerant 0.1 3 19 conservative 602234 1p36.3-p36.1 "caspase 9, apoptosis-related cysteine protease" 3511 rs2308950 CASP9 842 1 15578812 NM_001229 NP_001220 A/G R173H minus 6310860 693 EGP_SNPS PDR90 NIHPDR 172 0.01 0.01 0.01 1078 3 0.01 0.01 250 2 118 "by cluster,freq" Possibly damaging 1.567 10 Potentially intolerant 0.1 3 19 conservative 602234 1p36.3-p36.1 "caspase 9, apoptosis-related cysteine protease" 3512 rs2308950 CASP9 842 1 15578812 NM_001229 NP_001220 A/G R173H minus 12675300 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.03 0.01 0.01 1078 3 0.01 0.01 250 2 118 "by cluster,freq" Possibly damaging 1.567 10 Potentially intolerant 0.1 3 19 conservative 602234 1p36.3-p36.1 "caspase 9, apoptosis-related cysteine protease" 3513 rs2335052 GATA2 2624 3 129687649 NM_032638 NP_116027 A/G A164T minus 24645804 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.28 0.28 0 46 1 0.2 0.05 80 2 123 by freq Borderline 0.18 3.08 26 moderately conservative 137295 3q21.3 GATA binding protein 2 3514 rs2340601 MOV10L1 54456 22 48874930 NM_018995 NP_061868 A/G V650I plus 24214790 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.2 0.2 0 46 1 0.29 0.13 94 2 123 "by doubleHit,submitter,freq,cluster" Intolerant 0.02 3.14 22 conservative 605794 22q13.33 "Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)" 3515 rs2341097 SIX5 147912 19 50960742 NM_175875 NP_787071 C/T V693M plus 3294380 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.34 0.34 0 120 1 120 "HapMap,doubleHit,freq,cluster" conservative 600963 19q13.32 sine oculis homeobox homolog 5 (Drosophila) 3516 rs2356590 CUBN 8029 10 17019612 NM_001081 NP_001072 G/T P1971T plus 23891881 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.17 0 48 1 123 "by doubleHit,freq,cluster" Tolerant 0.93 2.76 8 conservative 602997 10p12.31 cubilin (intrinsic factor-cobalamin receptor) 3517 rs2360543 ZNF530 348327 19 62809035 NM_020880 NP_065931 A/T H110Q minus 3317190 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.22 0.32 0.11 304 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.25 11 conservative 19q13.43 zinc finger protein 530 3518 rs2360543 ZNF530 348327 19 62809035 NM_020880 NP_065931 A/T H110Q minus 24782962 1303 SEQUENOM CEPH CEPH (92) 184 0.38 0.32 0.11 304 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.25 11 conservative 19q13.43 zinc finger protein 530 3519 rs2366894 BIRC6 57448 2 32625357 NM_016252 NP_057336 A/T T2646S plus 3324641 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.31 0.3 0.01 168 2 0.26 0.06 92 2 123 "HapMap,doubleHit,freq,cluster" moderately conservative 605638 2p22-p21 baculoviral IAP repeat-containing 6 (apollon) 3520 rs2366894 BIRC6 57448 2 32625357 NM_016252 NP_057336 A/T T2646S plus 23165424 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.3 0.01 168 2 0.26 0.06 92 2 123 "HapMap,doubleHit,freq,cluster" moderately conservative 605638 2p22-p21 baculoviral IAP repeat-containing 6 (apollon) 3521 rs2372536 ATIC 471 2 216015526 NM_004044 NP_004035 C/G T116S plus 3331286 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.28 0.34 0.09 212 2 121 "HapMap,doubleHit,freq,cluster" Benign 0.607 34 Tolerant 0.35 2.82 85 moderately conservative 601731 2q35 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase 3522 rs2372536 ATIC 471 2 216015526 NM_004044 NP_004035 C/G T116S plus 3331286 1303 SEQUENOM CEPH CEPH (92) 92 0.41 0.34 0.09 212 2 121 "HapMap,doubleHit,freq,cluster" Benign 0.607 34 Tolerant 0.35 2.82 85 moderately conservative 601731 2q35 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase 3523 rs2401751 PTPN21 11099 14 88016375 NM_007039 NP_008970 C/T L385F minus 3366087 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.31 0.33 0.04 162 2 0.32 0.01 1572 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.418 5 conservative 603271 14q31.3 "protein tyrosine phosphatase, non-receptor type 21" 3524 rs2401751 PTPN21 11099 14 88016375 NM_007039 NP_008970 C/T L385F minus 24710652 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.37 0.33 0.04 162 2 0.32 0.01 1572 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.418 5 conservative 603271 14q31.3 "protein tyrosine phosphatase, non-receptor type 21" 3525 rs2412504 PAK6 56924 15 38345356 NM_020168 NP_064553 A/G M76V plus 23491700 1371 PERLEGEN AFD_EUR_PANEL European American (24) 40 0.1 0.1 0 40 1 0.15 0.04 806 3 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.44 2.81 32 conservative 608110 15q14 p21(CDKN1A)-activated kinase 6 3526 rs2429387 MRC2 9902 17 58120747 NM_006039 NP_006030 C/T R1156H minus 23607360 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.26 0.23 94 2 123 "by doubleHit,submitter,freq,cluster" conservative 17q24.1 "mannose receptor, C type 2" 3527 rs2434470 DEPC-1 221120 11 43897178 NM_139178 NP_631917 C/G D228E plus 24361788 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.29 0 48 1 0.08 0.04 94 2 123 "by cluster,freq" Potentially intolerant 0.1 2.84 18 conservative 11p11.2 prostate cancer antigen-1 3528 rs2441582 FOXD4L1 200350 2 113973431 NM_012184 NP_036316 C/T S123N minus 24809126 1303 SEQUENOM CEPH CEPH (92) 184 0.15 0.15 0 184 1 123 "by submitter,freq" Benign 0.03 13 Borderline 0.15 2.81 36 conservative 2q14.1 forkhead box D4 like 1 3529 rs2452600 LIM 10611 4 95854060 NM_006457 NP_006448 C/T S136F plus 23917011 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.23 0 48 1 0.31 0.25 94 2 123 "by submitter,freq,cluster" Potentially damaging 1.462 7 Intolerant 0.01 2.92 18 radical 605904 4q22 LIM protein (similar to rat protein kinase C-binding enigma) 3530 rs2455069 CD33 945 19 56420453 NM_001772 NP_001763 A/G R69G plus 3441316 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.47 0.48 0.02 144 2 0.31 0.23 94 2 123 "HapMap,doubleHit,freq,cluster" moderately radical 159590 19q13.3 CD33 antigen (gp67) 3531 rs2455069 CD33 945 19 56420453 NM_001772 NP_001763 A/G R69G plus 24686120 1371 PERLEGEN AFD_EUR_PANEL European American (24) 24 0.5 0.48 0.02 144 2 0.31 0.23 94 2 123 "HapMap,doubleHit,freq,cluster" moderately radical 159590 19q13.3 CD33 antigen (gp67) 3532 rs2464196 TCF1 6927 12 119898147 NM_000545 NP_000536 C/T S487N minus 3454712 885 TSC-CSHL HapMap-CEPH-30-trios 94 0.23 0.25 0.04 142 2 0.45 0.07 1590 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.183 16 Borderline 0.18 3.09 29 conservative 142410 12q24.2 "transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor" 3533 rs2464196 TCF1 6927 12 119898147 NM_000545 NP_000536 C/T S487N minus 23933092 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.25 0.04 142 2 0.45 0.07 1590 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.183 16 Borderline 0.18 3.09 29 conservative 142410 12q24.2 "transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor" 3534 rs2465811 PTPRB 5787 12 69276321 NM_002837 NP_002828 C/T S127G plus 11040632 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.32 0.3 0.05 166 2 0.35 0.06 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.004 5 moderately conservative 176882 12q15-q21 "protein tyrosine phosphatase, receptor type, B" 3535 rs2465811 PTPRB 5787 12 69276321 NM_002837 NP_002828 C/T S127G plus 23660787 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.24 0.3 0.05 166 2 0.35 0.06 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.004 5 moderately conservative 176882 12q15-q21 "protein tyrosine phosphatase, receptor type, B" 3536 rs2468844 SAA2 6289 11 18223603 NM_030754 NP_110381 A/G R89H minus 3460862 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.06 0.06 0 164 2 0.22 0.26 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.65 77 conservative 104751 11p15.1-p14 serum amyloid A2 3537 rs2468844 SAA2 6289 11 18223603 NM_030754 NP_110381 A/G R89H minus 23595249 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 164 2 0.22 0.26 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.65 77 conservative 104751 11p15.1-p14 serum amyloid A2 3538 rs2475298 SEC23IP 11196 10 121669003 NM_007190 NP_009121 C/T K644E minus 3468863 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.35 0.33 0.04 168 2 0.22 0.08 94 2 123 "HapMap,freq,cluster" Benign 0.061 7 Tolerant 0.75 2.89 18 moderately conservative 10q25-q26 SEC23 interacting protein 3539 rs2475298 SEC23IP 11196 10 121669003 NM_007190 NP_009121 C/T K644E minus 24330406 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.33 0.04 168 2 0.22 0.08 94 2 123 "HapMap,freq,cluster" Benign 0.061 7 Tolerant 0.75 2.89 18 moderately conservative 10q25-q26 SEC23 interacting protein 3540 rs2480345 GPR158 57512 10 25741347 NM_020752 NP_065803 C/G A422G minus 23466500 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.27 0 48 1 0.31 0.21 94 2 123 "by doubleHit,submitter,freq,cluster" moderately conservative 10p12.31 G protein-coupled receptor 158 3541 rs2485319 OVGP1 5016 1 111669735 NM_002557 NP_002548 A/G M477T plus 24266746 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.41 0.41 0 46 1 0.31 0.06 92 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.637 10 moderately conservative 603578 1p13 "oviductal glycoprotein 1, 120kDa (mucin 9, oviductin)" 3542 rs2487999 OBFC1 79991 10 105649816 NM_024928 NP_079204 C/T T151A plus 23611734 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 0.39 0 44 1 123 "by doubleHit,freq,cluster" Benign 0.075 6 moderately conservative 10q25.1 oligonucleotide/oligosaccharide-binding fold containing 1 3543 rs2498323 HGFAC 3083 4 3488078 NM_001528 NP_001519 C/T R644Q minus 3504677 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.11 0.13 0.04 168 2 0.07 0.08 94 2 123 "HapMap,submitter,freq" Potentially damaging 1.357 7 Tolerant 0.21 2.79 46 conservative 604552 4p16 HGF activator 3544 rs2498323 HGFAC 3083 4 3488078 NM_001528 NP_001519 C/T R644Q minus 24309742 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.13 0.04 168 2 0.07 0.08 94 2 123 "HapMap,submitter,freq" Potentially damaging 1.357 7 Tolerant 0.21 2.79 46 conservative 604552 4p16 HGF activator 3545 rs2502601 SYNJ2 8871 6 158487717 NM_003898 NP_003889 C/T E1468G minus 24460965 1371 PERLEGEN AFD_EUR_PANEL European American (24) 24 0.5 0.5 0 24 1 0.44 0.06 94 2 123 "by doubleHit,freq,cluster" moderately conservative 6q25.3 synaptojanin 2 3546 rs2511188 USP35 57558 11 77598578 XM_290527 XP_290527 C/T I433V minus 3520662 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.13 0.13 0 120 1 0.46 0 1470 1 108 "HapMap,doubleHit,freq,cluster" Tolerant 0.91 2.95 20 conservative 11q13.4 ubiquitin specific protease 35 3547 rs2532500 TAPBPL 55080 12 6433071 NM_018009 NP_060479 C/T T165A minus 23782900 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.23 0 48 1 0.33 0.11 94 2 123 "by doubleHit,freq,cluster" moderately conservative 607081 12p13.31 TAP binding protein-like 3548 rs2532501 TAPBPL 55080 12 6433014 NM_018009 NP_060479 C/T M146V minus 16340833 693 EGP_SNPS PDR90 NIHPDR 144 0.37 0.33 0.09 190 2 0.34 0.1 94 2 123 "by doubleHit,freq,cluster" conservative 607081 12p13.31 TAP binding protein-like 3549 rs2532501 TAPBPL 55080 12 6433014 NM_018009 NP_060479 C/T M146V minus 23782898 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.22 0.33 0.09 190 2 0.34 0.1 94 2 123 "by doubleHit,freq,cluster" conservative 607081 12p13.31 TAP binding protein-like 3550 rs2536512 SOD3 6649 4 24477584 NM_003102 NP_003093 A/G A58T plus 22887836 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.39 0.39 0 118 1 121 "HapMap,doubleHit,freq,cluster" Borderline 1.003 6 moderately conservative 185490 4p16.3-q21 "superoxide dismutase 3, extracellular" 3551 rs2543519 TMPRSS6 164656 22 35804769 NM_153019 NP_694564 C/T I430T minus 8296222 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.23 0.23 0 120 1 120 "HapMap,doubleHit,freq,cluster" moderately conservative 22q13.1 "transmembrane protease, serine 6" 3552 rs2544600 ZFYVE16 9765 5 79768835 NM_014733 NP_055548 C/T I192T plus 3568149 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.07 0.07 0 120 1 121 "HapMap,doubleHit,freq,cluster" moderately conservative 608880 5p15.2-q14.3 "zinc finger, FYVE domain containing 16" 3553 rs2573652 ADAMTS17 170691 15 98332137 NM_139057 NP_620688 C/T N1094S plus 3614339 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.35 0.35 0 118 1 0.5 0 1480 1 121 "HapMap,doubleHit,freq,cluster" conservative 607511 15q24 "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 17" 3554 rs2593943 MORC 27136 3 110172911 NM_014429 NP_055244 A/G H836Y plus 24375946 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.4 0 48 1 0.29 0.14 92 2 123 "by doubleHit,freq,cluster" moderately conservative 603205 3q13 microrchidia homolog (mouse) 3555 rs2602141 TP53BP1 7158 15 41511938 NM_005657 NP_005648 G/T K1136Q plus 23963734 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.35 0 48 1 0.32 0.21 94 2 123 "by doubleHit,submitter,freq,cluster" Tolerant 0.62 3.01 13 moderately conservative 605230 15q15-q21 "tumor protein p53 binding protein, 1" 3556 rs2608009 KRT7 3855 12 50925569 NM_005556 NP_005547 C/G G364A plus 16596101 1303 SEQUENOM CEPH CEPH (92) 92 0.21 0.21 0.01 138 2 0.09 0.01 1572 3 123 "by doubleHit,freq,cluster" Possibly damaging 1.76 157 moderately conservative 148059 12q12-q13 keratin 7 3557 rs2608009 KRT7 3855 12 50925569 NM_005556 NP_005547 C/G G364A plus 24342109 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.22 0.21 0.01 138 2 0.09 0.01 1572 3 123 "by doubleHit,freq,cluster" Possibly damaging 1.76 157 moderately conservative 148059 12q12-q13 keratin 7 3558 rs2617170 KLRC4 8302 12 10452224 NM_013431 NP_038459 C/T N104S plus 23787339 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.31 0 48 1 0.4 0.11 94 2 123 "by doubleHit,freq,cluster" Benign 0.775 53 Tolerant 0.45 2.77 76 conservative 602893 12p13.2-p12.3 "killer cell lectin-like receptor subfamily C, member 4" 3559 rs2641348 ADAM30 11085 1 120149926 NM_021794 NP_068566 C/T L359P minus 3721433 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.13 0.14 0.01 166 2 0.25 0.33 94 2 123 "HapMap,submitter,freq,cluster" Tolerant 0.29 2.78 12 moderately conservative 604779 1p13-p11 a disintegrin and metalloproteinase domain 30 3560 rs2641348 ADAM30 11085 1 120149926 NM_021794 NP_068566 C/T L359P minus 23668861 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.15 0.14 0.01 166 2 0.25 0.33 94 2 123 "HapMap,submitter,freq,cluster" Tolerant 0.29 2.78 12 moderately conservative 604779 1p13-p11 a disintegrin and metalloproteinase domain 30 3561 rs2652098 CSPG2 1462 5 82843828 NM_004385 NP_004376 A/G S300L minus 23989856 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.12 0.03 1548 2 123 "HapMap,submitter,freq,cluster" Borderline 0.17 2.78 21 moderately radical 118661 5q14.3 chondroitin sulfate proteoglycan 2 (versican) 3562 rs2657879 GLS2 27165 12 55151605 NM_013267 NP_037399 C/T L581P minus 24456482 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.19 0 48 1 0.08 0.08 94 2 123 "by doubleHit,submitter,freq" Benign 0.563 9 moderately conservative 606365 12q13 "glutaminase 2 (liver, mitochondrial)" 3563 rs2660744 PPAT 5471 4 57102538 NM_002703 NP_002694 A/G Q488X plus 2199804 773 TSC-CSHL SC_12_C CORIELL Caucasian (12) 14 0.43 0.41 0.06 196 3 0.41 0.05 46 2 113 by freq Probably damaging Intolerant radical 172450 4q12 phosphoribosyl pyrophosphate amidotransferase 3564 rs2660744 PPAT 5471 4 57102538 NM_002703 NP_002694 A/G Q488X plus 2199804 774 TSC-CSHL SC_95_C CORIELL Caucasian (95) 90 0.46 0.41 0.06 196 3 0.41 0.05 46 2 113 by freq Probably damaging Intolerant radical 172450 4q12 phosphoribosyl pyrophosphate amidotransferase 3565 rs2660744 PPAT 5471 4 57102538 NM_002703 NP_002694 A/G Q488X plus 2199804 1303 SEQUENOM CEPH CEPH (92) 92 0.36 0.41 0.06 196 3 0.41 0.05 46 2 113 by freq Probably damaging Intolerant radical 172450 4q12 phosphoribosyl pyrophosphate amidotransferase 3566 rs2661488 PKHD1 5314 6 51599825 NM_138694 NP_619639 A/T I3905N plus 23771062 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.05 0 42 1 123 "by cluster,freq" moderately radical 606702 6p12.2 polycystic kidney and hepatic disease 1 (autosomal recessive) 3567 rs2664538 MMP9 4318 20 44073632 NM_004994 NP_004985 A/G Q279R plus 3758674 687 TSC-SANGER SC_12_CA CEPH Caucasians (12) 14 0.39 0.35 0.12 258 5 0.37 0.1 116 4 123 "by doubleHit,submitter,freq,cluster" Benign 0.427 18 conservative 120361 20q11.2-q13.1 "matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)" 3568 rs2664538 MMP9 4318 20 44073632 NM_004994 NP_004985 A/G Q279R plus 5112470 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 40 0.43 0.35 0.12 258 5 0.37 0.1 116 4 123 "by doubleHit,submitter,freq,cluster" Benign 0.427 18 conservative 120361 20q11.2-q13.1 "matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)" 3569 rs2664538 MMP9 4318 20 44073632 NM_004994 NP_004985 A/G Q279R plus 8338714 1303 SEQUENOM CEPH CEPH (92) 92 0.22 0.35 0.12 258 5 0.37 0.1 116 4 123 "by doubleHit,submitter,freq,cluster" Benign 0.427 18 conservative 120361 20q11.2-q13.1 "matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)" 3570 rs2664538 MMP9 4318 20 44073632 NM_004994 NP_004985 A/G Q279R plus 16338512 1120 WIPGA POP-WIPGA-12-05-2003 CORIELL Mixed 64 0.47 0.35 0.12 258 5 0.37 0.1 116 4 123 "by doubleHit,submitter,freq,cluster" Benign 0.427 18 conservative 120361 20q11.2-q13.1 "matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)" 3571 rs2664538 MMP9 4318 20 44073632 NM_004994 NP_004985 A/G Q279R plus 23574543 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.35 0.12 258 5 0.37 0.1 116 4 123 "by doubleHit,submitter,freq,cluster" Benign 0.427 18 conservative 120361 20q11.2-q13.1 "matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)" 3572 rs2664581 PI3 5266 20 43237936 NM_002638 NP_002629 A/C T34P plus 3758733 687 TSC-SANGER SC_12_CA CEPH Caucasians (12) 4 0.09 0.17 0.06 172 3 0.13 0.09 96 3 123 "HapMap,submitter,freq" Benign 0.28 6 Tolerant 0.53 3.2 24 conservative 182257 20q12-q13 "protease inhibitor 3, skin-derived (SKALP)" 3573 rs2664581 PI3 5266 20 43237936 NM_002638 NP_002629 A/C T34P plus 3758733 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.14 0.17 0.06 172 3 0.13 0.09 96 3 123 "HapMap,submitter,freq" Benign 0.28 6 Tolerant 0.53 3.2 24 conservative 182257 20q12-q13 "protease inhibitor 3, skin-derived (SKALP)" 3574 rs2664581 PI3 5266 20 43237936 NM_002638 NP_002629 A/C T34P plus 24539452 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.17 0.06 172 3 0.13 0.09 96 3 123 "HapMap,submitter,freq" Benign 0.28 6 Tolerant 0.53 3.2 24 conservative 182257 20q12-q13 "protease inhibitor 3, skin-derived (SKALP)" 3575 rs2672785 MUC5B 4587 11 1203517 XM_039877 XP_039877 C/T E34G minus 3771887 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.24 0.24 0 120 1 120 "HapMap,doubleHit,freq" moderately conservative 600770 11p15 "mucin 5, subtype B, tracheobronchial" 3576 rs2706762 PCYOX1 51449 2 70400121 NM_016297 NP_057381 C/T S149F plus 3825043 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.15 0.17 0.04 168 2 0.02 0 46 1 123 "HapMap,submitter,freq" Potentially damaging 1.35 7 radical 2p13.3 prenylcysteine oxidase 1 3577 rs2706762 PCYOX1 51449 2 70400121 NM_016297 NP_057381 C/T S149F plus 24652156 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.17 0.04 168 2 0.02 0 46 1 123 "HapMap,submitter,freq" Potentially damaging 1.35 7 radical 2p13.3 prenylcysteine oxidase 1 3578 rs2711941 KLHL5 51088 4 38886728 NM_199039 NP_950240 G/T I10L minus 23718419 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.05 0 42 1 123 "by doubleHit,freq,cluster" conservative 608064 4p14 kelch-like 5 (Drosophila) 3579 rs2725362 WRN 7486 8 31118822 NM_000553 NP_000544 G/T L1074F plus 4318967 506 NCBI NIHPDR NIHPDR 178 0.46 0.46 0.02 552 5 0.45 0.03 440 6 123 "by doubleHit,submitter,freq,cluster" Benign 0.356 6 conservative 604611 8p12-p11.2 Werner syndrome 3580 rs2725362 WRN 7486 8 31118822 NM_000553 NP_000544 G/T L1074F plus 6903978 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.44 0.46 0.02 552 5 0.45 0.03 440 6 123 "by doubleHit,submitter,freq,cluster" Benign 0.356 6 conservative 604611 8p12-p11.2 Werner syndrome 3581 rs2725362 WRN 7486 8 31118822 NM_000553 NP_000544 G/T L1074F plus 16359562 693 EGP_SNPS PDR90 NIHPDR 172 0.43 0.46 0.02 552 5 0.45 0.03 440 6 123 "by doubleHit,submitter,freq,cluster" Benign 0.356 6 conservative 604611 8p12-p11.2 Werner syndrome 3582 rs2725362 WRN 7486 8 31118822 NM_000553 NP_000544 G/T L1074F plus 17206404 1303 SEQUENOM CEPH CEPH (92) 92 0.49 0.46 0.02 552 5 0.45 0.03 440 6 123 "by doubleHit,submitter,freq,cluster" Benign 0.356 6 conservative 604611 8p12-p11.2 Werner syndrome 3583 rs2725362 WRN 7486 8 31118822 NM_000553 NP_000544 G/T L1074F plus 24474132 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.46 0.02 552 5 0.45 0.03 440 6 123 "by doubleHit,submitter,freq,cluster" Benign 0.356 6 conservative 604611 8p12-p11.2 Werner syndrome 3584 rs2729835 LACTB 114294 15 61220819 NM_032857 NP_116246 C/T R469K minus 23514813 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.29 0 48 1 0.43 0 46 1 123 "by doubleHit,submitter,freq,cluster" Tolerant 1 2.92 13 conservative 608440 15q22.1 "lactamase, beta" 3585 rs2736654 GLO1 2739 6 38758606 NM_006708 NP_006699 A/C E111A minus 24369377 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.35 0 48 1 0.18 0.08 94 2 123 "by doubleHit,freq,cluster" Benign 0.3 22 moderately radical 138750 6p21.3-p21.1 glyoxalase I 3586 rs2740583 PCDHB8 56128 5 140540098 NM_019120 NP_061993 C/T F767L plus 24381608 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.42 0 48 1 0.13 0.04 90 2 123 "by submitter,freq" Potentially damaging 1.287 92 Intolerant 0.03 2.79 123 conservative 606334 5q31 protocadherin beta 8 3587 rs2756081 NQO2 4835 6 2955389 NM_000904 NP_000895 C/T L47F plus 14319725 1303 SEQUENOM CEPH CEPH (92) 92 0.17 0.2 0.05 140 2 0.15 0.18 94 2 123 "by doubleHit,freq,cluster" Probably damaging 2.001 6 conservative 160998 6pter-q12 "NAD(P)H dehydrogenase, quinone 2" 3588 rs2756081 NQO2 4835 6 2955389 NM_000904 NP_000895 C/T L47F plus 23984815 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.2 0.05 140 2 0.15 0.18 94 2 123 "by doubleHit,freq,cluster" Probably damaging 2.001 6 conservative 160998 6pter-q12 "NAD(P)H dehydrogenase, quinone 2" 3589 rs2782948 PLXNA2 5362 1 204779649 NM_025179 NP_079455 A/G R5Q minus 23845553 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.28 0.28 0 46 1 0.46 0.01 792 3 123 "by doubleHit,freq,cluster" conservative 601054 1q32.2 plexin A2 3590 rs2792751 GPAM 57678 10 113930319 NM_020918 NP_065969 A/G I43V minus 24326695 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.33 0 48 1 0.19 0.14 94 2 123 "by doubleHit,freq,cluster" Benign 0.225 5 conservative 602395 10q25.3 "glycerol-3-phosphate acyltransferase, mitochondrial" 3591 rs2805910 PRG1 5552 10 70526858 NM_002727 NP_002718 A/G R31Q plus 24096614 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 0.4 0.01 94 2 123 "by doubleHit,submitter,freq,cluster" conservative 177040 10q22.1 "proteoglycan 1, secretory granule" 3592 rs2820289 NAV1 89796 1 198508907 NM_020443 NP_065176 C/T S1270L plus 23846830 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.16 0.16 94 2 123 "by doubleHit,submitter,freq,cluster" moderately radical 1q32.3 neuron navigator 1 3593 rs2822785 SAMSN1 64092 21 14876399 NM_022136 NP_071419 A/G H64Y plus 3997266 634 PERLEGEN NCBI|NIHPDR NIHPDR 18 0.39 0.43 0.05 186 3 0.22 0.11 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 607978 21q11 "SAM domain, SH3 domain and nuclear localisation signals, 1" 3594 rs2822785 SAMSN1 64092 21 14876399 NM_022136 NP_071419 A/G H64Y plus 16908202 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.46 0.43 0.05 186 3 0.22 0.11 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 607978 21q11 "SAM domain, SH3 domain and nuclear localisation signals, 1" 3595 rs2822785 SAMSN1 64092 21 14876399 NM_022136 NP_071419 A/G H64Y plus 24719918 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.43 0.05 186 3 0.22 0.11 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" moderately conservative 607978 21q11 "SAM domain, SH3 domain and nuclear localisation signals, 1" 3596 rs2822786 SAMSN1 64092 21 14876464 NM_022136 NP_071419 A/G P42L plus 3997267 634 PERLEGEN NCBI|NIHPDR NIHPDR 18 0.22 0.37 0.13 66 2 0.18 0.19 94 2 123 "by submitter,freq" moderately conservative 607978 21q11 "SAM domain, SH3 domain and nuclear localisation signals, 1" 3597 rs2822786 SAMSN1 64092 21 14876464 NM_022136 NP_071419 A/G P42L plus 24719919 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.37 0.13 66 2 0.18 0.19 94 2 123 "by submitter,freq" moderately conservative 607978 21q11 "SAM domain, SH3 domain and nuclear localisation signals, 1" 3598 rs2822787 SAMSN1 64092 21 14876531 NM_022136 NP_071419 C/T N20D plus 3997268 634 PERLEGEN NCBI|NIHPDR NIHPDR 19 0.16 0.17 0.01 67 2 0.33 0.18 94 2 123 "by doubleHit,submitter,freq,cluster" conservative 607978 21q11 "SAM domain, SH3 domain and nuclear localisation signals, 1" 3599 rs2822787 SAMSN1 64092 21 14876531 NM_022136 NP_071419 C/T N20D plus 24226081 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.17 0.01 67 2 0.33 0.18 94 2 123 "by doubleHit,submitter,freq,cluster" conservative 607978 21q11 "SAM domain, SH3 domain and nuclear localisation signals, 1" 3600 rs2824721 PRSS7 5651 21 18591989 NM_002772 NP_002763 A/G P732S plus 4000059 634 PERLEGEN NCBI|NIHPDR NIHPDR 16 0.31 0.27 0.04 64 2 0.42 0.01 94 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.102 8 moderately conservative 606635 21q21.1 "protease, serine, 7 (enterokinase)" 3601 rs2824721 PRSS7 5651 21 18591989 NM_002772 NP_002763 A/G P732S plus 23778086 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.27 0.04 64 2 0.42 0.01 94 2 123 "by doubleHit,submitter,freq,cluster" Benign 0.102 8 moderately conservative 606635 21q21.1 "protease, serine, 7 (enterokinase)" 3602 rs2824790 PRSS7 5651 21 18677911 NM_002772 NP_002763 C/G E134Q plus 4000146 634 PERLEGEN NCBI|NIHPDR NIHPDR 19 0.16 0.31 0.14 65 2 0.19 0.08 92 2 123 "by doubleHit,submitter,freq,cluster" Borderline 1.067 7 conservative 606635 21q21.1 "protease, serine, 7 (enterokinase)" 3603 rs2824790 PRSS7 5651 21 18677911 NM_002772 NP_002763 C/G E134Q plus 24693964 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.37 0.31 0.14 65 2 0.19 0.08 92 2 123 "by doubleHit,submitter,freq,cluster" Borderline 1.067 7 conservative 606635 21q21.1 "protease, serine, 7 (enterokinase)" 3604 rs2824804 PRSS7 5651 21 18692433 NM_002772 NP_002763 C/T K77R plus 4000162 634 PERLEGEN NCBI|NIHPDR NIHPDR 19 0.21 0.08 0.06 183 3 0.03 0.01 90 2 123 "HapMap,submitter,freq" Borderline 1.047 5 conservative 606635 21q21.1 "protease, serine, 7 (enterokinase)" 3605 rs2824804 PRSS7 5651 21 18692433 NM_002772 NP_002763 C/T K77R plus 4000162 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.08 0.08 0.06 183 3 0.03 0.01 90 2 123 "HapMap,submitter,freq" Borderline 1.047 5 conservative 606635 21q21.1 "protease, serine, 7 (enterokinase)" 3606 rs2824804 PRSS7 5651 21 18692433 NM_002772 NP_002763 C/T K77R plus 24204741 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.08 0.06 183 3 0.03 0.01 90 2 123 "HapMap,submitter,freq" Borderline 1.047 5 conservative 606635 21q21.1 "protease, serine, 7 (enterokinase)" 3607 rs2829897 GABPA 2551 21 26058461 NM_002040 NP_002031 C/T A291V plus 4006980 634 PERLEGEN NCBI|NIHPDR NIHPDR 16 0.25 0.25 0 16 1 100 "by submitter,freq" Benign 0.091 6 Tolerant 0.34 2.9 101 moderately conservative 600609 21q21.3 "GA binding protein transcription factor, alpha subunit 60kDa" 3608 rs2829898 GABPA 2551 21 26058802 NM_002040 NP_002031 A/G W323X plus 4006981 634 PERLEGEN NCBI|NIHPDR NIHPDR 17 0.47 0.47 0 17 1 100 "by submitter,freq" Probably damaging Intolerant radical 600609 21q21.3 "GA binding protein transcription factor, alpha subunit 60kDa" 3609 rs2829900 GABPA 2551 21 26058866 NM_002040 NP_002031 A/G E345K plus 4006983 634 PERLEGEN NCBI|NIHPDR NIHPDR 8 0.5 0.5 0 8 1 100 "by submitter,freq" moderately conservative 600609 21q21.3 "GA binding protein transcription factor, alpha subunit 60kDa" 3610 rs2830585 ADAMTS5 11096 21 27227083 NM_007038 NP_008969 C/T R614H plus 4008065 634 PERLEGEN NCBI|NIHPDR NIHPDR 19 0.16 0.23 0.05 185 3 0.1 0.08 94 2 123 "HapMap,submitter,freq" Benign 0.32 7 Intolerant 0.01 2.76 33 conservative 605007 21q21.3 "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)" 3611 rs2830585 ADAMTS5 11096 21 27227083 NM_007038 NP_008969 C/T R614H plus 4008065 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.26 0.23 0.05 185 3 0.1 0.08 94 2 123 "HapMap,submitter,freq" Benign 0.32 7 Intolerant 0.01 2.76 33 conservative 605007 21q21.3 "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)" 3612 rs2830585 ADAMTS5 11096 21 27227083 NM_007038 NP_008969 C/T R614H plus 24474885 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.23 0.05 185 3 0.1 0.08 94 2 123 "HapMap,submitter,freq" Benign 0.32 7 Intolerant 0.01 2.76 33 conservative 605007 21q21.3 "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)" 3613 rs2834167 IL10RB 3588 21 33562658 NM_000628 NP_000619 A/G K47E plus 4013214 634 PERLEGEN NCBI|NIHPDR NIHPDR 5 0.4 0.33 0.09 201 4 0.29 0.17 120 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.871 5 Tolerant 1 2.78 11 moderately conservative 123889 21q22.11 "interleukin 10 receptor, beta" 3614 rs2834167 IL10RB 3588 21 33562658 NM_000628 NP_000619 A/G K47E plus 9806511 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 40 0.4 0.33 0.09 201 4 0.29 0.17 120 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.871 5 Tolerant 1 2.78 11 moderately conservative 123889 21q22.11 "interleukin 10 receptor, beta" 3615 rs2834167 IL10RB 3588 21 33562658 NM_000628 NP_000619 A/G K47E plus 9806511 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.27 0.33 0.09 201 4 0.29 0.17 120 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.871 5 Tolerant 1 2.78 11 moderately conservative 123889 21q22.11 "interleukin 10 receptor, beta" 3616 rs2834167 IL10RB 3588 21 33562658 NM_000628 NP_000619 A/G K47E plus 24115747 1371 PERLEGEN AFD_EUR_PANEL European American (24) 38 0.45 0.33 0.09 201 4 0.29 0.17 120 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.871 5 Tolerant 1 2.78 11 moderately conservative 123889 21q22.11 "interleukin 10 receptor, beta" 3617 rs2835285 CBR3 874 21 36429637 NM_001236 NP_001227 A/G V93I plus 4014820 634 PERLEGEN NCBI|NIHPDR NIHPDR 7 0.43 0.43 0 7 1 118 "by submitter,cluster" Potentially damaging 1.296 32 Tolerant 1 2.83 36 conservative 603608 21q22.2 carbonyl reductase 3 3618 rs2839223 PCNT2 5116 21 46601491 NM_006031 NP_006022 A/G G704E plus 4020284 634 PERLEGEN NCBI|NIHPDR NIHPDR 19 0.11 0.21 0.09 67 2 0.12 0.11 94 2 123 "by submitter,freq,cluster" moderately conservative 605925 21q22.3 pericentrin 2 (kendrin) 3619 rs2839223 PCNT2 5116 21 46601491 NM_006031 NP_006022 A/G G704E plus 24532983 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.21 0.09 67 2 0.12 0.11 94 2 123 "by submitter,freq,cluster" moderately conservative 605925 21q22.3 pericentrin 2 (kendrin) 3620 rs2839227 PCNT2 5116 21 46610952 NM_006031 NP_006022 A/G T879A plus 4020288 634 PERLEGEN NCBI|NIHPDR NIHPDR 17 0.24 0.21 0.03 183 3 0.33 0.21 94 2 123 "HapMap,submitter,freq,cluster" moderately conservative 605925 21q22.3 pericentrin 2 (kendrin) 3621 rs2839227 PCNT2 5116 21 46610952 NM_006031 NP_006022 A/G T879A plus 14438282 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.19 0.21 0.03 183 3 0.33 0.21 94 2 123 "HapMap,submitter,freq,cluster" moderately conservative 605925 21q22.3 pericentrin 2 (kendrin) 3622 rs2839227 PCNT2 5116 21 46610952 NM_006031 NP_006022 A/G T879A plus 23558055 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.21 0.03 183 3 0.33 0.21 94 2 123 "HapMap,submitter,freq,cluster" moderately conservative 605925 21q22.3 pericentrin 2 (kendrin) 3623 rs2839245 PCNT2 5116 21 46660550 NM_006031 NP_006022 C/T L2097P plus 4020311 634 PERLEGEN NCBI|NIHPDR NIHPDR 9 0.22 0.09 0.04 163 3 0.43 0 44 1 123 "HapMap,submitter,freq,cluster" moderately conservative 605925 21q22.3 pericentrin 2 (kendrin) 3624 rs2839245 PCNT2 5116 21 46660550 NM_006031 NP_006022 C/T L2097P plus 4020311 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.09 0.09 0.04 163 3 0.43 0 44 1 123 "HapMap,submitter,freq,cluster" moderately conservative 605925 21q22.3 pericentrin 2 (kendrin) 3625 rs2839245 PCNT2 5116 21 46660550 NM_006031 NP_006022 C/T L2097P plus 23558418 1371 PERLEGEN AFD_EUR_PANEL European American (24) 36 0.06 0.09 0.04 163 3 0.43 0 44 1 123 "HapMap,submitter,freq,cluster" moderately conservative 605925 21q22.3 pericentrin 2 (kendrin) 3626 rs2839256 PCNT2 5116 21 46672887 NM_006031 NP_006022 A/G A2549T plus 4020323 634 PERLEGEN NCBI|NIHPDR NIHPDR 6 0.33 0.33 0 6 1 100 "by submitter,freq" moderately conservative 605925 21q22.3 pericentrin 2 (kendrin) 3627 rs2839672 GAD2 2572 10 26548149 NM_000818 NP_000809 A/C P153Q plus 4020968 635 JDRF_WT_DIL UK UK 400 0.01 0.01 0 400 1 100 by freq Probably damaging 2.125 30 Intolerant 0.05 2.81 41 moderately conservative 138275 10p11.23 "glutamate decarboxylase 2 (pancreatic islets and brain, 65kDa)" 3628 rs2839673 GAD2 2572 10 26553557 NM_000818 NP_000809 A/G G232E plus 4020969 635 JDRF_WT_DIL UK UK 400 0.01 0.01 0 400 1 100 by freq Benign 0.127 32 Tolerant 0.43 2.89 36 moderately conservative 138275 10p11.23 "glutamate decarboxylase 2 (pancreatic islets and brain, 65kDa)" 3629 rs2839678 GAD2 2572 10 26599576 NM_000818 NP_000809 C/G G326A plus 4020974 635 JDRF_WT_DIL UK UK 400 0.1 0.1 0 400 1 100 by freq Possibly damaging 1.722 33 Intolerant 0 2.81 51 moderately conservative 138275 10p11.23 "glutamate decarboxylase 2 (pancreatic islets and brain, 65kDa)" 3630 rs2857713 LTA 4049 6 31648535 NM_000595 NP_000586 A/G C13R minus 4328792 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 42 0.29 0.18 0.1 432 4 0.27 0 44 1 123 "by doubleHit,freq,cluster" Benign 0.848 6 Borderline 0.16 3.23 64 radical 153440 6p21.3 "lymphotoxin alpha (TNF superfamily, member 1)" 3631 rs2857713 LTA 4049 6 31648535 NM_000595 NP_000586 A/G C13R minus 6312881 693 EGP_SNPS PDR90 NIHPDR 166 0.23 0.18 0.1 432 4 0.27 0 44 1 123 "by doubleHit,freq,cluster" Benign 0.848 6 Borderline 0.16 3.23 64 radical 153440 6p21.3 "lymphotoxin alpha (TNF superfamily, member 1)" 3632 rs2857713 LTA 4049 6 31648535 NM_000595 NP_000586 A/G C13R minus 16360680 649 FHCRC POPU1 USA (20) 40 0.3 0.18 0.1 432 4 0.27 0 44 1 123 "by doubleHit,freq,cluster" Benign 0.848 6 Borderline 0.16 3.23 64 radical 153440 6p21.3 "lymphotoxin alpha (TNF superfamily, member 1)" 3633 rs2857713 LTA 4049 6 31648535 NM_000595 NP_000586 A/G C13R minus 24797455 1303 SEQUENOM CEPH CEPH (92) 184 0.09 0.18 0.1 432 4 0.27 0 44 1 123 "by doubleHit,freq,cluster" Benign 0.848 6 Borderline 0.16 3.23 64 radical 153440 6p21.3 "lymphotoxin alpha (TNF superfamily, member 1)" 3634 rs2888782 STEAP 26872 7 89435192 NM_012449 NP_036581 C/G F169L plus 4081175 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.08 0.08 0 120 1 101 "HapMap,freq" Benign 0.793 9 conservative 604415 7q21 six transmembrane epithelial antigen of the prostate 3635 rs2896399 METTL2 55798 7 127713330 NM_018396 NP_060866 C/T C59R plus 5250439 1303 SEQUENOM CEPH CEPH (92) 92 0.47 0.47 0 92 1 108 by freq Probably damaging 2.715 5 Tolerant 0.34 2.99 11 radical 607846 7q32.2 methyltransferase like 2 3636 rs2903250 IGSF11 152404 3 120131750 NM_152538 NP_689751 G/T P38T plus 4097786 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.24 0.27 0.06 166 2 0.11 0.09 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 608351 3q13.33 "immunoglobulin superfamily, member 11" 3637 rs2903250 IGSF11 152404 3 120131750 NM_152538 NP_689751 G/T P38T plus 24288729 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.27 0.06 166 2 0.11 0.09 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 608351 3q13.33 "immunoglobulin superfamily, member 11" 3638 rs2910313 PCDHB7 56129 5 140533765 NM_018940 NP_061763 C/G V389L plus 4106385 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.44 0.45 0.03 164 2 0.28 0.04 1562 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.558 104 Tolerant 1 2.78 130 conservative 606333 5q31 protocadherin beta 7 3639 rs2910313 PCDHB7 56129 5 140533765 NM_018940 NP_061763 C/G V389L plus 24621856 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.45 0.03 164 2 0.28 0.04 1562 3 123 "HapMap,doubleHit,submitter,freq,cluster" Benign 0.558 104 Tolerant 1 2.78 130 conservative 606333 5q31 protocadherin beta 7 3640 rs2912444 ZNF529 57711 19 41730909 NM_020951 NP_066002 A/C L26V plus 4109075 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.31 0.31 0 120 1 121 "HapMap,submitter,freq,cluster" Borderline 1.178 6 Tolerant 0.74 2.84 76 conservative 19q13.13 zinc finger protein 529 3641 rs2917782 STARD6 147323 18 50109719 NM_139171 NP_631910 A/G E159K minus 5180962 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.09 0.09 0 120 1 108 "HapMap,doubleHit,freq" Tolerant 1 2.86 18 moderately conservative 607051 18q21.2 START domain containing 6 3642 rs2920048 ZFPM2 23414 8 106883832 NM_012082 NP_036214 C/G E782D plus 24524275 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.02 0 46 1 123 "by submitter,freq" conservative 603693 8q23 "zinc finger protein, multitype 2" 3643 rs2920217 ZNF509 166793 4 4422594 NM_145291 NP_660334 G/T Y320S minus 4119325 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.28 0.29 0.02 168 2 0.18 0.04 92 2 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 1 2.77 265 moderately radical 4p16.2 zinc finger protein 509 3644 rs2920217 ZNF509 166793 4 4422594 NM_145291 NP_660334 G/T Y320S minus 24383050 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.29 0.02 168 2 0.18 0.04 92 2 123 "HapMap,doubleHit,submitter,freq,cluster" Tolerant 1 2.77 265 moderately radical 4p16.2 zinc finger protein 509 3645 rs2941256 RRN3 54700 16 15074392 NM_018427 NP_060897 A/G I348M minus 4146849 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.08 0.08 0 120 1 101 "HapMap,freq" Benign 0.89 7 Potentially intolerant 0.07 2.8 10 conservative 605121 16p12 RNA polymerase I transcription factor RRN3 3646 rs2946994 CTBP2 1488 10 126704704 NM_022802 NP_073713 C/G Q539E minus 24583930 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.48 0 48 1 0.33 0.04 94 2 123 "by doubleHit,submitter,freq,cluster" conservative 602619 10q26.2 C-terminal binding protein 2 3647 rs3012075 CTBP2 1488 10 126704956 NM_022802 NP_073713 A/G Y455H plus 24583936 1371 PERLEGEN AFD_EUR_PANEL European American (24) 23 0.5 0.5 0 23 1 0.3 0.06 80 2 123 "by doubleHit,freq,cluster" moderately conservative 602619 10q26.2 C-terminal binding protein 2 3648 rs3024477 F13A1 2162 6 6196119 NM_000129 NP_000120 A/T Y205F minus 4250362 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.04 0.04 0 46 1 102 by freq Borderline 0.17 2.78 18 conservative 134570 6p25.3-p24.3 "coagulation factor XIII, A1 polypeptide" 3649 rs3024678 IL4R 3566 16 27282197 NM_000418 NP_000409 C/T P675S plus 4250600 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 44 0.02 0.02 0 92 2 0.02 0 92 2 123 "by cluster,freq" Possibly damaging 1.951 18 moderately conservative 147781 16p11.2-12.1 interleukin 4 receptor 3650 rs3024678 IL4R 3566 16 27282197 NM_000418 NP_000409 C/T P675S plus 23444688 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 92 2 0.02 0 92 2 123 "by cluster,freq" Possibly damaging 1.951 18 moderately conservative 147781 16p11.2-12.1 interleukin 4 receptor 3651 rs3024772 PROZ 8858 13 112874101 NM_003891 NP_003882 A/G R295H plus 4250711 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.02 0.02 0 46 1 0.02 0 48 1 102 by freq Tolerant 0.24 2.76 23 conservative 176895 13q34 "protein Z, vitamin K-dependent plasma glycoprotein" 3652 rs3027956 SLC1A5 6510 19 51983014 NM_005628 NP_005619 C/G P17A minus 23991299 1371 PERLEGEN AFD_EUR_PANEL European American (24) 38 0.21 0.21 0 38 1 0.27 0.17 234 3 123 "by cluster,freq" Possibly damaging 1.668 7 conservative 109190 19q13.3 "solute carrier family 1 (neutral amino acid transporter), member 5" 3653 rs3027961 SLC1A5 6510 19 51970699 NM_005628 NP_005619 C/G V512L minus 4258977 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.23 0.27 0.07 212 2 0.2 0 138 1 120 "HapMap,freq,cluster" Benign 0.144 21 Tolerant 0.5 3.1 42 conservative 109190 19q13.3 "solute carrier family 1 (neutral amino acid transporter), member 5" 3654 rs3027961 SLC1A5 6510 19 51970699 NM_005628 NP_005619 C/G V512L minus 16790225 1303 SEQUENOM CEPH CEPH (92) 92 0.33 0.27 0.07 212 2 0.2 0 138 1 120 "HapMap,freq,cluster" Benign 0.144 21 Tolerant 0.5 3.1 42 conservative 109190 19q13.3 "solute carrier family 1 (neutral amino acid transporter), member 5" 3655 rs3087366 POLD2 5425 7 43929065 NM_006230 NP_006221 A/G N303S minus 4318902 506 NCBI NIHPDR NIHPDR 164 0.01 0.01 0 342 2 106 "HapMap,freq,cluster" Potentially damaging 1.494 5 Intolerant 0.02 2.84 19 conservative 600815 7p13 "polymerase (DNA directed), delta 2, regulatory subunit 50kDa" 3656 rs3087366 POLD2 5425 7 43929065 NM_006230 NP_006221 A/G N303S minus 4479012 693 EGP_SNPS PDR90 NIHPDR 178 0.01 0.01 0 342 2 106 "HapMap,freq,cluster" Potentially damaging 1.494 5 Intolerant 0.02 2.84 19 conservative 600815 7p13 "polymerase (DNA directed), delta 2, regulatory subunit 50kDa" 3657 rs3087374 POLG 5428 15 87660998 NM_002693 NP_002684 G/T Q1236H minus 4318910 506 NCBI NIHPDR NIHPDR 176 0.04 0.04 0.02 396 3 123 "by cluster,freq" conservative 174763 15q25 "polymerase (DNA directed), gamma" 3658 rs3087374 POLG 5428 15 87660998 NM_002693 NP_002684 G/T Q1236H minus 4388391 693 EGP_SNPS PDR90 NIHPDR 172 0.04 0.04 0.02 396 3 123 "by cluster,freq" conservative 174763 15q25 "polymerase (DNA directed), gamma" 3659 rs3087374 POLG 5428 15 87660998 NM_002693 NP_002684 G/T Q1236H minus 24511209 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.04 0.02 396 3 123 "by cluster,freq" conservative 174763 15q25 "polymerase (DNA directed), gamma" 3660 rs3087386 REV1L 51455 2 99514024 NM_016316 NP_057400 C/T F257S minus 4318922 506 NCBI NIHPDR NIHPDR 176 0.42 0.42 0 176 1 0.32 0 1276 1 119 "by doubleHit,freq,cluster" radical 606134 2q11.1-q11.2 REV1-like (yeast) 3661 rs3087399 REV1L 51455 2 99513676 NM_016316 NP_057400 A/G N373S minus 4318938 506 NCBI NIHPDR NIHPDR 174 0.11 0.11 0 336 3 0.15 0.17 142 4 123 "HapMap,submitter,freq,cluster" Tolerant 0.73 3.07 15 conservative 606134 2q11.1-q11.2 REV1-like (yeast) 3662 rs3087399 REV1L 51455 2 99513676 NM_016316 NP_057400 A/G N373S minus 4318938 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.11 0.11 0 336 3 0.15 0.17 142 4 123 "HapMap,submitter,freq,cluster" Tolerant 0.73 3.07 15 conservative 606134 2q11.1-q11.2 REV1-like (yeast) 3663 rs3087399 REV1L 51455 2 99513676 NM_016316 NP_057400 A/G N373S minus 23232246 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.12 0.11 0 336 3 0.15 0.17 142 4 123 "HapMap,submitter,freq,cluster" Tolerant 0.73 3.07 15 conservative 606134 2q11.1-q11.2 REV1-like (yeast) 3664 rs3087401 REV1L 51455 2 99479463 NM_016316 NP_057400 A/G A1003T minus 4318940 506 NCBI NIHPDR NIHPDR 174 0.08 0.08 0 174 1 102 by freq Benign 0.206 5 Tolerant 0.6 2.97 11 moderately conservative 606134 2q11.1-q11.2 REV1-like (yeast) 3665 rs3087403 REV1L 51455 2 99517388 NM_016316 NP_057400 A/G V138M minus 4318942 506 NCBI NIHPDR NIHPDR 178 0.26 0.26 0 346 3 0.12 0.11 94 2 123 "HapMap,submitter,freq" Borderline 0.13 2.82 16 conservative 606134 2q11.1-q11.2 REV1-like (yeast) 3666 rs3087403 REV1L 51455 2 99517388 NM_016316 NP_057400 A/G V138M minus 4318942 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.26 0.26 0 346 3 0.12 0.11 94 2 123 "HapMap,submitter,freq" Borderline 0.13 2.82 16 conservative 606134 2q11.1-q11.2 REV1-like (yeast) 3667 rs3087403 REV1L 51455 2 99517388 NM_016316 NP_057400 A/G V138M minus 24295357 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.26 0 346 3 0.12 0.11 94 2 123 "HapMap,submitter,freq" Borderline 0.13 2.82 16 conservative 606134 2q11.1-q11.2 REV1-like (yeast) 3668 rs3087414 WRN 7486 8 31119686 NM_000553 NP_000544 C/T S1079L plus 4318962 506 NCBI NIHPDR NIHPDR 178 0.02 0.02 0 354 2 120 "by cluster,freq" Possibly damaging 1.773 6 Potentially intolerant 0.09 2.9 82 moderately radical 604611 8p12-p11.2 Werner syndrome 3669 rs3087414 WRN 7486 8 31119686 NM_000553 NP_000544 C/T S1079L plus 16359568 693 EGP_SNPS PDR90 NIHPDR 176 0.02 0.02 0 354 2 120 "by cluster,freq" Possibly damaging 1.773 6 Potentially intolerant 0.09 2.9 82 moderately radical 604611 8p12-p11.2 Werner syndrome 3670 rs3087425 WRN 7486 8 31097352 NM_000553 NP_000544 C/T R834C plus 4318975 506 NCBI NIHPDR NIHPDR 176 0.01 0.01 0 354 2 120 "by cluster,freq" Probably damaging 2.257 6 Intolerant 0 2.84 115 radical 604611 8p12-p11.2 Werner syndrome 3671 rs3087425 WRN 7486 8 31097352 NM_000553 NP_000544 C/T R834C plus 16359516 693 EGP_SNPS PDR90 NIHPDR 178 0.01 0.01 0 354 2 120 "by cluster,freq" Probably damaging 2.257 6 Intolerant 0 2.84 115 radical 604611 8p12-p11.2 Werner syndrome 3672 rs3087469 NTHL1 4913 16 2037789 NM_002528 NP_002519 C/T R21W minus 4319036 506 NCBI NIHPDR NIHPDR 166 0.01 0.01 0 316 2 106 "by cluster,freq" moderately radical 602656 16p13.3 nth endonuclease III-like 1 (E. coli) 3673 rs3087469 NTHL1 4913 16 2037789 NM_002528 NP_002519 C/T R21W minus 4442835 693 EGP_SNPS PDR90 NIHPDR 150 0.01 0.01 0 316 2 106 "by cluster,freq" moderately radical 602656 16p13.3 nth endonuclease III-like 1 (E. coli) 3674 rs3088142 DUSP13 51207 10 76524570 NM_016364 NP_057448 C/T C156Y plus 19160101 1303 SEQUENOM CEPH CEPH (92) 92 0.36 0.39 0.05 140 2 0.09 0.05 1554 3 123 "by doubleHit,freq,cluster" Possibly damaging 1.641 6 Tolerant 1 2.77 34 radical 10q22.3 dual specificity phosphatase 13 3675 rs3088142 DUSP13 51207 10 76524570 NM_016364 NP_057448 C/T C156Y plus 24591929 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.39 0.05 140 2 0.09 0.05 1554 3 123 "by doubleHit,freq,cluster" Possibly damaging 1.641 6 Tolerant 1 2.77 34 radical 10q22.3 dual specificity phosphatase 13 3676 rs3092857 ATM 472 11 107648509 NM_000051 NP_000042 A/G M1040V plus 4479922 506 NCBI NIHPDR NIHPDR 168 0.02 0.02 0 346 2 0.01 0 484 4 123 "by cluster,freq" Benign 0.702 5 conservative 607585 11q22-q23 "ataxia telangiectasia mutated (includes complementation groups A, C and D)" 3677 rs3092857 ATM 472 11 107648509 NM_000051 NP_000042 A/G M1040V plus 6904921 693 EGP_SNPS PDR90 NIHPDR 178 0.02 0.02 0 346 2 0.01 0 484 4 123 "by cluster,freq" Benign 0.702 5 conservative 607585 11q22-q23 "ataxia telangiectasia mutated (includes complementation groups A, C and D)" 3678 rs3093543 LTA 4049 6 31648736 NM_000595 NP_000586 A/C H51P plus 4328794 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.15 0.07 0.05 304 4 0.04 0 48 1 120 "by cluster,freq" Benign 0.907 15 Tolerant 0.23 2.82 79 moderately conservative 153440 6p21.3 "lymphotoxin alpha (TNF superfamily, member 1)" 3679 rs3093543 LTA 4049 6 31648736 NM_000595 NP_000586 A/C H51P plus 6312882 693 EGP_SNPS PDR90 NIHPDR 178 0.03 0.07 0.05 304 4 0.04 0 48 1 120 "by cluster,freq" Benign 0.907 15 Tolerant 0.23 2.82 79 moderately conservative 153440 6p21.3 "lymphotoxin alpha (TNF superfamily, member 1)" 3680 rs3093543 LTA 4049 6 31648736 NM_000595 NP_000586 A/C H51P plus 16360681 649 FHCRC POPU1 USA (20) 40 0.1 0.07 0.05 304 4 0.04 0 48 1 120 "by cluster,freq" Benign 0.907 15 Tolerant 0.23 2.82 79 moderately conservative 153440 6p21.3 "lymphotoxin alpha (TNF superfamily, member 1)" 3681 rs3093543 LTA 4049 6 31648736 NM_000595 NP_000586 A/C H51P plus 16360731 649 FHCRC POPU1 USA (20) 40 0.1 0.07 0.05 304 4 0.04 0 48 1 120 "by cluster,freq" Benign 0.907 15 Tolerant 0.23 2.82 79 moderately conservative 153440 6p21.3 "lymphotoxin alpha (TNF superfamily, member 1)" 3682 rs3093905 ADPRTL2 10038 14 19889067 NM_005484 NP_005475 A/G S112N plus 4329216 693 EGP_SNPS PDR90 NIHPDR 168 0.02 0.02 0 168 1 103 by freq Borderline 1.098 7 Tolerant 0.73 2.78 30 conservative 607725 14q11.2-q12 ADP-ribosyltransferase (NAD+; poly(ADP-ribose) polymerase)-like 2 3683 rs3093906 ADPRTL2 10038 14 19889088 NM_005484 NP_005475 A/G N119S plus 4329217 693 EGP_SNPS PDR90 NIHPDR 168 0.01 0.01 0 168 1 103 by freq Potentially damaging 1.265 7 Tolerant 1 2.78 30 conservative 607725 14q11.2-q12 ADP-ribosyltransferase (NAD+; poly(ADP-ribose) polymerase)-like 2 3684 rs3093921 ADPRTL2 10038 14 19892148 NM_005484 NP_005475 A/G D186G plus 4329237 693 EGP_SNPS PDR90 NIHPDR 174 0.01 0.01 0 174 1 103 by freq Possibly damaging 1.886 8 Potentially intolerant 0.08 2.78 30 moderately conservative 607725 14q11.2-q12 ADP-ribosyltransferase (NAD+; poly(ADP-ribose) polymerase)-like 2 3685 rs3104233 GZMA 3001 5 54439714 NM_006144 NP_006135 A/G M121T minus 23349387 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.09 0 46 1 123 "by cluster,freq" Potentially damaging 1.279 7 moderately conservative 140050 5q11-q12 "granzyme A (granzyme 1, cytotoxic T-lymphocyte-associated serine esterase 3)" 3686 rs3107275 PHACS 84680 11 44061557 NM_032592 NP_115981 C/T P421L plus 24597866 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.46 0 48 1 0.33 0.07 94 2 123 "by doubleHit,submitter,freq,cluster" Intolerant 0.05 2.8 217 moderately conservative 608405 11p11 1-aminocyclopropane-1-carboxylate synthase 3687 rs3125001 NOTCH1 4851 9 136681098 NM_017617 NP_060087 C/T A863T plus 16360575 649 FHCRC POPU1 USA (20) 40 0.4 0.4 0 80 2 121 "by doubleHit,freq,cluster" moderately conservative 190198 9q34.3 "Notch homolog 1, translocation-associated (Drosophila)" 3688 rs3125001 NOTCH1 4851 9 136681098 NM_017617 NP_060087 C/T A863T plus 16360576 649 FHCRC POPU1 USA (20) 40 0.4 0.4 0 80 2 121 "by doubleHit,freq,cluster" moderately conservative 190198 9q34.3 "Notch homolog 1, translocation-associated (Drosophila)" 3689 rs3125630 SIL 6491 1 47479934 NM_003035 NP_003026 A/G A86V plus 24246172 1371 PERLEGEN AFD_EUR_PANEL European American (24) 36 0.47 0.47 0 36 1 0.33 0.14 82 2 123 "by doubleHit,submitter,freq,cluster" moderately conservative 181590 1p32 TAL1 (SCL) interrupting locus 3690 rs3127328 T 6862 6 166542456 NM_003181 NP_003172 C/T G356S plus 23676534 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.16 0.17 94 2 123 "by doubleHit,freq,cluster" Benign 0.577 25 Tolerant 1 2.94 34 moderately conservative 601397 6q27 "T, brachyury homolog (mouse)" 3691 rs3130618 BAT4 7918 6 31740113 NM_033177 NP_149417 A/C R41L plus 23324092 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.09 0.09 0 44 1 0.15 0.2 92 2 123 "by cluster,freq" Possibly damaging 1.575 5 Tolerant 0.39 3.19 13 moderately radical 142610 6p21.3 HLA-B associated transcript 4 3692 rs3136797 POLB 5423 8 42345962 NM_002690 NP_002681 C/G P242R plus 4385180 693 EGP_SNPS PDR90 NIHPDR 168 0.01 0.01 0 322 3 0.01 0.01 250 2 113 "by cluster,freq" Possibly damaging 1.742 29 Intolerant 0.02 2.96 24 moderately radical 174760 8p11.2 "polymerase (DNA directed), beta" 3693 rs3136797 POLB 5423 8 42345962 NM_002690 NP_002681 C/G P242R plus 5586843 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.02 0.01 0 322 3 0.01 0.01 250 2 113 "by cluster,freq" Possibly damaging 1.742 29 Intolerant 0.02 2.96 24 moderately radical 174760 8p11.2 "polymerase (DNA directed), beta" 3694 rs3136797 POLB 5423 8 42345962 NM_002690 NP_002681 C/G P242R plus 5586843 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.01 0 322 3 0.01 0.01 250 2 113 "by cluster,freq" Possibly damaging 1.742 29 Intolerant 0.02 2.96 24 moderately radical 174760 8p11.2 "polymerase (DNA directed), beta" 3695 rs3138505 GADD45G 10912 9 89450314 NM_006705 NP_006696 A/G G112S plus 4387007 693 EGP_SNPS PDR90 NIHPDR 178 0.01 0.01 0 178 1 0.02 0 46 1 123 "by cluster,freq" Benign 0.076 22 Tolerant 1 2.84 48 moderately conservative 604949 9q22.1-q22.2 "growth arrest and DNA-damage-inducible, gamma" 3696 rs3174720 TRIM16 10626 17 15472872 NM_006470 NP_006461 C/T R493W minus 24820442 1303 SEQUENOM CEPH CEPH (92) 184 0.31 0.31 0 184 1 123 by freq Borderline 1.205 7 Intolerant 0.03 2.78 7 moderately radical 17p11.2 tripartite motif-containing 16 3697 rs3176311 TAF10 6881 11 6589583 NM_006284 NP_006275 C/T I92T minus 4388458 693 EGP_SNPS PDR90 NIHPDR 168 0.01 0.01 0 168 1 105 by freq Tolerant 0.47 3.01 10 moderately conservative 600475 11p15.3 "TAF10 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 30kDa" 3698 rs3176750 XPA 7507 9 97517344 NM_000380 NP_000371 C/G L252V minus 4390360 693 EGP_SNPS PDR90 NIHPDR 174 0.01 0.01 0 174 1 105 "HapMap,freq" Benign 0.101 9 Tolerant 1 2.85 12 conservative 278700 9q22.3 "xeroderma pigmentosum, complementation group A" 3699 rs3176975 APOH 350 17 61641219 NM_000042 NP_000033 G/T V266L minus 9807040 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 42 0.26 0.27 0.01 90 2 0.36 0.18 117 3 123 "by submitter,freq,cluster" Benign 0.172 12 conservative 138700 17q23-qter apolipoprotein H (beta-2-glycoprotein I) 3700 rs3176975 APOH 350 17 61641219 NM_000042 NP_000033 G/T V266L minus 23636032 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.27 0.01 90 2 0.36 0.18 117 3 123 "by submitter,freq,cluster" Benign 0.172 12 conservative 138700 17q23-qter apolipoprotein H (beta-2-glycoprotein I) 3701 rs3177253 PECI 10455 6 4078854 NM_006117 NP_006108 A/G M17I minus 22454455 1303 SEQUENOM CEPH CEPH (92) 92 0.28 0.28 0 92 1 121 by freq Possibly damaging 1.682 8 conservative 608024 6p24.3 "peroxisomal D3,D2-enoyl-CoA isomerase" 3702 rs3177459 SLC2A4RG 56731 20 61844151 NM_020062 NP_064446 G/T E233D plus 8309960 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.31 0.42 0.12 302 2 123 "HapMap,doubleHit,freq,cluster" conservative 20q13.33 SLC2A4 regulator 3703 rs3177459 SLC2A4RG 56731 20 61844151 NM_020062 NP_064446 G/T E233D plus 24796618 1303 SEQUENOM CEPH CEPH (92) 184 0.49 0.42 0.12 302 2 123 "HapMap,doubleHit,freq,cluster" conservative 20q13.33 SLC2A4 regulator 3704 rs3177751 ETFB 2109 19 56542102 NM_001985 NP_001976 C/T T154M minus 12470968 1303 SEQUENOM CEPH CEPH (92) 92 0.21 0.21 0 92 1 121 "by doubleHit,freq,cluster" Benign 0.347 88 Potentially intolerant 0.06 2.82 78 moderately conservative 130410 19q13.3 "electron-transfer-flavoprotein, beta polypeptide" 3705 rs3177979 OAS1 4938 12 111819929 NM_016816 NP_058132 A/G A352T plus 24415240 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.42 0 48 1 0.17 0.08 94 2 123 "by doubleHit,submitter,freq,cluster" moderately conservative 164350 12q24.1 "2',5'-oligoadenylate synthetase 1, 40/46kDa" 3706 rs3177980 SELL 6402 1 166408144 NM_000655 NP_000646 C/T F193L minus 6904124 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.26 0.28 0.03 186 3 0.19 0.01 94 2 123 "by doubleHit,freq,cluster" Possibly damaging 1.864 10 Tolerant 0.33 2.88 110 conservative 153240 1q23-q25 selectin L (lymphocyte adhesion molecule 1) 3707 rs3177980 SELL 6402 1 166408144 NM_000655 NP_000646 C/T F193L minus 6904124 1303 SEQUENOM CEPH CEPH (92) 92 0.31 0.28 0.03 186 3 0.19 0.01 94 2 123 "by doubleHit,freq,cluster" Possibly damaging 1.864 10 Tolerant 0.33 2.88 110 conservative 153240 1q23-q25 selectin L (lymphocyte adhesion molecule 1) 3708 rs3177980 SELL 6402 1 166408144 NM_000655 NP_000646 C/T F193L minus 24266135 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.28 0.03 186 3 0.19 0.01 94 2 123 "by doubleHit,freq,cluster" Possibly damaging 1.864 10 Tolerant 0.33 2.88 110 conservative 153240 1q23-q25 selectin L (lymphocyte adhesion molecule 1) 3709 rs3179861 DDX5 1655 17 59927132 NM_004396 NP_004387 G/T S480A minus 4400893 1303 SEQUENOM CEPH CEPH (92) 92 0.07 0.07 0 92 1 105 by freq Benign 0.156 13 Tolerant 0.54 2.91 30 moderately conservative 180630 17q21 DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 3710 rs3180408 USP18 11274 22 17025236 NM_017414 NP_059110 C/T T169M plus 8286364 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.35 0.35 0 168 2 0.35 0.03 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.273 5 Borderline 0.15 2.77 22 moderately conservative 607057 22q11.21 ubiquitin specific protease 18 3711 rs3180408 USP18 11274 22 17025236 NM_017414 NP_059110 C/T T169M plus 23787905 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.35 0 168 2 0.35 0.03 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.273 5 Borderline 0.15 2.77 22 moderately conservative 607057 22q11.21 ubiquitin specific protease 18 3712 rs3181179 CASP5 838 11 104379251 NM_004347 NP_004338 A/G R152H minus 4402959 649 FHCRC POPU1 USA (20) 40 0.05 0.05 0 40 1 0.02 0 46 1 123 "HapMap,submitter,cluster" Benign 0.967 9 Tolerant 0.57 2.79 32 conservative 602665 11q22.2-q22.3 "caspase 5, apoptosis-related cysteine protease" 3713 rs3181320 CASP5 838 11 104384838 NM_004347 NP_004338 C/G F13L minus 4403101 649 FHCRC POPU1 USA (20) 40 0.08 0.08 0 40 1 0.12 0.21 60 2 116 "by doubleHit,freq,cluster" conservative 602665 11q22.2-q22.3 "caspase 5, apoptosis-related cysteine protease" 3714 rs3181326 CASP5 838 11 104378033 NM_004347 NP_004338 C/G V201L minus 4403108 649 FHCRC POPU1 USA (20) 38 0.05 0.05 0 38 1 105 by freq Benign 0.134 10 Tolerant 0.31 2.79 34 conservative 602665 11q22.2-q22.3 "caspase 5, apoptosis-related cysteine protease" 3715 rs3182535 PITRM1 10531 10 3190292 NM_014889 NP_055704 C/T A397V minus 5374954 1303 SEQUENOM CEPH CEPH (92) 92 0.25 0.3 0.1 140 2 0.41 0 92 2 123 "by doubleHit,submitter,freq,cluster" Potentially damaging 1.336 7 Tolerant 0.31 2.85 13 moderately conservative 10p15.3 pitrilysin metalloproteinase 1 3716 rs3182535 PITRM1 10531 10 3190292 NM_014889 NP_055704 C/T A397V minus 23542079 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.3 0.1 140 2 0.41 0 92 2 123 "by doubleHit,submitter,freq,cluster" Potentially damaging 1.336 7 Tolerant 0.31 2.85 13 moderately conservative 10p15.3 pitrilysin metalloproteinase 1 3717 rs3190103 HCCR1 25875 12 49729211 NM_015416 NP_056231 A/G V84I plus 11046295 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.38 0.38 0 168 2 0.32 0.22 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 12q13.13 cervical cancer 1 protooncogene 3718 rs3190103 HCCR1 25875 12 49729211 NM_015416 NP_056231 A/G V84I plus 23404206 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.38 0 168 2 0.32 0.22 94 2 123 "HapMap,doubleHit,submitter,freq,cluster" conservative 12q13.13 cervical cancer 1 protooncogene 3719 rs3192149 TOPBP1 11073 3 134851060 NM_007027 NP_008958 A/C K370Q minus 10069328 1303 SEQUENOM CEPH CEPH (92) 92 0.22 0.22 0.01 140 2 0.33 0.07 94 2 123 "by doubleHit,submitter,freq,cluster" Potentially damaging 1.479 7 moderately conservative 607760 3q22.1 topoisomerase (DNA) II binding protein 3720 rs3192149 TOPBP1 11073 3 134851060 NM_007027 NP_008958 A/C K370Q minus 23915201 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.22 0.01 140 2 0.33 0.07 94 2 123 "by doubleHit,submitter,freq,cluster" Potentially damaging 1.479 7 moderately conservative 607760 3q22.1 topoisomerase (DNA) II binding protein 3721 rs3192151 TOPBP1 11073 3 134818781 NM_007027 NP_008958 A/C H1140P minus 4417612 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.04 0 92 1 105 by freq Benign 0.901 7 moderately conservative 607760 3q22.1 topoisomerase (DNA) II binding protein 3722 rs3194051 IL7R 3575 5 35912031 NM_002185 NP_002176 A/G I356V plus 16336738 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 44 0.32 0.3 0.02 184 3 0.26 0.22 138 3 123 "by submitter,freq,cluster" Tolerant 0.66 3.04 35 conservative 146661 5p13 interleukin 7 receptor 3723 rs3194051 IL7R 3575 5 35912031 NM_002185 NP_002176 A/G I356V plus 16336738 1303 SEQUENOM CEPH CEPH (92) 92 0.29 0.3 0.02 184 3 0.26 0.22 138 3 123 "by submitter,freq,cluster" Tolerant 0.66 3.04 35 conservative 146661 5p13 interleukin 7 receptor 3724 rs3194051 IL7R 3575 5 35912031 NM_002185 NP_002176 A/G I356V plus 23289765 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.3 0.02 184 3 0.26 0.22 138 3 123 "by submitter,freq,cluster" Tolerant 0.66 3.04 35 conservative 146661 5p13 interleukin 7 receptor 3725 rs3200107 HLA-A 3105 6 30018560 NM_002116 NP_002107 A/C R41S plus 24797195 1303 SEQUENOM CEPH CEPH (92) 184 0.1 0.1 0 184 1 123 by freq Borderline 1.057 442 moderately radical 142800 6p21.3 "major histocompatibility complex, class I, A" 3726 rs3200156 HLA-A 3105 6 30018740 NM_002116 NP_002107 A/G D101N plus 24798360 1303 SEQUENOM CEPH CEPH (92) 184 0.46 0.46 0 184 1 123 "by cluster,freq" Benign 0.31 442 conservative 142800 6p21.3 "major histocompatibility complex, class I, A" 3727 rs3204145 IKBKAP 8518 9 108731175 NM_003640 NP_003631 A/T C1072S minus 14367338 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.13 0.13 0 168 2 0.33 0.11 90 2 123 "HapMap,freq,cluster" Probably damaging 2.385 8 Potentially intolerant 0.06 2.83 14 moderately radical 603722 9q31 "inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein" 3728 rs3204145 IKBKAP 8518 9 108731175 NM_003640 NP_003631 A/T C1072S minus 23784430 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 168 2 0.33 0.11 90 2 123 "HapMap,freq,cluster" Probably damaging 2.385 8 Potentially intolerant 0.06 2.83 14 moderately radical 603722 9q31 "inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein" 3729 rs3204953 REV3L 5980 6 111735319 NM_002912 NP_002903 A/G V2986I minus 4479756 506 NCBI NIHPDR NIHPDR 158 0.04 0.04 0 158 1 106 "by cluster,freq" conservative 602776 6q21 "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)" 3730 rs3205421 CHPT1 56994 12 100610813 NM_020244 NP_064629 C/T F162S plus 16596920 1303 SEQUENOM CEPH CEPH (92) 92 0.28 0.28 0 92 1 120 "by doubleHit,freq,cluster" Benign 0.99 16 Intolerant 0.04 2.79 36 radical 12q choline phosphotransferase 1 3731 rs3205537 PDZRN3 23024 3 73516059 XM_041363 XP_041363 C/T A880V minus 21887288 1303 SEQUENOM CEPH CEPH (92) 92 0.17 0.17 0 92 1 121 "by cluster,freq" Borderline 1.227 7 moderately conservative 3p14.1 PDZ domain containing RING finger 3 3732 rs3207090 FLVCR 28982 1 209456990 NM_014053 NP_054772 C/T T544M plus 15720718 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.44 0 92 1 121 "by doubleHit,freq,cluster" moderately conservative 1q32.3 feline leukemia virus subgroup C cellular receptor 3733 rs3208856 CBLC 23624 19 49988646 NM_012116 NP_036248 C/T H405Y plus 4439298 1303 SEQUENOM CEPH CEPH (92) 92 0.07 0.07 0 92 1 105 by freq Potentially damaging 1.31 5 moderately conservative 608453 19q13.2 Cas-Br-M (murine) ecotropic retroviral transforming sequence c 3734 rs3210400 SCLY 51540 2 238772388 NM_016510 NP_057594 A/G A175T plus 16863111 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.42 0.42 0 120 1 0.28 0 1498 1 120 "HapMap,freq,cluster" Borderline 1.124 7 moderately conservative 2q37.3 selenocysteine lyase 3735 rs3211371 CYP2B6 1555 19 46214555 NM_000767 NP_000758 C/T R487C plus 24815467 1303 SEQUENOM CEPH CEPH (92) 184 0.36 0.36 0 184 1 0.1 0.08 566 3 123 "by cluster,freq" Borderline 1.22 87 Tolerant 1 2.81 156 radical 123930 19q13.2 "cytochrome P450, family 2, subfamily B, polypeptide 6" 3736 rs3211612 CDK4 1019 12 56431366 NM_000075 NP_000066 A/G R82Q minus 4442433 693 EGP_SNPS PDR90 NIHPDR 180 0.01 0.01 0 180 1 105 HapMap Possibly damaging 1.715 16 Tolerant 0.38 2.74 97 conservative 123829 12q14 cyclin-dependent kinase 4 3737 rs3211772 F10 2159 13 112843317 NM_000504 NP_000495 A/G A152T plus 4442594 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 42 0.05 0.05 0 42 1 0.02 0 44 1 105 by freq Benign 0.043 11 Tolerant 0.55 2.76 27 moderately conservative 227600 13q34 coagulation factor X 3738 rs3212057 XRCC3 7517 14 103243218 NM_005432 NP_005423 A/G R94H minus 4472428 693 EGP_SNPS PDR90 NIHPDR 156 0.03 0.03 0 156 1 105 "HapMap,freq" Borderline 0.19 2.79 12 conservative 600675 14q32.3 X-ray repair complementing defective repair in Chinese hamster cells 3 3739 rs3212254 RIPK3 11035 14 23875303 NM_006871 NP_006862 A/C P492Q minus 4472638 649 FHCRC POPU1 USA (20) 40 0.05 0.05 0 40 1 119 "by doubleHit,freq,cluster" moderately conservative 605817 14q11.2 receptor-interacting serine-threonine kinase 3 3740 rs3212298 PODXL 5420 7 130650994 NM_005397 NP_005388 A/G V326I minus 4472682 713 POLLAK MASTERPLATE1 "North American, South American, European, Asian, African (individuals diagnosed with focal segmental glomerulosclerosis)" 180 0.01 0.02 0.03 228 2 0.16 0.19 94 2 123 "by submitter,freq,cluster" Tolerant 1 2.89 7 conservative 602632 7q32-q33 podocalyxin-like 3741 rs3212298 PODXL 5420 7 130650994 NM_005397 NP_005388 A/G V326I minus 24048080 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.02 0.03 228 2 0.16 0.19 94 2 123 "by submitter,freq,cluster" Tolerant 1 2.89 7 conservative 602632 7q32-q33 podocalyxin-like 3742 rs3213096 IL12B 3593 5 158682907 NM_002187 NP_002178 A/G V33I minus 4473627 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 44 0.02 0.02 0 90 2 0.02 0 92 2 123 by freq Benign 0.98 26 Borderline 0.15 2.85 34 conservative 161561 5q31.1-q33.1 "interleukin 12B (natural killer cell stimulatory factor 2, cytotoxic lymphocyte maturation factor 2, p40)" 3743 rs3213096 IL12B 3593 5 158682907 NM_002187 NP_002178 A/G V33I minus 23489583 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.02 0.02 0 90 2 0.02 0 92 2 123 by freq Benign 0.98 26 Borderline 0.15 2.85 34 conservative 161561 5q31.1-q33.1 "interleukin 12B (natural killer cell stimulatory factor 2, cytotoxic lymphocyte maturation factor 2, p40)" 3744 rs3213173 E2F1 1869 20 31728907 NM_005225 NP_005216 A/G V276M minus 4473742 693 EGP_SNPS PDR90 NIHPDR 176 0.02 0.02 0 176 1 106 by freq Intolerant 0.01 2.75 43 conservative 189971 20q11.2 E2F transcription factor 1 3745 rs3213190 NID 4811 1 232467215 NM_002508 NP_002499 A/G Q1246R minus 6414337 885 TSC-CSHL HapMap-CEPH-30-trios 106 0.17 0.17 0 154 2 0.35 0.03 1872 4 123 "HapMap,doubleHit,freq,cluster" conservative 131390 1q43 nidogen (enactin) 3746 rs3213190 NID 4811 1 232467215 NM_002508 NP_002499 A/G Q1246R minus 23863110 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.17 0 154 2 0.35 0.03 1872 4 123 "HapMap,doubleHit,freq,cluster" conservative 131390 1q43 nidogen (enactin) 3747 rs3213409 JAK3 3718 19 17806696 NM_000215 NP_000206 A/G V722I minus 4474050 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 40 0.05 0.05 0 40 1 106 "HapMap,freq" Benign 0.225 10 Intolerant 0 2.81 44 conservative 600173 19p13.1 "Janus kinase 3 (a protein tyrosine kinase, leukocyte)" 3748 rs3213422 DHODH 1723 16 70600183 NM_001361 NP_001352 A/C K7Q plus 6607932 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.48 0.47 0.01 166 2 0.31 0.02 1566 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.168 6 moderately conservative 126064 16q22 dihydroorotate dehydrogenase 3749 rs3213422 DHODH 1723 16 70600183 NM_001361 NP_001352 A/C K7Q plus 24576205 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.46 0.47 0.01 166 2 0.31 0.02 1566 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.168 6 moderately conservative 126064 16q22 dihydroorotate dehydrogenase 3750 rs3213542 HELIC1 10973 6 101072727 NM_006828 NP_006819 C/T V1930M plus 17895515 1303 SEQUENOM CEPH CEPH (92) 92 0.11 0.11 0 92 1 0.11 0 1492 1 120 "by doubleHit,freq,cluster" Benign 0.952 6 Intolerant 0.02 2.77 20 conservative 6q16 "helicase, ATP binding 1" 3751 rs3213764 ATF7IP 55729 12 14478568 NM_018179 NP_060649 A/G K530R plus 24339064 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.46 0 48 1 0.36 0.03 1578 3 123 "by doubleHit,freq,cluster" conservative 12p13.2 activating transcription factor 7 interacting protein 3752 rs3213837 ERBB2IP 55914 5 65357067 NM_018695 NP_061165 A/G S274L minus 24316604 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.25 0 48 1 0.08 0.01 1534 3 123 by freq Possibly damaging 1.754 5 moderately radical 606944 5q13.1 erbb2 interacting protein 3753 rs3217921 CCND2 894 12 4279368 NM_001759 NP_001750 A/G G268R plus 4478949 693 EGP_SNPS PDR90 NIHPDR 180 0.01 0.01 0 180 1 106 HapMap Borderline 1.141 30 Tolerant 0.51 3.14 30 moderately radical 123833 12p13 cyclin D2 3754 rs3218089 CCND3 896 6 42016100 NM_001760 NP_001751 C/T P134S minus 4479154 693 EGP_SNPS PDR90 NIHPDR 176 0.01 0.01 0 176 1 106 by freq Probably damaging 2.307 28 Tolerant 0.31 2.86 37 moderately conservative 123834 6p21 cyclin D3 3755 rs3218170 E2F2 1870 1 23592835 NM_004091 NP_004082 A/G G205R minus 4479249 693 EGP_SNPS PDR90 NIHPDR 174 0.01 0.01 0 174 1 106 by freq Potentially damaging 1.298 7 Tolerant 0.4 2.86 26 moderately radical 600426 1p36 E2F transcription factor 2 3756 rs3218171 E2F2 1870 1 23592770 NM_004091 NP_004082 G/T Q226H minus 4479250 693 EGP_SNPS PDR90 NIHPDR 170 0.4 0.4 0 170 1 121 "by doubleHit,freq,cluster" Potentially damaging 1.432 7 Tolerant 0.24 2.77 38 conservative 600426 1p36 E2F transcription factor 2 3757 rs3218536 XRCC2 7516 7 151783655 NM_005431 NP_005422 A/G R188H minus 4479697 693 EGP_SNPS PDR90 NIHPDR 178 0.05 0.05 0.01 240 2 0.04 0.01 294 3 116 "by cluster,freq" Borderline 0.16 2.84 15 conservative 600375 7q36.1 X-ray repair complementing defective repair in Chinese hamster cells 2 3758 rs3218536 XRCC2 7516 7 151783655 NM_005431 NP_005422 A/G R188H minus 5586982 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.06 0.05 0.01 240 2 0.04 0.01 294 3 116 "by cluster,freq" Borderline 0.16 2.84 15 conservative 600375 7q36.1 X-ray repair complementing defective repair in Chinese hamster cells 2 3759 rs3218578 REV3L 5980 6 111802401 NM_002912 NP_002903 A/C T1206P minus 4479741 506 NCBI NIHPDR NIHPDR 148 0.02 0.02 0 148 1 106 by freq conservative 602776 6q21 "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)" 3760 rs3218595 REV3L 5980 6 111802324 NM_002912 NP_002903 G/T Q1231H minus 4479765 506 NCBI NIHPDR NIHPDR 148 0.03 0.03 0 148 1 0.15 0 46 1 123 "by cluster,freq" conservative 602776 6q21 "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)" 3761 rs3218599 REV3L 5980 6 111800817 NM_002912 NP_002903 C/G D1734H minus 4479769 506 NCBI NIHPDR NIHPDR 178 0.02 0.03 0.02 226 2 0.02 0 46 1 123 "by cluster,freq" moderately conservative 602776 6q21 "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)" 3762 rs3218599 REV3L 5980 6 111800817 NM_002912 NP_002903 C/G D1734H minus 24491669 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.03 0.02 226 2 0.02 0 46 1 123 "by cluster,freq" moderately conservative 602776 6q21 "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)" 3763 rs3218600 REV3L 5980 6 111802592 NM_002912 NP_002903 C/T S1142L minus 4479770 506 NCBI NIHPDR NIHPDR 142 0.05 0.04 0.02 190 2 0.02 0 46 1 123 by freq moderately radical 602776 6q21 "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)" 3764 rs3218600 REV3L 5980 6 111802592 NM_002912 NP_002903 C/T S1142L minus 23497114 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.04 0.02 190 2 0.02 0 46 1 123 by freq moderately radical 602776 6q21 "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)" 3765 rs3218606 REV3L 5980 6 111795775 NM_002912 NP_002903 A/G R1892H minus 4479777 506 NCBI NIHPDR NIHPDR 154 0.03 0.03 0 154 1 106 by freq conservative 602776 6q21 "REV3-like, catalytic subunit of DNA polymerase zeta (yeast)" 3766 rs3218622 PTGS2 5743 1 183377662 NM_000963 NP_000954 A/G R228H minus 4479797 506 NCBI NIHPDR NIHPDR 66 0.02 0.01 0.01 234 2 121 "by cluster,freq" Potentially damaging 1.389 64 Tolerant 1 2.87 60 conservative 600262 1q25.2-q25.3 prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase) 3767 rs3218622 PTGS2 5743 1 183377662 NM_000963 NP_000954 A/G R228H minus 6396180 693 EGP_SNPS PDR90 NIHPDR 168 0.01 0.01 0.01 234 2 121 "by cluster,freq" Potentially damaging 1.389 64 Tolerant 1 2.87 60 conservative 600262 1q25.2-q25.3 prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase) 3768 rs3218625 PTGS2 5743 1 183375198 NM_000963 NP_000954 A/G G587R minus 4479800 506 NCBI NIHPDR NIHPDR 148 0.01 0.01 0 318 2 0.02 0 48 1 123 "by cluster,freq" Benign 0.533 26 moderately radical 600262 1q25.2-q25.3 prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase) 3769 rs3218625 PTGS2 5743 1 183375198 NM_000963 NP_000954 A/G G587R minus 6396202 693 EGP_SNPS PDR90 NIHPDR 170 0.01 0.01 0 318 2 0.02 0 48 1 123 "by cluster,freq" Benign 0.533 26 moderately radical 600262 1q25.2-q25.3 prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase) 3770 rs3218673 ATM 472 11 107643255 NM_000051 NP_000042 C/T P872S plus 4479863 506 NCBI NIHPDR NIHPDR 176 0.01 0.01 0 348 2 0.02 0.03 298 3 123 "by cluster,freq" Benign 0.051 5 moderately conservative 607585 11q22-q23 "ataxia telangiectasia mutated (includes complementation groups A, C and D)" 3771 rs3218673 ATM 472 11 107643255 NM_000051 NP_000042 C/T P872S plus 6904893 693 EGP_SNPS PDR90 NIHPDR 172 0.01 0.01 0 348 2 0.02 0.03 298 3 123 "by cluster,freq" Benign 0.051 5 moderately conservative 607585 11q22-q23 "ataxia telangiectasia mutated (includes complementation groups A, C and D)" 3772 rs3218684 ATM 472 11 107603773 NM_000051 NP_000042 C/T R45W plus 4479877 506 NCBI NIHPDR NIHPDR 174 0.01 0.01 0 346 2 113 "by cluster,freq" Probably damaging 2.156 5 moderately radical 607585 11q22-q23 "ataxia telangiectasia mutated (includes complementation groups A, C and D)" 3773 rs3218684 ATM 472 11 107603773 NM_000051 NP_000042 C/T R45W plus 6904782 693 EGP_SNPS PDR90 NIHPDR 172 0.01 0.01 0 346 2 113 "by cluster,freq" Probably damaging 2.156 5 moderately radical 607585 11q22-q23 "ataxia telangiectasia mutated (includes complementation groups A, C and D)" 3774 rs3218688 ATM 472 11 107644532 NM_000051 NP_000042 C/T L942F plus 4479883 506 NCBI NIHPDR NIHPDR 174 0.01 0.01 0 346 2 113 "by cluster,freq" Borderline 1.242 5 conservative 607585 11q22-q23 "ataxia telangiectasia mutated (includes complementation groups A, C and D)" 3775 rs3218688 ATM 472 11 107644532 NM_000051 NP_000042 C/T L942F plus 6904901 693 EGP_SNPS PDR90 NIHPDR 172 0.01 0.01 0 346 2 113 "by cluster,freq" Borderline 1.242 5 conservative 607585 11q22-q23 "ataxia telangiectasia mutated (includes complementation groups A, C and D)" 3776 rs3218695 ATM 472 11 107634988 NM_000051 NP_000042 A/C D814E plus 4479895 506 NCBI NIHPDR NIHPDR 170 0.01 0.01 0 336 2 0.02 0 46 1 123 "by cluster,freq" Borderline 1.211 5 conservative 607585 11q22-q23 "ataxia telangiectasia mutated (includes complementation groups A, C and D)" 3777 rs3218695 ATM 472 11 107634988 NM_000051 NP_000042 A/C D814E plus 6904886 693 EGP_SNPS PDR90 NIHPDR 166 0.01 0.01 0 336 2 0.02 0 46 1 123 "by cluster,freq" Borderline 1.211 5 conservative 607585 11q22-q23 "ataxia telangiectasia mutated (includes complementation groups A, C and D)" 3778 rs3218707 ATM 472 11 107619937 NM_000051 NP_000042 C/G V182L plus 4479916 506 NCBI NIHPDR NIHPDR 178 0.01 0.01 0 178 1 106 by freq Benign 0.723 5 conservative 607585 11q22-q23 "ataxia telangiectasia mutated (includes complementation groups A, C and D)" 3779 rs3218708 ATM 472 11 107644512 NM_000051 NP_000042 C/T T935M plus 4479919 506 NCBI NIHPDR NIHPDR 172 0.01 0.01 0 344 2 113 "by cluster,freq" Borderline 1.002 5 moderately conservative 607585 11q22-q23 "ataxia telangiectasia mutated (includes complementation groups A, C and D)" 3780 rs3218708 ATM 472 11 107644512 NM_000051 NP_000042 C/T T935M plus 6904900 693 EGP_SNPS PDR90 NIHPDR 172 0.01 0.01 0 344 2 113 "by cluster,freq" Borderline 1.002 5 moderately conservative 607585 11q22-q23 "ataxia telangiectasia mutated (includes complementation groups A, C and D)" 3781 rs3218750 POLD1 5424 19 55597134 NM_002691 NP_002682 A/G R177H plus 4480017 506 NCBI NIHPDR NIHPDR 158 0.01 0.01 0 328 2 108 "by cluster,freq" Possibly damaging 1.895 17 Borderline 0.13 2.96 22 conservative 174761 19q13.3 "polymerase (DNA directed), delta 1, catalytic subunit 125kDa" 3782 rs3218750 POLD1 5424 19 55597134 NM_002691 NP_002682 A/G R177H plus 4480824 693 EGP_SNPS PDR90 NIHPDR 170 0.01 0.01 0 328 2 108 "by cluster,freq" Possibly damaging 1.895 17 Borderline 0.13 2.96 22 conservative 174761 19q13.3 "polymerase (DNA directed), delta 1, catalytic subunit 125kDa" 3783 rs3218772 POLD1 5424 19 55594008 NM_002691 NP_002682 C/T R30W plus 4480058 506 NCBI NIHPDR NIHPDR 158 0.01 0.01 0 338 2 118 "by cluster,freq" moderately radical 174761 19q13.3 "polymerase (DNA directed), delta 1, catalytic subunit 125kDa" 3784 rs3218772 POLD1 5424 19 55594008 NM_002691 NP_002682 C/T R30W plus 4480809 693 EGP_SNPS PDR90 NIHPDR 180 0.01 0.01 0 338 2 118 "by cluster,freq" moderately radical 174761 19q13.3 "polymerase (DNA directed), delta 1, catalytic subunit 125kDa" 3785 rs3218773 POLD1 5424 19 55593976 NM_002691 NP_002682 A/G R19H plus 4480059 506 NCBI NIHPDR NIHPDR 160 0.04 0.03 0.01 340 2 0.03 0.02 244 2 118 "by cluster,freq" conservative 174761 19q13.3 "polymerase (DNA directed), delta 1, catalytic subunit 125kDa" 3786 rs3218773 POLD1 5424 19 55593976 NM_002691 NP_002682 A/G R19H plus 4480808 693 EGP_SNPS PDR90 NIHPDR 180 0.03 0.03 0.01 340 2 0.03 0.02 244 2 118 "by cluster,freq" conservative 174761 19q13.3 "polymerase (DNA directed), delta 1, catalytic subunit 125kDa" 3787 rs3218775 POLD1 5424 19 55610041 NM_002691 NP_002682 A/G R849H plus 4480062 506 NCBI NIHPDR NIHPDR 176 0.01 0.02 0.01 356 2 108 "by cluster,freq" Benign 0.214 30 Tolerant 0.22 2.77 32 conservative 174761 19q13.3 "polymerase (DNA directed), delta 1, catalytic subunit 125kDa" 3788 rs3218775 POLD1 5424 19 55610041 NM_002691 NP_002682 A/G R849H plus 4480892 693 EGP_SNPS PDR90 NIHPDR 180 0.02 0.02 0.01 356 2 108 "by cluster,freq" Benign 0.214 30 Tolerant 0.22 2.77 32 conservative 174761 19q13.3 "polymerase (DNA directed), delta 1, catalytic subunit 125kDa" 3789 rs3218778 POLI 11201 18 50054338 NM_007195 NP_009126 A/G R71G plus 4480070 506 NCBI NIHPDR NIHPDR 172 0.01 0.01 0 328 2 108 "by cluster,freq" Possibly damaging 1.575 5 Intolerant 0 2.83 26 moderately radical 605252 18q21.1 polymerase (DNA directed) iota 3790 rs3218778 POLI 11201 18 50054338 NM_007195 NP_009126 A/G R71G plus 4916669 693 EGP_SNPS PDR90 NIHPDR 156 0.01 0.01 0 328 2 108 "by cluster,freq" Possibly damaging 1.575 5 Intolerant 0 2.83 26 moderately radical 605252 18q21.1 polymerase (DNA directed) iota 3791 rs3218783 POLI 11201 18 50063234 NM_007195 NP_009126 A/G E251K plus 4480076 506 NCBI NIHPDR NIHPDR 178 0.01 0.01 0 338 2 108 "by cluster,freq" Benign 0.9 6 Tolerant 0.42 2.83 27 moderately conservative 605252 18q21.1 polymerase (DNA directed) iota 3792 rs3218783 POLI 11201 18 50063234 NM_007195 NP_009126 A/G E251K plus 4916708 693 EGP_SNPS PDR90 NIHPDR 160 0.01 0.01 0 338 2 108 "by cluster,freq" Benign 0.9 6 Tolerant 0.42 2.83 27 moderately conservative 605252 18q21.1 polymerase (DNA directed) iota 3793 rs3218784 POLI 11201 18 50061258 NM_007195 NP_009126 A/G I236M plus 4480078 506 NCBI NIHPDR NIHPDR 180 0.02 0.02 0.01 474 3 108 "HapMap,freq,cluster" Benign 0.675 6 Intolerant 0.01 2.85 26 conservative 605252 18q21.1 polymerase (DNA directed) iota 3794 rs3218784 POLI 11201 18 50061258 NM_007195 NP_009126 A/G I236M plus 4916703 693 EGP_SNPS PDR90 NIHPDR 174 0.02 0.02 0.01 474 3 108 "HapMap,freq,cluster" Benign 0.675 6 Intolerant 0.01 2.85 26 conservative 605252 18q21.1 polymerase (DNA directed) iota 3795 rs3218784 POLI 11201 18 50061258 NM_007195 NP_009126 A/G I236M plus 4916703 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.01 0.02 0.01 474 3 108 "HapMap,freq,cluster" Benign 0.675 6 Intolerant 0.01 2.85 26 conservative 605252 18q21.1 polymerase (DNA directed) iota 3796 rs3218786 POLI 11201 18 50074207 NM_007195 NP_009126 C/T F507S plus 4480080 506 NCBI NIHPDR NIHPDR 156 0.01 0.01 0.01 502 4 123 "HapMap,freq,cluster" Possibly damaging 1.8 5 radical 605252 18q21.1 polymerase (DNA directed) iota 3797 rs3218786 POLI 11201 18 50074207 NM_007195 NP_009126 C/T F507S plus 4916787 693 EGP_SNPS PDR90 NIHPDR 178 0.01 0.01 0.01 502 4 123 "HapMap,freq,cluster" Possibly damaging 1.8 5 radical 605252 18q21.1 polymerase (DNA directed) iota 3798 rs3218786 POLI 11201 18 50074207 NM_007195 NP_009126 C/T F507S plus 4916787 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.01 0.01 0.01 502 4 123 "HapMap,freq,cluster" Possibly damaging 1.8 5 radical 605252 18q21.1 polymerase (DNA directed) iota 3799 rs3218786 POLI 11201 18 50074207 NM_007195 NP_009126 C/T F507S plus 24531260 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.01 0.01 502 4 123 "HapMap,freq,cluster" Possibly damaging 1.8 5 radical 605252 18q21.1 polymerase (DNA directed) iota 3800 rs3218787 POLI 11201 18 50074290 NM_007195 NP_009126 C/T C535R plus 4480081 506 NCBI NIHPDR NIHPDR 156 0.01 0.01 0 334 2 108 "by cluster,freq" Probably damaging 2.7 5 radical 605252 18q21.1 polymerase (DNA directed) iota 3801 rs3218787 POLI 11201 18 50074290 NM_007195 NP_009126 C/T C535R plus 4916788 693 EGP_SNPS PDR90 NIHPDR 178 0.01 0.01 0 334 2 108 "by cluster,freq" Probably damaging 2.7 5 radical 605252 18q21.1 polymerase (DNA directed) iota 3802 rs3218790 POLE2 5427 14 49186903 NM_002692 NP_002683 A/T K443X minus 4480085 506 NCBI NIHPDR NIHPDR 170 0.01 0.01 0 170 1 106 "HapMap,freq" Probably damaging Intolerant radical 602670 14q21-q22 "polymerase (DNA directed), epsilon 2 (p59 subunit)" 3803 rs3219057 ADPRT 142 1 222879951 NM_001618 NP_001609 A/G V334I minus 4480443 693 EGP_SNPS PDR90 NIHPDR 176 0.01 0.01 0 176 1 106 by freq Benign 0.62 8 Tolerant 0.59 2.81 20 conservative 173870 1q41-q42 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase) 3804 rs3219145 ADPRT 142 1 222857564 NM_001618 NP_001609 A/G K940R minus 4480554 693 EGP_SNPS PDR90 NIHPDR 176 0.01 0.01 0 176 1 0.01 0.01 252 2 121 "by cluster,freq" Borderline 1.047 13 conservative 173870 1q41-q42 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase) 3805 rs3219484 MUTYH 4595 1 45469249 NM_012222 NP_036354 A/G V22M minus 4911242 693 EGP_SNPS PDR90 NIHPDR 180 0.02 0.03 0.02 228 2 123 by freq conservative 604933 1p34.3-p32.1 mutY homolog (E. coli) 3806 rs3219484 MUTYH 4595 1 45469249 NM_012222 NP_036354 A/G V22M minus 24607457 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.03 0.02 228 2 123 by freq conservative 604933 1p34.3-p32.1 mutY homolog (E. coli) 3807 rs3219489 MUTYH 4595 1 45466598 NM_012222 NP_036354 C/G Q335H minus 4911247 693 EGP_SNPS PDR90 NIHPDR 180 0.41 0.41 0 180 1 0.44 0 1488 1 120 "by doubleHit,freq,cluster" Borderline 1.125 6 conservative 604933 1p34.3-p32.1 mutY homolog (E. coli) 3808 rs3729961 IL6ST 3572 5 55287688 NM_002184 NP_002175 C/G L397V minus 16360316 649 FHCRC POPU1 USA (20) 40 0.18 0.18 0 40 1 120 "by cluster,freq" Borderline 1.075 5 Tolerant 0.57 2.76 17 conservative 600694 5q11 "interleukin 6 signal transducer (gp130, oncostatin M receptor)" 3809 rs3729986 MYBPC3 4607 11 47328174 NM_000256 NP_000247 A/G V158M minus 16341813 693 EGP_SNPS PDR90 NIHPDR 178 0.03 0.03 0 178 1 120 "by cluster,freq" Benign 0.68 9 Intolerant 0.02 3.04 25 conservative 600958 11p11.2 "myosin binding protein C, cardiac" 3810 rs3729989 MYBPC3 4607 11 47326617 NM_000256 NP_000247 A/G S236G minus 16341824 693 EGP_SNPS PDR90 NIHPDR 164 0.09 0.09 0 164 1 120 "by cluster,freq" Potentially damaging 1.38 11 Tolerant 0.74 2.99 27 moderately conservative 600958 11p11.2 "myosin binding protein C, cardiac" 3811 rs3730463 POLL 27343 10 103334579 NM_013274 NP_037406 A/C T221P minus 4916425 693 EGP_SNPS PDR90 NIHPDR 180 0.07 0.07 0 180 1 111 "by cluster,freq" Potentially damaging 1.294 7 Intolerant 0.05 2.94 11 conservative 606343 10q23 "polymerase (DNA directed), lambda" 3812 rs3730477 POLL 27343 10 103330046 NM_013274 NP_037406 C/T R438W minus 4916439 693 EGP_SNPS PDR90 NIHPDR 168 0.13 0.13 0.01 216 2 0.02 0 94 2 123 "by doubleHit,freq,cluster" Possibly damaging 1.835 10 Intolerant 0.03 2.8 21 moderately radical 606343 10q23 "polymerase (DNA directed), lambda" 3813 rs3730477 POLL 27343 10 103330046 NM_013274 NP_037406 C/T R438W minus 24493023 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.13 0.01 216 2 0.02 0 94 2 123 "by doubleHit,freq,cluster" Possibly damaging 1.835 10 Intolerant 0.03 2.8 21 moderately radical 606343 10q23 "polymerase (DNA directed), lambda" 3814 rs3730911 LIG1 3978 19 53344862 NM_000234 NP_000225 A/G G249E minus 4916883 693 EGP_SNPS PDR90 NIHPDR 180 0.01 0.01 0 180 1 0.01 0.01 250 2 113 "by cluster,freq" Tolerant 1 2.89 19 moderately conservative 126391 19q13.2-q13.3 "ligase I, DNA, ATP-dependent" 3815 rs3730933 LIG1 3978 19 53339009 NM_000234 NP_000225 A/G N267S minus 4916905 693 EGP_SNPS PDR90 NIHPDR 160 0.02 0.02 0 160 1 0.01 0.01 246 2 113 "HapMap,freq,cluster" Possibly damaging 1.512 6 Tolerant 0.66 2.92 19 conservative 126391 19q13.2-q13.3 "ligase I, DNA, ATP-dependent" 3816 rs3730980 LIG1 3978 19 53330834 NM_000234 NP_000225 A/G M480V minus 4916952 693 EGP_SNPS PDR90 NIHPDR 176 0.01 0.01 0 176 1 0.01 0.01 252 2 113 "by cluster,freq" Borderline 1.07 6 Tolerant 1 2.99 18 conservative 126391 19q13.2-q13.3 "ligase I, DNA, ATP-dependent" 3817 rs3731003 LIG1 3978 19 53323070 NM_000234 NP_000225 C/T T614I minus 4916978 693 EGP_SNPS PDR90 NIHPDR 176 0.01 0.01 0 176 1 0.02 0.03 298 3 123 "by cluster,freq" Possibly damaging 1.54 6 Intolerant 0.03 2.79 27 moderately conservative 126391 19q13.2-q13.3 "ligase I, DNA, ATP-dependent" 3818 rs3731008 LIG1 3978 19 53318362 NM_000234 NP_000225 G/T R677L minus 4916985 693 EGP_SNPS PDR90 NIHPDR 180 0.01 0.01 0 180 1 107 HapMap Possibly damaging 1.622 6 Borderline 0.13 2.79 27 moderately radical 126391 19q13.2-q13.3 "ligase I, DNA, ATP-dependent" 3819 rs3731249 CDKN2A 1029 9 21960916 NM_000077 NP_000068 A/G A148T minus 4917238 693 EGP_SNPS PDR90 NIHPDR 172 0.03 0.05 0.02 326 3 0.04 0 248 2 116 "by cluster,freq" Potentially damaging 1.32 9 Borderline 0.11 2.97 19 moderately conservative 600160 9p21 "cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)" 3820 rs3731249 CDKN2A 1029 9 21960916 NM_000077 NP_000068 A/G A148T minus 4917238 1303 SEQUENOM CEPH CEPH (92) 92 0.06 0.05 0.02 326 3 0.04 0 248 2 116 "by cluster,freq" Potentially damaging 1.32 9 Borderline 0.11 2.97 19 moderately conservative 600160 9p21 "cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)" 3821 rs3731249 CDKN2A 1029 9 21960916 NM_000077 NP_000068 A/G A148T minus 8819697 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.08 0.05 0.02 326 3 0.04 0 248 2 116 "by cluster,freq" Potentially damaging 1.32 9 Borderline 0.11 2.97 19 moderately conservative 600160 9p21 "cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)" 3822 rs3731877 TTLL4 9654 2 219428004 NM_014640 NP_055455 C/G E34Q minus 23727607 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.44 0 48 1 0.14 0.07 1588 3 123 "by cluster,freq" conservative 2p24.3-p24.1 "tubulin tyrosine ligase-like family, member 4" 3823 rs3732235 ZFML 27332 2 71542764 NM_014497 NP_055312 C/T N980S minus 23216673 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 0.15 0.01 92 2 123 "by cluster,freq" conservative 2p13.2-p13.1 NP220 nuclear protein 3824 rs3732299 HK2 3099 2 75011132 NM_000189 NP_000180 A/T Q142H minus 4918290 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.23 0.23 0 120 1 0.24 0 1496 1 107 "HapMap,freq" Borderline 1.224 34 Tolerant 0.24 2.77 55 conservative 601125 2p13 hexokinase 2 3825 rs3732378 CX3CR1 1524 3 39282166 NM_001337 NP_001328 A/G T280M plus 5586363 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.15 0.15 0 110 2 0.06 0.02 1942 7 123 "by cluster,freq" Possibly damaging 1.711 5 Intolerant 0.02 2.92 256 moderately conservative 601470 3p21.3 chemokine (C-X3-C motif) receptor 1 3826 rs3732378 CX3CR1 1524 3 39282166 NM_001337 NP_001328 A/G T280M plus 24299415 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 110 2 0.06 0.02 1942 7 123 "by cluster,freq" Possibly damaging 1.711 5 Intolerant 0.02 2.92 256 moderately conservative 601470 3p21.3 chemokine (C-X3-C motif) receptor 1 3827 rs3732379 CX3CR1 1524 3 39282260 NM_001337 NP_001328 C/T V249I plus 5586362 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.24 0.22 0.04 110 2 0.07 0.04 1940 7 123 "by cluster,freq" Benign 0.089 5 Tolerant 1 2.92 256 conservative 601470 3p21.3 chemokine (C-X3-C motif) receptor 1 3828 rs3732379 CX3CR1 1524 3 39282260 NM_001337 NP_001328 C/T V249I plus 24299422 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.22 0.04 110 2 0.07 0.04 1940 7 123 "by cluster,freq" Benign 0.089 5 Tolerant 1 2.92 256 conservative 601470 3p21.3 chemokine (C-X3-C motif) receptor 1 3829 rs3732401 GTF2E1 2960 3 121982783 NM_005513 NP_005504 C/T P366S plus 23900015 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 0.43 0.08 1584 3 123 "by doubleHit,freq,cluster" Possibly damaging 1.74 6 Tolerant 0.28 3.08 12 moderately conservative 189962 3q21-q24 "general transcription factor IIE, polypeptide 1, alpha 56kDa" 3830 rs3732675 TIP120B 23066 3 12833028 XM_371617 XP_371617 C/T S440P plus 24304654 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.42 0 48 1 0.46 0.06 1576 3 123 "by doubleHit,freq,cluster" Probably damaging 2.1 15 Tolerant 1 2.83 33 moderately conservative 3p25.2 TBP-interacting protein 3831 rs3732781 ZNF80 7634 3 115437877 NM_007136 NP_009067 G/T Y245X minus 24377860 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.3 0.3 0 44 1 0.11 0.01 78 2 123 by freq Probably damaging Intolerant radical 194553 3p12-qter zinc finger protein 80 (pT17) 3832 rs3733011 HRG 3273 3 187872261 NM_000412 NP_000403 C/T I180T plus 23914231 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.07 0.07 0 44 1 0.11 0.03 1580 3 123 "by doubleHit,freq,cluster" Intolerant 0.02 2.84 51 moderately conservative 142640 3q27 histidine-rich glycoprotein 3833 rs3733227 SCD4 79966 4 83939390 NM_024906 NP_079182 C/G E197Q minus 23836003 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.23 0 48 1 0.4 0.02 1586 3 123 "by doubleHit,freq,cluster" Potentially intolerant 0.1 2.87 56 conservative 608370 4q21.3 stearoyl-CoA desaturase 4 3834 rs3733228 SCD4 79966 4 83939243 NM_024906 NP_079182 A/C L246M minus 23836000 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.4 0 48 1 0.45 0.07 1590 3 123 "by doubleHit,freq,cluster" conservative 608370 4q21.3 stearoyl-CoA desaturase 4 3835 rs3733617 ANK2 287 4 114635881 NM_001148 NP_001139 C/T P2835S plus 4919612 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.03 0.03 0.01 168 2 0.14 0.06 1586 3 123 "HapMap,freq,cluster" moderately conservative 106410 4q25-q27 "ankyrin 2, neuronal" 3836 rs3733617 ANK2 287 4 114635881 NM_001148 NP_001139 C/T P2835S plus 23730944 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.03 0.01 168 2 0.14 0.06 1586 3 123 "HapMap,freq,cluster" moderately conservative 106410 4q25-q27 "ankyrin 2, neuronal" 3837 rs3733694 PCDHB8 56128 5 140538712 NM_019120 NP_061993 C/T K305E minus 4919689 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.09 0.09 0.01 166 2 0.07 0.03 1596 3 123 "HapMap,freq" Possibly damaging 1.545 100 Tolerant 0.8 2.77 132 moderately conservative 606334 5q31 protocadherin beta 8 3838 rs3733694 PCDHB8 56128 5 140538712 NM_019120 NP_061993 C/T K305E minus 23351119 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.09 0.01 166 2 0.07 0.03 1596 3 123 "HapMap,freq" Possibly damaging 1.545 100 Tolerant 0.8 2.77 132 moderately conservative 606334 5q31 protocadherin beta 8 3839 rs3733699 PCDHB3 56132 5 140461659 NM_018937 NP_061760 A/T R414S minus 19610355 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.1 0.1 0 120 1 0.11 0 1494 1 120 "HapMap,freq,cluster" Borderline 1.153 105 Tolerant 0.86 2.77 132 moderately radical 606329 5q31 protocadherin beta 3 3840 rs3733890 BHMT 635 5 78457715 NM_001713 NP_001704 A/G R239Q plus 10251468 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.28 0.27 0.01 162 2 0.23 0.04 1588 3 123 "HapMap,doubleHit,freq,cluster" Borderline 1.117 13 conservative 602888 5q13.1-q15 betaine-homocysteine methyltransferase 3841 rs3733890 BHMT 635 5 78457715 NM_001713 NP_001704 A/G R239Q plus 23976493 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.26 0.27 0.01 162 2 0.23 0.04 1588 3 123 "HapMap,doubleHit,freq,cluster" Borderline 1.117 13 conservative 602888 5q13.1-q15 betaine-homocysteine methyltransferase 3842 rs3734166 CDC25C 995 5 137693222 NM_001790 NP_001781 A/G R70C plus 16338848 693 EGP_SNPS PDR90 NIHPDR 180 0.34 0.31 0.07 228 2 0.44 0.01 1576 3 123 "by cluster,freq" Benign 0.507 6 radical 157680 5q31 cell division cycle 25C 3843 rs3734166 CDC25C 995 5 137693222 NM_001790 NP_001781 A/G R70C plus 23675035 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.31 0.07 228 2 0.44 0.01 1576 3 123 "by cluster,freq" Benign 0.507 6 radical 157680 5q31 cell division cycle 25C 3844 rs3734313 IMPG1 3617 6 76697501 NM_001563 NP_001554 A/G R711H minus 23973202 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.17 0 48 1 0.28 0.04 1580 3 123 "by cluster,freq" Possibly damaging 1.582 5 conservative 602870 6q14.2-q15 interphotoreceptor matrix proteoglycan 1 3845 rs3734354 SIM1 6492 6 100975500 NM_005068 NP_005059 A/C P352T minus 23985113 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.47 0.09 1584 3 123 "by cluster,freq" Possibly damaging 1.595 7 Borderline 0.11 2.78 95 conservative 603128 6q16.3-q21 single-minded homolog 1 (Drosophila) 3846 rs3734355 SIM1 6492 6 100975442 NM_005068 NP_005059 C/T A371V minus 23985102 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.47 0.09 1570 3 123 "by cluster,freq" Benign 0.098 7 Borderline 0.2 2.78 87 moderately conservative 603128 6q16.3-q21 single-minded homolog 1 (Drosophila) 3847 rs3735007 ZC3HAV1 56829 7 138189752 NM_020119 NP_064504 C/T T851I minus 14566264 885 TSC-CSHL HapMap-CEPH-30-trios 60 0.5 0.48 0.03 108 2 0.33 0.03 1574 3 123 "HapMap,doubleHit,freq,cluster" Tolerant 0.53 2.96 61 moderately conservative 607312 7q34 "zinc finger CCCH type, antiviral 1" 3848 rs3735007 ZC3HAV1 56829 7 138189752 NM_020119 NP_064504 C/T T851I minus 24478660 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.48 0.03 108 2 0.33 0.03 1574 3 123 "HapMap,doubleHit,freq,cluster" Tolerant 0.53 2.96 61 moderately conservative 607312 7q34 "zinc finger CCCH type, antiviral 1" 3849 rs3735099 CHST12 55501 7 2245670 NM_018641 NP_061111 A/C P52H plus 23918419 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.02 0.02 0 46 1 0.18 0.01 1544 2 123 "by cluster,freq" Benign 0.099 5 moderately conservative 7p22 carbohydrate (chondroitin 4) sulfotransferase 12 3850 rs3735156 MLL3 58508 7 151386716 NM_170606 NP_733751 C/G R526P minus 14582202 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.03 0.03 0 120 1 0.09 0 1480 1 120 "HapMap,doubleHit,freq,cluster" moderately radical 606833 7q34-q36 myeloid/lymphoid or mixed-lineage leukemia 3 3851 rs3735252 LMTK2 22853 7 97381228 NM_014916 NP_055731 C/G P30A plus 23911891 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.1 0.01 1010 3 123 "by doubleHit,freq,cluster" conservative 7q22.1 lemur tyrosine kinase 2 3852 rs3736001 PSCA 8000 8 143759809 NM_005672 NP_005663 A/G E39K plus 23962047 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.11 0 1526 2 123 "by cluster,freq" Tolerant 0.68 2.9 11 moderately conservative 602470 8q24.2 prostate stem cell antigen 3853 rs3736228 LRP5 4041 11 67957871 NM_002335 NP_002326 C/T A1330V plus 6905351 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.12 0.12 0 118 1 0.27 0 1498 1 113 "HapMap,freq,cluster" Benign 0.071 6 Tolerant 1 2.77 21 moderately conservative 603506 11q13.4 low density lipoprotein receptor-related protein 5 3854 rs3736563 UBP1 7342 3 33433270 NM_014517 NP_055332 C/T N109S plus 23873858 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.35 0 48 1 0.47 0.01 94 2 123 "by cluster,freq" Benign 0.725 23 Tolerant 0.81 2.99 53 conservative 3p22.3 upstream binding protein 1 (LBP-1a) 3855 rs3736930 ATP6V1G3 127124 1 195237487 NM_133326 NP_579872 C/T R36Q plus 23868951 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.05 0 1522 2 123 "by cluster,freq" conservative 1q31.3 "ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G isoform 3" 3856 rs3737657 ETNK2 55224 1 200842204 NM_018208 NP_060678 A/G R227Q minus 24158552 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.06 0.02 1590 3 123 "by cluster,freq" Benign 0.084 5 Tolerant 0.46 2.76 35 conservative 1q32.1 putative ethanolamine kinase 3857 rs3738099 ALPL 249 1 21640041 NM_000478 NP_000469 A/G Y263H minus 23844815 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 0.45 0.03 1588 3 123 "by cluster,freq" Benign 0.654 54 Tolerant 0.59 2.87 50 moderately conservative 171760 1p36.1-p34 "alkaline phosphatase, liver/bone/kidney" 3858 rs3738372 CAPN2 824 1 220260815 NM_001748 NP_001739 G/T K568Q minus 24635280 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.25 0 48 1 0.21 0.06 92 2 123 "by doubleHit,freq,cluster" Possibly damaging 1.762 62 Intolerant 0.01 2.88 80 moderately conservative 114230 1q41-q42 "calpain 2, (m/II) large subunit" 3859 rs3738671 TRIT1 54802 1 39984981 NM_017646 NP_060116 A/T F202L minus 4924671 902 AFFY Caucasian 24 0.04 0.12 0.17 34 2 0.34 0.05 1548 4 107 by freq Potentially damaging 1.31 10 Tolerant 0.76 2.77 14 conservative 1p35.3-p34.1 tRNA isopentenyltransferase 1 3860 rs3738671 TRIT1 54802 1 39984981 NM_017646 NP_060116 A/T F202L minus 4924671 904 AFFY CEPH 10 0.3 0.12 0.17 34 2 0.34 0.05 1548 4 107 by freq Potentially damaging 1.31 10 Tolerant 0.76 2.77 14 conservative 1p35.3-p34.1 tRNA isopentenyltransferase 1 3861 rs3738888 BARD1 580 2 215420670 NM_000465 NP_000456 C/T R658C minus 5586279 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.05 0.02 0.02 200 3 0.02 0 346 4 123 "by cluster,freq" radical 601593 2q34-q35 BRCA1 associated RING domain 1 3862 rs3738888 BARD1 580 2 215420670 NM_000465 NP_000456 C/T R658C minus 5586279 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.02 0.02 200 3 0.02 0 346 4 123 "by cluster,freq" radical 601593 2q34-q35 BRCA1 associated RING domain 1 3863 rs3738888 BARD1 580 2 215420670 NM_000465 NP_000456 C/T R658C minus 24349914 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.02 0.02 0.02 200 3 0.02 0 346 4 123 "by cluster,freq" radical 601593 2q34-q35 BRCA1 associated RING domain 1 3864 rs3738952 CUL3 8452 2 225187983 NM_003590 NP_003581 A/G V567I minus 24165575 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.31 0.02 1524 2 123 "by doubleHit,freq,cluster" Benign 0.648 5 Tolerant 0.5 2.9 32 conservative 603136 2q36.3 cullin 3 3865 rs3739038 LRRFIP1 9208 2 238454703 NM_004735 NP_004726 C/G H759D minus 23887289 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.27 0 48 1 0.41 0.11 94 2 123 "by doubleHit,freq,cluster" moderately conservative 603256 2q37.3 leucine rich repeat (in FLII) interacting protein 1 3866 rs3739124 PTPN18 26469 2 130843881 NM_014369 NP_055184 C/T M193V minus 24265289 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.02 0.02 0 46 1 0.03 0 1546 2 123 by freq Possibly damaging 1.713 6 Tolerant 0.48 2.76 56 conservative 606587 2q21.2 "protein tyrosine phosphatase, non-receptor type 18 (brain-derived)" 3867 rs3739168 PNKP 11284 19 55062216 NM_007254 NP_009185 C/T P20S minus 4925169 693 EGP_SNPS PDR90 NIHPDR 180 0.02 0.02 0 180 1 107 by freq moderately conservative 605610 19q13.3-q13.4 polynucleotide kinase 3'-phosphatase 3868 rs3739185 PNKP 11284 19 55059433 NM_007254 NP_009185 A/C R180S minus 4925187 693 EGP_SNPS PDR90 NIHPDR 178 0.01 0.01 0 178 1 107 by freq Potentially damaging 1.35 5 Tolerant 0.31 2.8 34 moderately radical 605610 19q13.3-q13.4 polynucleotide kinase 3'-phosphatase 3869 rs3739186 PNKP 11284 19 55059298 NM_007254 NP_009185 A/T Y196N minus 4925188 693 EGP_SNPS PDR90 NIHPDR 176 0.02 0.02 0 176 1 107 by freq Probably damaging 2.025 6 Borderline 0.13 2.82 32 moderately radical 605610 19q13.3-q13.4 polynucleotide kinase 3'-phosphatase 3870 rs3739407 MTUS1 57509 8 17657155 XM_372031 XP_372031 C/T C148R minus 23735805 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.17 0 48 1 0.39 0.02 1567 3 123 "by doubleHit,freq,cluster" radical 8p22 mitochondrial tumor suppressor 1 3871 rs3739510 LAMC3 10319 9 130966125 NM_006059 NP_006050 C/G R770G minus 6245797 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.17 0.14 0.06 168 2 0.41 0.07 1554 3 123 "HapMap,freq,cluster" Tolerant 0.49 3.19 14 moderately radical 604349 9q31-q34 "laminin, gamma 3" 3872 rs3739510 LAMC3 10319 9 130966125 NM_006059 NP_006050 C/G R770G minus 23895341 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.14 0.06 168 2 0.41 0.07 1554 3 123 "HapMap,freq,cluster" Tolerant 0.49 3.19 14 moderately radical 604349 9q31-q34 "laminin, gamma 3" 3873 rs3739722 GRIN3A 116443 9 101415237 NM_133445 NP_597702 A/G R1041Q minus 24052112 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.23 0.02 1594 3 123 "by cluster,freq" conservative 606650 9q31.1 "glutamate receptor, ionotropic, N-methyl-D-aspartate 3A" 3874 rs3739915 TTF1 7270 9 132306684 NM_007344 NP_031370 G/T G360V minus 10513831 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.07 0.07 0 120 1 0.2 0 1498 1 120 "HapMap,doubleHit,freq,cluster" moderately radical 600777 9q34.3 "transcription termination factor, RNA polymerase I" 3875 rs3739916 TTF1 7270 9 132306561 NM_007344 NP_031370 A/G R401Q minus 4925919 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.06 0.06 0 120 1 0.03 0 1494 1 107 "HapMap,freq" conservative 600777 9q34.3 "transcription termination factor, RNA polymerase I" 3876 rs3739922 KIAA0625 23064 9 132233084 NM_015046 NP_055861 G/T F1152C minus 4925925 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.02 0.03 0.01 168 2 0.16 0.16 94 2 123 "HapMap,doubleHit,freq,cluster" radical 608465 9q34.3 senataxin 3877 rs3739922 KIAA0625 23064 9 132233084 NM_015046 NP_055861 G/T F1152C minus 24002638 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.03 0.01 168 2 0.16 0.16 94 2 123 "HapMap,doubleHit,freq,cluster" radical 608465 9q34.3 senataxin 3878 rs3740015 DHTKD1 55526 10 12171087 NM_018706 NP_061176 G/T Y272D plus 24302960 1371 PERLEGEN AFD_EUR_PANEL European American (24) 23 0.5 0.5 0 23 1 0.46 0.03 1200 3 123 "by doubleHit,freq,cluster" radical 10p14 dehydrogenase E1 and transketolase domain containing 1 3879 rs3740231 MYO3A 53904 10 26503049 NM_017433 NP_059129 A/T T1284S minus 24688625 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.38 0 48 1 0.31 0.04 94 2 123 "by doubleHit,freq,cluster" moderately conservative 606808 10p11.1 myosin IIIA 3880 rs3740469 SLK 9748 10 105753016 NM_014720 NP_055535 A/G T697I minus 23510995 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.17 0 48 1 0.12 0.02 1572 3 123 "by cluster,freq" Possibly damaging 1.77 8 Tolerant 0.44 3.04 20 moderately conservative 10q25.1 SNF1 sucrose nonfermenting like kinase (yeast) 3881 rs3740526 MMS19L 64210 10 99210697 NM_022362 NP_071757 A/G G790D minus 24090459 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.39 0.39 0 46 1 0.4 0.03 1590 3 123 "by doubleHit,freq,cluster" Benign 0.096 9 Tolerant 0.63 3.04 12 moderately conservative 10q24-q25 "MMS19-like (MET18 homolog, S. cerevisiae)" 3882 rs3740753 PGR 5241 11 100503981 NM_000926 NP_000917 C/G S344T plus 16343360 693 EGP_SNPS PDR90 NIHPDR 174 0.09 0.09 0 174 1 120 "by cluster,freq" Borderline 1.149 11 moderately conservative 607311 11q22-q23 progesterone receptor 3883 rs3740909 CDON 50937 11 125394736 NM_016952 NP_058648 C/T E162K plus 10699381 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.07 0.09 0.04 168 2 0.11 0.01 1578 3 123 "HapMap,doubleHit,freq,cluster" Tolerant 1 2.77 31 moderately conservative 608707 11q23-q24 cell adhesion molecule-related/down-regulated by oncogenes 3884 rs3740909 CDON 50937 11 125394736 NM_016952 NP_058648 C/T E162K plus 23329308 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.09 0.04 168 2 0.11 0.01 1578 3 123 "HapMap,doubleHit,freq,cluster" Tolerant 1 2.77 31 moderately conservative 608707 11q23-q24 cell adhesion molecule-related/down-regulated by oncogenes 3885 rs3740912 CDON 50937 11 125396479 NM_016952 NP_058648 C/T V75I plus 24364299 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.39 0.39 0 46 1 0.23 0.08 94 2 123 "by doubleHit,freq,cluster" conservative 608707 11q23-q24 cell adhesion molecule-related/down-regulated by oncogenes 3886 rs3740955 RAG1 5896 11 36552176 NM_000448 NP_000439 A/G H249R plus 5606000 693 EGP_SNPS PDR90 NIHPDR 164 0.38 0.38 0.02 332 3 0.23 0.02 1596 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.013 331 conservative 179615 11p13 recombination activating gene 1 3887 rs3740955 RAG1 5896 11 36552176 NM_000448 NP_000439 A/G H249R plus 5606000 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.39 0.38 0.02 332 3 0.23 0.02 1596 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.013 331 conservative 179615 11p13 recombination activating gene 1 3888 rs3740955 RAG1 5896 11 36552176 NM_000448 NP_000439 A/G H249R plus 24569612 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.38 0.02 332 3 0.23 0.02 1596 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.013 331 conservative 179615 11p13 recombination activating gene 1 3889 rs3741056 ACAT1 38 11 107497556 NM_000019 NP_000010 C/G A5P plus 24610906 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.25 0.25 0 44 1 0.33 0.06 1582 3 123 "by doubleHit,freq,cluster" Potentially damaging 1.452 5 conservative 607809 11q22.3-q23.1 acetyl-Coenzyme A acetyltransferase 1 (acetoacetyl Coenzyme A thiolase) 3890 rs3741367 CD164L1 57124 11 65839705 NM_020404 NP_065137 C/T H457R plus 4927371 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.41 0.44 0.05 210 2 0.22 0 1476 1 120 "HapMap,freq,cluster" conservative 606064 11q13 CD164 sialomucin-like 1 3891 rs3741367 CD164L1 57124 11 65839705 NM_020404 NP_065137 C/T H457R plus 4927371 1303 SEQUENOM CEPH CEPH (92) 92 0.48 0.44 0.05 210 2 0.22 0 1476 1 120 "HapMap,freq,cluster" conservative 606064 11q13 CD164 sialomucin-like 1 3892 rs3741395 HSMDPKIN 55561 11 64354082 XM_290516 XP_290516 A/G Q1091R minus 24507709 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.44 0 48 1 0.2 0.23 94 2 123 "by doubleHit,freq,cluster" conservative 11q13.1 myotonic dystrophy protein kinase like protein 3893 rs3741626 MLL2 8085 12 47720676 NM_003482 NP_003473 A/G P2107S plus 4927630 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.01 0.01 0 120 1 107 HapMap moderately conservative 602113 12q12-q14 myeloid/lymphoid or mixed-lineage leukemia 2 3894 rs3741927 DYRK4 8798 12 4578460 NM_003845 NP_003836 A/G N189S plus 23779469 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.09 0.01 1590 3 123 "HapMap,freq,cluster" Intolerant 0.01 2.77 47 conservative 12p13.32 dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 4 3895 rs3742636 SIX4 51804 14 60250410 NM_017420 NP_059116 A/C H584P minus 4928642 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.26 0.26 0.01 168 2 0.48 0.05 1582 3 123 "HapMap,doubleHit,freq,cluster" moderately conservative 606342 14q23 sine oculis homeobox homolog 4 (Drosophila) 3896 rs3742636 SIX4 51804 14 60250410 NM_017420 NP_059116 A/C H584P minus 23667451 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.26 0.01 168 2 0.48 0.05 1582 3 123 "HapMap,doubleHit,freq,cluster" moderately conservative 606342 14q23 sine oculis homeobox homolog 4 (Drosophila) 3897 rs3742883 ZFYVE26 23503 14 67304292 NM_015346 NP_056161 C/T N1891S plus 4928890 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.03 0.03 0.01 168 2 0.15 0.02 1580 3 123 "HapMap,freq,cluster" conservative 14q24.1 "zinc finger, FYVE domain containing 26" 3898 rs3742883 ZFYVE26 23503 14 67304292 NM_015346 NP_056161 C/T N1891S plus 23796081 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.03 0.01 168 2 0.15 0.02 1580 3 123 "HapMap,freq,cluster" conservative 14q24.1 "zinc finger, FYVE domain containing 26" 3899 rs3742884 ZFYVE26 23503 14 67321687 NM_015346 NP_056161 A/G A1122V plus 4928891 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.03 0.03 0.01 166 2 0.07 0.04 1480 2 123 "HapMap,freq,cluster" moderately conservative 14q24.1 "zinc finger, FYVE domain containing 26" 3900 rs3742884 ZFYVE26 23503 14 67321687 NM_015346 NP_056161 A/G A1122V plus 23796122 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.04 0.03 0.01 166 2 0.07 0.04 1480 2 123 "HapMap,freq,cluster" moderately conservative 14q24.1 "zinc finger, FYVE domain containing 26" 3901 rs3742885 ZFYVE26 23503 14 67321744 NM_015346 NP_056161 A/G P1103L plus 4928892 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.03 0.03 0.01 168 2 0.14 0.04 1194 3 123 "HapMap,freq,cluster" moderately conservative 14q24.1 "zinc finger, FYVE domain containing 26" 3902 rs3742885 ZFYVE26 23503 14 67321744 NM_015346 NP_056161 A/G P1103L plus 23796124 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.03 0.01 168 2 0.14 0.04 1194 3 123 "HapMap,freq,cluster" moderately conservative 14q24.1 "zinc finger, FYVE domain containing 26" 3903 rs3743135 PAK6 56924 15 38345774 NM_020168 NP_064553 A/G H215R plus 6092636 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.07 0.08 0.02 168 2 0.17 0.03 1590 3 123 "HapMap,doubleHit,freq,cluster" Tolerant 0.53 3.18 15 conservative 608110 15q14 p21(CDKN1A)-activated kinase 6 3904 rs3743135 PAK6 56924 15 38345774 NM_020168 NP_064553 A/G H215R plus 23491720 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.08 0.02 168 2 0.17 0.03 1590 3 123 "HapMap,doubleHit,freq,cluster" Tolerant 0.53 3.18 15 conservative 608110 15q14 p21(CDKN1A)-activated kinase 6 3905 rs3743563 MMP15 4324 16 56636666 NM_002428 NP_002419 A/G G609R plus 4929570 885 TSC-CSHL HapMap-CEPH-30-trios 114 0.25 0.25 0 114 1 0.4 0 1496 1 107 "HapMap,freq" Tolerant 0.33 3.14 30 moderately radical 602261 16q13-q21 matrix metalloproteinase 15 (membrane-inserted) 3906 rs3743715 TK2 7084 16 65141495 NM_004614 NP_004605 C/G P33A plus 28458631 549 KYUGEN CP CEPH (78) 156 0.01 0.01 0 156 1 0.16 0 200 1 123 "by cluster,freq" conservative 188250 16q22-q23.1 "thymidine kinase 2, mitochondrial" 3907 rs3743716 TK2 7084 16 65141503 NM_004614 NP_004605 C/T K30R plus 28458630 549 KYUGEN CP CEPH (78) 156 0.12 0.12 0 156 1 0.29 0 200 1 123 "by doubleHit,freq,cluster" conservative 188250 16q22-q23.1 "thymidine kinase 2, mitochondrial" 3908 rs3743749 ADAMTS18 170692 16 75880736 NM_199355 NP_955387 C/G S1159T minus 4929756 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.19 0.19 0.01 160 2 0.2 0.02 1578 3 123 "HapMap,freq" Benign 0.354 5 Tolerant 0.61 2.83 13 moderately conservative 607512 16q23 "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18" 3909 rs3743749 ADAMTS18 170692 16 75880736 NM_199355 NP_955387 C/G S1159T minus 24680151 1371 PERLEGEN AFD_EUR_PANEL European American (24) 40 0.18 0.19 0.01 160 2 0.2 0.02 1578 3 123 "HapMap,freq" Benign 0.354 5 Tolerant 0.61 2.83 13 moderately conservative 607512 16q23 "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18" 3910 rs3743887 TMEM8 58986 16 364278 NM_021259 NP_067082 A/G R567W plus 13399974 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.05 0.05 0 118 1 0.08 0 1108 1 119 "HapMap,freq,cluster" Borderline 1.106 6 moderately radical 16p13.3 transmembrane protein 8 (five membrane-spanning domains) 3911 rs3744032 ACOX1 51 17 71481430 NM_007292 NP_009223 C/T G101S plus 4930040 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.05 0.04 0.02 160 2 0.14 0.03 1556 3 123 "HapMap,freq,cluster" Potentially damaging 1.396 13 Tolerant 0.59 2.8 34 moderately conservative 264470 17q24-17q25 "acyl-Coenzyme A oxidase 1, palmitoyl" 3912 rs3744032 ACOX1 51 17 71481430 NM_007292 NP_009223 C/T G101S plus 24019961 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.02 0.04 0.02 160 2 0.14 0.03 1556 3 123 "HapMap,freq,cluster" Potentially damaging 1.396 13 Tolerant 0.59 2.8 34 moderately conservative 264470 17q24-17q25 "acyl-Coenzyme A oxidase 1, palmitoyl" 3913 rs3744108 MTMR4 9110 17 53940871 NM_004687 NP_004678 C/G L170V plus 6615637 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.41 0.41 0 120 1 0.49 0 1498 1 111 "HapMap,freq,cluster" Borderline 1.022 5 Tolerant 0.24 2.82 36 conservative 603559 17q22-q23 myotubularin related protein 4 3914 rs3744124 BHD 201163 17 17065540 NM_144606 NP_653207 A/G G303R minus 14279451 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.06 0.06 0 118 1 0.18 0 1500 1 119 "HapMap,doubleHit,freq,cluster" moderately radical 607273 17p11.2 folliculin 3915 rs3744376 ABC1 63897 17 55510846 NM_022070 NP_071353 A/G A71V plus 4930384 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.08 0.09 0.02 164 2 0.06 0.04 1378 3 123 "HapMap,freq,cluster" moderately conservative 17q23.2-q23.3 amplified in breast cancer 1 3916 rs3744376 ABC1 63897 17 55510846 NM_022070 NP_071353 A/G A71V plus 23598375 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.11 0.09 0.02 164 2 0.06 0.04 1378 3 123 "HapMap,freq,cluster" moderately conservative 17q23.2-q23.3 amplified in breast cancer 1 3917 rs3744581 DNAH9 1770 17 11591782 NM_001372 NP_001363 A/G N2195S plus 4930589 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.25 0.25 0 118 1 0.37 0 1500 1 121 "HapMap,freq,cluster" Possibly damaging 1.736 11 Intolerant 0.03 2.79 20 conservative 603330 17p12 "dynein, axonemal, heavy polypeptide 9" 3918 rs3744679 ITGAE 3682 17 3582489 NM_002208 NP_002199 C/G Q892H minus 23792099 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 0.03 0.02 1574 3 123 "by cluster,freq" Possibly damaging 1.517 6 Tolerant 0.52 2.81 24 conservative 604682 17p13 "integrin, alpha E (antigen CD103, human mucosal lymphocyte antigen 1; alpha polypeptide)" 3919 rs3745202 PRX 57716 19 45592851 NM_181882 NP_870998 C/G P1083R plus 4931212 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.2 0.21 0.03 166 2 0.02 0 1550 2 123 "HapMap,freq,cluster" Tolerant 0.64 2.82 11 moderately radical 605725 19q13.13-q13.2 periaxin 3920 rs3745202 PRX 57716 19 45592851 NM_181882 NP_870998 C/G P1083R plus 24595997 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.21 0.03 166 2 0.02 0 1550 2 123 "HapMap,freq,cluster" Tolerant 0.64 2.82 11 moderately radical 605725 19q13.13-q13.2 periaxin 3921 rs3745764 HKR1 284459 19 42546420 NM_181786 NP_861451 A/G T628I minus 4931784 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.26 0.25 0.01 162 2 0.16 0.01 1590 3 123 "HapMap,freq" Possibly damaging 1.711 5 Tolerant 0.68 2.78 31 moderately conservative 165250 19q13.13 GLI-Kruppel family member HKR1 3922 rs3745764 HKR1 284459 19 42546420 NM_181786 NP_861451 A/G T628I minus 24575192 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.24 0.25 0.01 162 2 0.16 0.01 1590 3 123 "HapMap,freq" Possibly damaging 1.711 5 Tolerant 0.68 2.78 31 moderately conservative 165250 19q13.13 GLI-Kruppel family member HKR1 3923 rs3745765 HKR1 284459 19 42546075 NM_181786 NP_861451 A/C S513I minus 23613519 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.19 0 48 1 0.35 0.02 1570 3 123 "by doubleHit,freq,cluster" Benign 0.412 5 Tolerant 1 2.8 32 moderately radical 165250 19q13.13 GLI-Kruppel family member HKR1 3924 rs3745902 KIR3DL2 3812 19 60069820 NM_006737 NP_006728 C/T T397M plus 4931922 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.29 0.29 0 120 1 0.35 0 1466 1 107 "HapMap,freq" Benign 0.056 126 Intolerant 0.01 2.93 154 moderately conservative 604947 19q13.4 "killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 2" 3925 rs3745925 MADCAM1 8174 19 452900 NM_130760 NP_570116 G/T P300H minus 4931945 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.17 0.17 0 120 1 0.32 0 1462 1 107 "HapMap,freq" moderately conservative 102670 19p13.3 mucosal vascular addressin cell adhesion molecule 1 3926 rs3746638 SN 6614 20 3623333 NM_023068 NP_075556 A/G A974V plus 24496983 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.46 0 48 1 0.35 0.02 1392 3 123 "by doubleHit,freq,cluster" Borderline 1.227 6 Tolerant 0.39 2.83 9 moderately conservative 600751 20p13 sialoadhesin 3927 rs3746731 C1QR1 22918 20 23013209 NM_012072 NP_036204 A/G P541S plus 24690182 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.46 0 48 1 0.31 0.07 90 2 123 "by doubleHit,freq,cluster" moderately conservative 120577 20p11.22 "complement component 1, q subcomponent, receptor 1" 3928 rs3746891 RIPK4 54101 21 42034426 NM_020639 NP_065690 C/T M666V plus 10983985 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.01 0.03 0.04 164 2 0.11 0.02 1578 3 123 "HapMap,freq,cluster" Benign 0.676 8 Tolerant 0.41 2.75 100 conservative 605706 21q22.3 ankyrin repeat domain 3 3929 rs3746891 RIPK4 54101 21 42034426 NM_020639 NP_065690 C/T M666V plus 24132507 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.07 0.03 0.04 164 2 0.11 0.02 1578 3 123 "HapMap,freq,cluster" Benign 0.676 8 Tolerant 0.41 2.75 100 conservative 605706 21q22.3 ankyrin repeat domain 3 3930 rs3747258 CERK 64781 22 45402542 NM_182661 NP_872602 A/G P159S plus 4933280 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.04 0.04 0 120 1 0.01 0 1500 1 107 "HapMap,doubleHit,freq" moderately conservative 22q13.31 ceramide kinase 3931 rs3747517 IFIH1 64135 2 162954331 NM_022168 NP_071451 A/G H843R minus 6120212 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.21 0.23 0.04 164 2 0.38 0.01 1540 3 123 "HapMap,doubleHit,freq,cluster" Tolerant 1 2.79 27 conservative 606951 2p24.3-q24.3 melanoma differentiation associated protein-5 3932 rs3747517 IFIH1 64135 2 162954331 NM_022168 NP_071451 A/G H843R minus 23232650 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.27 0.23 0.04 164 2 0.38 0.01 1540 3 123 "HapMap,doubleHit,freq,cluster" Tolerant 1 2.79 27 conservative 606951 2p24.3-q24.3 melanoma differentiation associated protein-5 3933 rs3747532 CER1 9350 9 14712477 NM_005454 NP_005445 C/G A65G plus 24522596 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.4 0 48 1 0.06 0.03 1590 3 123 "by doubleHit,freq,cluster" moderately conservative 603777 9p23-p22 "cerberus 1 homolog, cysteine knot superfamily (Xenopus laevis)" 3934 rs3747539 FRMPD1 22844 9 37682654 NM_014907 NP_055722 A/C T6P plus 4933561 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.23 0.23 0.01 166 2 0.09 0.04 838 3 123 "HapMap,freq" conservative 9p13.1 FERM and PDZ domain containing 1 3935 rs3747539 FRMPD1 22844 9 37682654 NM_014907 NP_055722 A/C T6P plus 24552125 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.22 0.23 0.01 166 2 0.09 0.04 838 3 123 "HapMap,freq" conservative 9p13.1 FERM and PDZ domain containing 1 3936 rs3747787 AIM1 202 6 107074471 XM_166300 XP_166300 C/T C1114R plus 24360629 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.21 0 48 1 0.11 0.01 1594 3 123 "by doubleHit,freq,cluster" radical 601797 6q21 absent in melanoma 1 3937 rs3748022 IKBKE 9641 1 203057860 XM_375834 XP_375834 C/T P713L plus 24642261 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.28 0.28 0 46 1 0.18 0.03 1580 3 123 by freq moderately conservative 605048 1q32.1 "inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase epsilon" 3938 rs3748034 HGFAC 3083 4 3483060 NM_001528 NP_001519 A/C A218S minus 23895565 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 0.06 0.06 90 2 123 "by cluster,freq" Benign 0.117 7 Tolerant 0.42 2.95 28 moderately conservative 604552 4p16 HGF activator 3939 rs3748178 AKNA 80709 9 114189600 NM_030767 NP_110394 A/G R1119Q minus 24511196 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.15 0.15 0 46 1 0.03 0.02 1594 3 123 "by cluster,freq" Benign 0.066 7 conservative 605729 9q32 AT-hook transcription factor 3940 rs3748400 ZCCHC14 23174 16 86003340 NM_015144 NP_055959 C/T V693M plus 10820982 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.22 0.22 0 118 1 0.31 0 1096 1 121 "HapMap,doubleHit,freq,cluster" Borderline 0.17 2.98 42 conservative 16q24.2 BDG-29 proten 3941 rs3748433 CEP2 11190 20 33553933 NM_007186 NP_009117 C/T R1441Q minus 24079477 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.09 0.09 0 46 1 0.11 0.01 1584 3 123 "by doubleHit,freq,cluster" conservative 20q11.22-q12 centrosomal protein 2 3942 rs3748735 PLXNA2 5362 1 204778864 NM_025179 NP_079455 C/T A267T plus 23845546 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.21 0 48 1 0.13 0.02 1562 3 123 "by cluster,freq" Benign 0.209 7 Tolerant 0.65 3.08 10 moderately conservative 601054 1q32.2 plexin A2 3943 rs3749191 CDCP1 64866 3 45109826 NM_022842 NP_073753 C/T Q525R plus 23338673 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.35 0 48 1 0.21 0.26 92 2 123 "by doubleHit,freq,cluster" Benign 0.101 5 conservative 3p21.32 CUB domain-containing protein 1 3944 rs3749195 TGM4 7047 3 44923483 NM_003241 NP_003232 A/G R372C minus 14238026 885 TSC-CSHL HapMap-CEPH-30-trios 102 0.49 0.49 0.01 150 2 0.18 0.03 1570 3 123 "HapMap,freq,cluster" Intolerant 0 2.78 17 radical 600585 3p22-p21.33 transglutaminase 4 (prostate) 3945 rs3749195 TGM4 7047 3 44923483 NM_003241 NP_003232 A/G R372C minus 24370786 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.49 0.01 150 2 0.18 0.03 1570 3 123 "HapMap,freq,cluster" Intolerant 0 2.78 17 radical 600585 3p22-p21.33 transglutaminase 4 (prostate) 3946 rs3749930 NOX3 50508 6 155853359 NM_015718 NP_056533 G/T T171K plus 24047947 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.49 0.02 1522 2 123 "by cluster,freq" Potentially damaging 1.38 28 Potentially intolerant 0.09 2.97 37 moderately conservative 607105 6q25.1-q26 NADPH oxidase 3 3947 rs3750009 PAPOLB 56903 7 4674626 NM_020144 NP_064529 G/T N19K minus 24050452 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.27 0 48 1 0.43 0.04 88 2 123 "by doubleHit,freq,cluster" Potentially damaging 1.261 13 Tolerant 1 2.97 39 moderately conservative 607436 7p22.2 poly(A) polymerase beta (testis specific) 3948 rs3750010 PAPOLB 56903 7 4674432 NM_020144 NP_064529 A/G K84R minus 10400843 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.1 0.08 0.04 168 2 0.09 0.03 1368 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.063 34 Tolerant 0.41 2.8 42 conservative 607436 7p22.2 poly(A) polymerase beta (testis specific) 3949 rs3750010 PAPOLB 56903 7 4674432 NM_020144 NP_064529 A/G K84R minus 23516430 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.08 0.04 168 2 0.09 0.03 1368 3 123 "HapMap,doubleHit,freq,cluster" Benign 0.063 34 Tolerant 0.41 2.8 42 conservative 607436 7p22.2 poly(A) polymerase beta (testis specific) 3950 rs3750050 PTPN12 5782 7 76901364 NM_002835 NP_002826 A/G T573A plus 24001266 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.31 0.03 1580 3 123 "by cluster,freq" Potentially damaging 1.344 7 moderately conservative 600079 7q11.23 "protein tyrosine phosphatase, non-receptor type 12" 3951 rs3750208 ZC3HDC3 23144 8 144692178 NM_015117 NP_055932 C/T R168W minus 4936234 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.13 0.13 0 120 1 107 "HapMap,freq" moderately radical 8q24.3 zinc finger CCCH type domain containing 3 3952 rs3750300 PADI3 51702 1 17331440 NM_016233 NP_057317 A/G I52V plus 23845366 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.16 0.03 1588 3 123 "by cluster,freq" Benign 0.021 25 Tolerant 1 3.05 31 conservative 606755 1p36.13 "peptidyl arginine deiminase, type III" 3953 rs3750425 TRPM6 140803 9 74606964 NM_017662 NP_060132 C/T V1393I plus 4936451 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.07 0.07 0 120 1 0.15 0 1474 1 107 "HapMap,freq" conservative 607009 9q21.13 "transient receptor potential cation channel, subfamily M, member 6" 3954 rs3750898 DCLRE1A 9937 10 115599905 NM_014881 NP_055696 C/G D317H minus 4936925 902 AFFY Caucasian 24 0.17 0.17 0 128 3 0.25 0.03 1562 4 121 "by doubleHit,freq,cluster" moderately conservative 10q25.1 "DNA cross-link repair 1A (PSO2 homolog, S. cerevisiae)" 3955 rs3750898 DCLRE1A 9937 10 115599905 NM_014881 NP_055696 C/G D317H minus 4936925 904 AFFY CEPH 12 0.17 0.17 0 128 3 0.25 0.03 1562 4 121 "by doubleHit,freq,cluster" moderately conservative 10q25.1 "DNA cross-link repair 1A (PSO2 homolog, S. cerevisiae)" 3956 rs3750898 DCLRE1A 9937 10 115599905 NM_014881 NP_055696 C/G D317H minus 15587118 1303 SEQUENOM CEPH CEPH (92) 92 0.17 0.17 0 128 3 0.25 0.03 1562 4 121 "by doubleHit,freq,cluster" moderately conservative 10q25.1 "DNA cross-link repair 1A (PSO2 homolog, S. cerevisiae)" 3957 rs3752095 DSG1 1828 18 27188679 NM_001942 NP_001933 A/T Y841F plus 24686132 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.09 0.01 1592 3 123 "by doubleHit,freq,cluster" Potentially damaging 1.282 9 Intolerant 0 3.08 21 conservative 125670 18q12.1 desmoglein 1 3958 rs3752199 ZNF317 57693 19 9128319 NM_020933 NP_065984 G/T Q19H plus 24719235 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.23 0 48 1 0.14 0.02 1588 3 123 by freq conservative 19p13 zinc finger protein 317 3959 rs3752302 DHX35 60625 20 37100596 NM_021931 NP_068750 C/T P703L plus 24050331 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.13 0.13 0 46 1 0.24 0.02 1180 3 123 "by cluster,freq" moderately conservative 20q11.22-q12 DEAH (Asp-Glu-Ala-His) box polypeptide 35 3960 rs3752365 ZNF573 126231 19 42922560 NM_152360 NP_689573 C/G G166A plus 16788341 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.19 0.18 0.03 166 2 0.07 0.01 1560 3 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.659 13 Intolerant 0.02 2.76 73 moderately conservative 19q13.13 zinc finger protein 573 3961 rs3752365 ZNF573 126231 19 42922560 NM_152360 NP_689573 C/G G166A plus 24575689 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.15 0.18 0.03 166 2 0.07 0.01 1560 3 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.659 13 Intolerant 0.02 2.76 73 moderately conservative 19q13.13 zinc finger protein 573 3962 rs3753565 TPR 7175 1 183048145 NM_003292 NP_003283 A/G S960N minus 23859490 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.16 0.02 1368 3 123 "by cluster,freq" Benign 0.675 5 Tolerant 0.32 2.97 10 conservative 189940 1q25 translocated promoter region (to activated MET oncogene) 3963 rs3754274 DLAD 58511 1 84579631 NM_021233 NP_067056 C/T R47K minus 24258206 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.29 0 48 1 0.2 0.13 92 2 123 "by cluster,freq" Tolerant 0.98 2.86 8 conservative 608057 1p22.3 DNase II-like acid DNase 3964 rs3754413 ITPKB 3707 1 223230931 NM_002221 NP_002212 C/T A322T plus 28460841 549 KYUGEN CP CEPH (78) 156 0.06 0.06 0 156 1 0.08 0 1488 2 123 "by cluster,freq" Benign 0.937 5 moderately conservative 147522 1q42.13 "inositol 1,4,5-trisphosphate 3-kinase B" 3965 rs3755321 UGT1A5 54579 2 234403825 NM_019078 NP_061951 A/G L63P minus 4941353 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.13 0.13 0 120 1 0.11 0 1104 1 120 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.623 78 Tolerant 1 2.8 155 moderately conservative 606430 2q37 "UDP glycosyltransferase 1 family, polypeptide A5" 3966 rs3756323 PCDHB11 56125 5 140559542 NM_018931 NP_061754 C/T Q4R minus 23351559 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.06 0.05 1584 3 123 "by doubleHit,freq,cluster" Benign 0.329 50 Tolerant 0.7 2.86 73 conservative 606337 5q31 protocadherin beta 11 3967 rs3758449 MYO3A 53904 10 26486318 NM_017433 NP_059129 C/T S956N minus 10635383 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.46 0.47 0.01 166 2 0.35 0.01 1558 3 123 "HapMap,doubleHit,freq,cluster" Tolerant 0.6 2.74 19 conservative 606808 10p11.1 myosin IIIA 3968 rs3758449 MYO3A 53904 10 26486318 NM_017433 NP_059129 C/T S956N minus 24688584 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.48 0.47 0.01 166 2 0.35 0.01 1558 3 123 "HapMap,doubleHit,freq,cluster" Tolerant 0.6 2.74 19 conservative 606808 10p11.1 myosin IIIA 3969 rs3758938 TBX10 347853 11 67158938 NM_005995 NP_005986 G/T K101T plus 24564262 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.48 0.48 0 44 1 0.1 0.02 1538 3 123 "by doubleHit,freq,cluster" Possibly damaging 1.927 10 Intolerant 0.03 2.8 40 moderately conservative 604648 11q13.1 T-box 10 3970 rs3759259 STYK1 55359 12 10673382 NM_018423 NP_060893 A/G S204G minus 24701076 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.4 0 48 1 0.19 0.03 1572 3 123 "by doubleHit,freq,cluster" moderately conservative 12p13.31 protein kinase STYK1 3971 rs3762697 MORC 27136 3 110236904 NM_014429 NP_055244 A/G M478V minus 23272638 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.19 0 48 1 0.17 0.06 94 2 123 "by cluster,freq" Tolerant 0.23 2.8 21 conservative 603205 3q13 microrchidia homolog (mouse) 3972 rs3764340 WWOX 51741 16 77023938 NM_018560 NP_061030 C/G P282A plus 12346211 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.04 0.04 0 118 1 0.08 0 1488 1 116 "HapMap,freq,cluster" Tolerant 0.53 2.87 94 conservative 605131 16q23.3-q24.1 WW domain containing oxidoreductase 3973 rs3764795 GML 2765 8 143919622 NM_002066 NP_002057 C/T R54C plus 4950834 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.05 0.05 0 120 1 107 "HapMap,freq" radical 602370 8q24.3 GPI anchored molecule like protein 3974 rs3764897 PLD2 5338 17 4669842 NM_002663 NP_002654 C/T G821S minus 6611005 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.17 0.18 0.03 168 2 0.13 0.03 1558 3 123 "HapMap,doubleHit,freq,cluster" Potentially damaging 1.323 6 Tolerant 0.59 2.8 20 moderately conservative 602384 17p13.1 phospholipase D2 3975 rs3764897 PLD2 5338 17 4669842 NM_002663 NP_002654 C/T G821S minus 23434145 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.18 0.03 168 2 0.13 0.03 1558 3 123 "HapMap,doubleHit,freq,cluster" Potentially damaging 1.323 6 Tolerant 0.59 2.8 20 moderately conservative 602384 17p13.1 phospholipase D2 3976 rs3765148 DHDH 27294 19 54139525 NM_014475 NP_055290 C/T G282R minus 4951188 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.07 0.07 0 120 1 0.07 0 1478 1 107 "HapMap,freq" Possibly damaging 1.938 9 Tolerant 0.38 2.78 22 moderately radical 606377 19q13.3 dihydrodiol dehydrogenase (dimeric) 3977 rs3768235 BCL10 8915 1 85445395 NM_003921 NP_003912 A/G G213E minus 23839855 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 0.14 0.01 1520 2 123 "by cluster,freq" moderately conservative 603517 1p22 B-cell CLL/lymphoma 10 3978 rs3769148 ZAK 51776 2 173954020 NM_016653 NP_057737 A/G S531L minus 24290044 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.44 0 48 1 0.13 0.06 1580 3 123 "by cluster,freq" moderately radical 2q24.2 sterile alpha motif and leucine zipper containing kinase AZK 3979 rs3770213 ZNF142 7701 2 219333877 XM_376172 XP_376172 A/T L1278H plus 24658561 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.38 0 48 1 0.1 0.08 92 2 123 by freq moderately conservative 604083 2q34-q35 zinc finger protein 142 (clone pHZ-49) 3980 rs3770214 ZNF142 7701 2 219334493 XM_376172 XP_376172 C/T S1073G plus 9977579 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.31 0.33 0.04 168 2 0.06 0.02 1582 3 123 "HapMap,freq,cluster" moderately conservative 604083 2q34-q35 zinc finger protein 142 (clone pHZ-49) 3981 rs3770214 ZNF142 7701 2 219334493 XM_376172 XP_376172 C/T S1073G plus 24658564 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.33 0.04 168 2 0.06 0.02 1582 3 123 "HapMap,freq,cluster" moderately conservative 604083 2q34-q35 zinc finger protein 142 (clone pHZ-49) 3982 rs3774729 SCA7 6314 3 63957122 NM_000333 NP_000324 A/G V862M plus 10083927 902 AFFY Caucasian 22 0.36 0.35 0.02 78 3 0.45 0.04 904 6 123 "by doubleHit,freq,cluster" Benign 0.427 6 conservative 607640 3p21.1-p12 spinocerebellar ataxia 7 (olivopontocerebellar atrophy with retinal degeneration) 3983 rs3774729 SCA7 6314 3 63957122 NM_000333 NP_000324 A/G V862M plus 10083927 904 AFFY CEPH 10 0.3 0.35 0.02 78 3 0.45 0.04 904 6 123 "by doubleHit,freq,cluster" Benign 0.427 6 conservative 607640 3p21.1-p12 spinocerebellar ataxia 7 (olivopontocerebellar atrophy with retinal degeneration) 3984 rs3774729 SCA7 6314 3 63957122 NM_000333 NP_000324 A/G V862M plus 23295729 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.35 0.35 0.02 78 3 0.45 0.04 904 6 123 "by doubleHit,freq,cluster" Benign 0.427 6 conservative 607640 3p21.1-p12 spinocerebellar ataxia 7 (olivopontocerebellar atrophy with retinal degeneration) 3985 rs3775291 TLR3 7098 4 187379223 NM_003265 NP_003256 A/G L412F minus 7987148 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.3 0.28 0.06 46 2 0.25 0.05 1552 2 114 "by cluster,freq" Intolerant 0 2.88 10 conservative 603029 4q35 toll-like receptor 3 3986 rs3775291 TLR3 7098 4 187379223 NM_003265 NP_003256 A/G L412F minus 7987148 848 IIPGA-WEISS-MARTINEZ E-1 CEPH 6 0.17 0.28 0.06 46 2 0.25 0.05 1552 2 114 "by cluster,freq" Intolerant 0 2.88 10 conservative 603029 4q35 toll-like receptor 3 3987 rs3776096 PCDHB6 56130 5 140510713 NM_018939 NP_061762 C/T V231I minus 4962162 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.31 0.28 0.06 166 2 0.41 0.08 1564 3 123 "HapMap,freq,cluster" Benign 0.321 105 Borderline 0.11 2.77 131 conservative 606332 5q31 protocadherin beta 6 3988 rs3776096 PCDHB6 56130 5 140510713 NM_018939 NP_061762 C/T V231I minus 23951288 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.28 0.06 166 2 0.41 0.08 1564 3 123 "HapMap,freq,cluster" Benign 0.321 105 Borderline 0.11 2.77 131 conservative 606332 5q31 protocadherin beta 6 3989 rs3778005 IMPG1 3617 6 76690105 NM_001563 NP_001554 A/G S761N minus 17099388 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.23 0.23 0 120 1 0.05 0 1488 1 121 "HapMap,doubleHit,freq,cluster" Benign 0.929 5 conservative 602870 6q14.2-q15 interphotoreceptor matrix proteoglycan 1 3990 rs3781408 CTBP2 1488 10 126705682 NM_022802 NP_073713 A/G D213N minus 23625792 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.07 0.01 1594 3 123 "by cluster,freq" conservative 602619 10q26.2 C-terminal binding protein 2 3991 rs3781409 CTBP2 1488 10 126705619 NM_022802 NP_073713 A/G V234M minus 24583969 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.29 0 48 1 0.3 0.05 1204 3 123 "by cluster,freq" conservative 602619 10q26.2 C-terminal binding protein 2 3992 rs3781411 CTBP2 1488 10 126705426 NM_022802 NP_073713 A/G R298Q minus 23625764 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 0.07 0.02 1584 3 123 "by cluster,freq" conservative 602619 10q26.2 C-terminal binding protein 2 3993 rs3781412 CTBP2 1488 10 126705144 NM_022802 NP_073713 C/T L392P minus 24583952 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.42 0 48 1 0.37 0.03 1554 3 123 by freq moderately conservative 602619 10q26.2 C-terminal binding protein 2 3994 rs3790549 WARS2 10352 1 119287860 NM_015836 NP_056651 C/G A267P plus 24141868 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.09 0.09 0 46 1 0.17 0.03 1182 3 123 "by cluster,freq" Intolerant 0.03 2.78 79 conservative 604733 1p13.3-p13.1 tryptophanyl tRNA synthetase 2 (mitochondrial) 3995 rs3792234 SBLF 11037 2 48721244 NM_006873 NP_006864 G/T Q607H plus 24156954 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.42 0 48 1 0.38 0.02 1596 3 123 "by doubleHit,freq,cluster" Tolerant 0.24 2.9 42 conservative 605357 2p16.3 stoned B-like factor 3996 rs3792683 MTP 4547 4 100868081 NM_000253 NP_000244 A/G N166S plus 23331396 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 0.23 0.02 1586 3 123 "by cluster,freq" Benign 0.567 9 Tolerant 0.97 2.78 15 conservative 157147 4q24 "microsomal triglyceride transfer protein (large polypeptide, 88kDa)" 3997 rs3793524 PTPN3 5774 9 109299029 NM_002829 NP_002820 C/G A90P minus 4979898 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.38 0.35 0.06 166 2 0.37 0.02 1592 3 123 "HapMap,freq,cluster" Probably damaging 2.274 8 Tolerant 1 2.78 69 conservative 176877 9q31 "protein tyrosine phosphatase, non-receptor type 3" 3998 rs3793524 PTPN3 5774 9 109299029 NM_002829 NP_002820 C/G A90P minus 23785111 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.28 0.35 0.06 166 2 0.37 0.02 1592 3 123 "HapMap,freq,cluster" Probably damaging 2.274 8 Tolerant 1 2.78 69 conservative 176877 9q31 "protein tyrosine phosphatase, non-receptor type 3" 3999 rs3793771 WNT8B 7479 10 102212947 NM_003393 NP_003384 C/G C11S minus 24488585 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.27 0 48 1 0.19 0.02 1592 3 123 "by doubleHit,freq,cluster" moderately radical 601396 10q24 "wingless-type MMTV integration site family, member 8B" 4000 rs3794873 ZNF236 7776 18 72745362 NM_007345 NP_031371 C/T S643G minus 4981248 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.03 0.03 0 120 1 0.02 0 48 1 123 "HapMap,freq,cluster" Tolerant 0.28 2.89 38 moderately conservative 604760 18q22-q23 zinc finger protein 236 4001 rs3795003 USP29 57663 19 62333611 NM_020903 NP_065954 C/T E586K minus 19404203 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.03 0.04 0.02 166 2 0.44 0.11 996 3 123 "HapMap,doubleHit,freq,cluster" Tolerant 0.62 2.97 10 moderately conservative 19q13.43 ubiquitin specific protease 29 4002 rs3795003 USP29 57663 19 62333611 NM_020903 NP_065954 C/T E586K minus 24225802 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.04 0.02 166 2 0.44 0.11 996 3 123 "HapMap,doubleHit,freq,cluster" Tolerant 0.62 2.97 10 moderately conservative 19q13.43 ubiquitin specific protease 29 4003 rs3795244 ZNF207 7756 17 27716509 NM_003457 NP_003448 G/T A224S plus 4981621 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.05 0.05 0 120 1 0.05 0 914 1 107 "HapMap,freq" Tolerant 0.36 3.01 24 moderately conservative 603428 17q12 zinc finger protein 207 4004 rs3795299 IL22RA1 58985 1 24192774 NM_021258 NP_067081 C/G R518G minus 24616886 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.42 0 48 1 0.25 0.02 1592 3 123 "by doubleHit,freq,cluster" moderately radical 605457 1p36.11 "interleukin 22 receptor, alpha 1" 4005 rs3795498 MGC4796 83931 1 36476574 NM_032017 NP_114406 A/G A395T minus 4981875 1303 SEQUENOM CEPH CEPH (92) 92 0.31 0.31 0 92 1 107 by freq Benign 0.039 10 Tolerant 0.37 3.07 30 moderately conservative 1p34.3 Ser/Thr-like kinase 4006 rs3800324 PGBD1 84547 6 28372660 NM_032507 NP_115896 A/G G244E plus 23916026 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.2 0.1 94 2 123 "by cluster,freq" moderately conservative 6p21.33 piggyBac transposable element derived 1 4007 rs3800325 PGBD1 84547 6 28372671 NM_032507 NP_115896 C/G Q248E plus 23290726 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.24 0.26 94 2 123 "by cluster,freq" conservative 6p21.33 piggyBac transposable element derived 1 4008 rs3800962 PRPS1L1 221823 7 17839809 NM_175886 NP_787082 G/T E279D minus 16336072 902 AFFY Caucasian 22 0.14 0.18 0.07 34 2 0.22 0.04 1158 4 123 "by doubleHit,freq,cluster" Benign 0.209 59 Tolerant 0.53 2.78 194 conservative 7p21.1 phosphoribosyl pyrophosphate synthetase 1-like 1 4009 rs3800962 PRPS1L1 221823 7 17839809 NM_175886 NP_787082 G/T E279D minus 16336072 904 AFFY CEPH 12 0.25 0.18 0.07 34 2 0.22 0.04 1158 4 123 "by doubleHit,freq,cluster" Benign 0.209 59 Tolerant 0.53 2.78 194 conservative 7p21.1 phosphoribosyl pyrophosphate synthetase 1-like 1 4010 rs3802264 ZHX2 22882 8 124035266 NM_014943 NP_055758 A/G G779S plus 23991981 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.35 0 48 1 123 "by cluster,freq" moderately conservative 8q24.13 zinc fingers and homeoboxes 2 4011 rs3803430 ALDH1A3 220 15 99263338 NM_000693 NP_000684 C/T M386V minus 12343035 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.01 0.01 0.01 164 2 0.09 0.04 1588 3 123 "HapMap,freq,cluster" Benign 0.289 131 Tolerant 0.51 2.82 151 conservative 600463 15q26.3 "aldehyde dehydrogenase 1 family, member A3" 4012 rs3803430 ALDH1A3 220 15 99263338 NM_000693 NP_000684 C/T M386V minus 23641698 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.02 0.01 0.01 164 2 0.09 0.04 1588 3 123 "HapMap,freq,cluster" Benign 0.289 131 Tolerant 0.51 2.82 151 conservative 600463 15q26.3 "aldehyde dehydrogenase 1 family, member A3" 4013 rs3803716 TNRC6 27327 16 24709826 NM_014494 NP_055309 A/G P535S minus 24405143 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.08 0.04 94 2 123 "by cluster,freq" Benign 0.442 5 Potentially intolerant 0.09 3.13 11 moderately conservative 16p11.2 trinucleotide repeat containing 6 4014 rs3805466 ERBB2IP 55914 5 65386237 NM_018695 NP_061165 A/G S1112L minus 19640840 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.03 0.03 0.01 168 2 0.25 0.03 1342 2 123 "HapMap,freq,cluster" Possibly damaging 1.773 6 moderately radical 606944 5q13.1 erbb2 interacting protein 4015 rs3805466 ERBB2IP 55914 5 65386237 NM_018695 NP_061165 A/G S1112L minus 23901330 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.03 0.01 168 2 0.25 0.03 1342 2 123 "HapMap,freq,cluster" Possibly damaging 1.773 6 moderately radical 606944 5q13.1 erbb2 interacting protein 4016 rs3806995 ENPP5 59084 6 46243943 NM_021572 NP_067547 A/C L6I minus 24000787 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.44 0 48 1 0.35 0.05 1386 3 123 "by doubleHit,freq,cluster" conservative 6p21.1-p11.2 ectonucleotide pyrophosphatase/phosphodiesterase 5 (putative function) 4017 rs3808553 FZD6 8323 8 104406543 NM_003506 NP_003497 G/T M345L minus 4994954 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.41 0.4 0.02 432 3 0.44 0.01 400 2 123 "HapMap,freq,cluster" Potentially damaging 1.488 5 Tolerant 0.52 2.78 98 conservative 603409 8q22.3-q23.1 frizzled homolog 6 (Drosophila) 4018 rs3808553 FZD6 8323 8 104406543 NM_003506 NP_003497 G/T M345L minus 28459824 549 KYUGEN CP CEPH (78) 156 0.41 0.4 0.02 432 3 0.44 0.01 400 2 123 "HapMap,freq,cluster" Potentially damaging 1.488 5 Tolerant 0.52 2.78 98 conservative 603409 8q22.3-q23.1 frizzled homolog 6 (Drosophila) 4019 rs3808553 FZD6 8323 8 104406543 NM_003506 NP_003497 G/T M345L minus 28459825 549 KYUGEN CP CEPH (78) 156 0.38 0.4 0.02 432 3 0.44 0.01 400 2 123 "HapMap,freq,cluster" Potentially damaging 1.488 5 Tolerant 0.52 2.78 98 conservative 603409 8q22.3-q23.1 frizzled homolog 6 (Drosophila) 4020 rs3810110 SIGLECL1 89858 19 56696555 NM_053003 NP_443729 A/G A82V plus 23813009 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.3 0.3 0 44 1 0.35 0.09 86 2 123 "by cluster,freq" moderately conservative 606094 19q13.4 SIGLEC-like 1 4021 rs3810151 ZNF526 116115 19 47420676 NM_133444 NP_597701 A/G V94A minus 4996554 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.08 0.08 0 118 1 0.06 0 1306 1 107 "HapMap,freq" Tolerant 0.61 2.79 45 moderately conservative 19q13.31 zinc finger protein 526 4022 rs3810971 MOV10L1 54456 22 48849123 NM_018995 NP_061868 C/T R182C plus 6683249 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.32 0.29 0.08 166 2 0.29 0.03 1590 3 123 "HapMap,doubleHit,freq,cluster" radical 605794 22q13.33 "Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)" 4023 rs3810971 MOV10L1 54456 22 48849123 NM_018995 NP_061868 C/T R182C plus 24214744 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.2 0.29 0.08 166 2 0.29 0.03 1590 3 123 "HapMap,doubleHit,freq,cluster" radical 605794 22q13.33 "Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)" 4024 rs3811635 MERTK 10461 2 112471232 NM_006343 NP_006334 A/G I518V plus 24311093 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.44 0 48 1 0.21 0.03 1588 3 123 "by doubleHit,freq,cluster" Tolerant 0.76 2.76 37 conservative 604705 2q14.1 c-mer proto-oncogene tyrosine kinase 4025 rs3811740 PLK4 10733 4 129164824 NM_014264 NP_055079 A/T S232T minus 23985363 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.29 0 48 1 0.37 0.05 1584 3 123 "by doubleHit,freq,cluster" Benign 0.225 8 moderately conservative 605031 4q27-q28 polo-like kinase 4 (Drosophila) 4026 rs3812138 NT5E 4907 6 86255952 NM_002526 NP_002517 C/T T376A minus 24010796 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.36 0.36 0 44 1 0.35 0.08 1400 3 123 "by doubleHit,freq,cluster" Benign 0.844 9 Tolerant 0.73 2.86 19 moderately conservative 129190 6q14-q21 "5'-nucleotidase, ecto (CD73)" 4027 rs3812179 CDYL 9425 6 4661015 NM_004824 NP_004815 C/T T2A minus 23989412 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.13 0.13 0 46 1 0.28 0.02 94 2 123 "by doubleHit,freq,cluster" moderately conservative 603778 6p25.1 "chromodomain protein, Y-like" 4028 rs3812561 SNAPC4 6621 9 136546713 NM_003086 NP_003077 A/G P1448S plus 4998970 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.04 0.04 0 168 2 0.09 0 1542 2 123 "HapMap,freq,cluster" moderately conservative 602777 9q34.3 "small nuclear RNA activating complex, polypeptide 4, 190kDa" 4029 rs3812561 SNAPC4 6621 9 136546713 NM_003086 NP_003077 A/G P1448S plus 24102256 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 168 2 0.09 0 1542 2 123 "HapMap,freq,cluster" moderately conservative 602777 9q34.3 "small nuclear RNA activating complex, polypeptide 4, 190kDa" 4030 rs3812571 SNAPC4 6621 9 136551131 NM_003086 NP_003077 C/G H799Q plus 4998980 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.46 0.47 0.01 168 2 0.31 0.08 94 2 123 "HapMap,doubleHit,freq,cluster" conservative 602777 9q34.3 "small nuclear RNA activating complex, polypeptide 4, 190kDa" 4031 rs3812571 SNAPC4 6621 9 136551131 NM_003086 NP_003077 C/G H799Q plus 24566900 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.47 0.01 168 2 0.31 0.08 94 2 123 "HapMap,doubleHit,freq,cluster" conservative 602777 9q34.3 "small nuclear RNA activating complex, polypeptide 4, 190kDa" 4032 rs3812577 SDCCAG3 10807 9 136575474 NM_006643 NP_006634 C/T R223Q plus 4998986 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.16 0.16 0 120 1 120 "HapMap,freq,cluster" Benign 0.192 9 conservative 9q34.3 serologically defined colon cancer antigen 3 4033 rs3812813 USP44 84101 12 94430230 NM_032147 NP_115523 A/G T91A minus 12183870 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.41 0.41 0 120 1 120 "HapMap,doubleHit,freq,cluster" Benign 0.042 11 moderately conservative 12q23.1 ubiquitin specific protease 44 4034 rs3813135 PGLYRP2 114770 19 15448345 NM_052890 NP_443122 C/T T46A plus 4999544 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.37 0.37 0 120 1 121 "HapMap,doubleHit,freq,cluster" Benign 0.039 6 moderately conservative 608199 19p13.12 peptidoglycan recognition protein 2 4035 rs3814160 ZNF488 118738 10 47991283 NM_153034 NP_694579 C/T P249S plus 5000571 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.09 0.09 0 120 1 107 "HapMap,freq" moderately conservative 10q11.22 zinc finger protein 488 4036 rs3814995 NPHS1 4868 19 41034052 NM_004646 NP_004637 C/T E117K plus 5001407 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.33 0.31 0.04 166 2 0.36 0.06 1584 3 123 "HapMap,freq,cluster" Benign 0.9 7 Borderline 0.16 2.94 15 moderately conservative 602716 19q13.1 "nephrosis 1, congenital, Finnish type (nephrin)" 4037 rs3814995 NPHS1 4868 19 41034052 NM_004646 NP_004637 C/T E117K plus 24108670 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.26 0.31 0.04 166 2 0.36 0.06 1584 3 123 "HapMap,freq,cluster" Benign 0.9 7 Borderline 0.16 2.94 15 moderately conservative 602716 19q13.1 "nephrosis 1, congenital, Finnish type (nephrin)" 4038 rs3816183 HAAO 23498 2 42927370 NM_012205 NP_036337 C/T I37V plus 23842878 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.27 0 48 1 0.27 0.09 94 2 123 "by doubleHit,freq,cluster" Benign 0.835 6 conservative 604521 2p22.1 "3-hydroxyanthranilate 3,4-dioxygenase" 4039 rs3816300 T 6862 6 166542416 NM_003181 NP_003172 A/G N369S minus 24146227 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.47 0.09 802 3 123 "by cluster,freq" Benign 0.028 24 Tolerant 1 2.99 33 conservative 601397 6q27 "T, brachyury homolog (mouse)" 4040 rs3816665 LAMA2 3908 6 129613023 NM_000426 NP_000417 C/T R619H minus 23373554 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.11 0.11 0 46 1 0.26 0.23 88 2 123 "by doubleHit,freq,cluster" Borderline 0.15 2.9 8 conservative 156225 6q22-q23 "laminin, alpha 2 (merosin, congenital muscular dystrophy)" 4041 rs3816800 ATP10A 57194 15 23476187 NM_024490 NP_077816 C/G R1298S minus 5951761 1303 SEQUENOM CEPH CEPH (92) 92 0.14 0.14 0 92 1 0.34 0 748 1 120 "by cluster,freq" Benign 0.175 7 Tolerant 1 2.78 16 moderately radical 605855 15q11-q13 "ATPase, Class V, type 10A" 4042 rs3816873 MTP 4547 4 100861842 NM_000253 NP_000244 C/T I128T plus 24365816 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.26 0.26 0 46 1 0.16 0.02 1590 3 123 "by cluster,freq" Borderline 1.154 9 Tolerant 0.81 2.85 14 moderately conservative 157147 4q24 "microsomal triglyceride transfer protein (large polypeptide, 88kDa)" 4043 rs3816988 TLN2 83660 15 60898792 NM_015059 NP_055874 A/G F2266L minus 5003403 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.13 0.13 0 168 2 0.08 0.04 1584 3 123 "HapMap,freq,cluster" Benign 0.209 17 Tolerant 0.77 2.96 20 conservative 607349 15q15-q21 talin 2 4044 rs3816988 TLN2 83660 15 60898792 NM_015059 NP_055874 A/G F2266L minus 23510605 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 168 2 0.08 0.04 1584 3 123 "HapMap,freq,cluster" Benign 0.209 17 Tolerant 0.77 2.96 20 conservative 607349 15q15-q21 talin 2 4045 rs3817121 TIP120B 23066 3 12836608 XM_371617 XP_371617 A/G V897I plus 19524606 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.18 0.16 0.05 168 2 0.12 0.05 90 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.62 15 Borderline 0.17 2.83 33 conservative 3p25.2 TBP-interacting protein 4046 rs3817121 TIP120B 23066 3 12836608 XM_371617 XP_371617 A/G V897I plus 23891031 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.16 0.05 168 2 0.12 0.05 90 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.62 15 Borderline 0.17 2.83 33 conservative 3p25.2 TBP-interacting protein 4047 rs3817405 PLXDC2 84898 10 20546424 NM_032812 NP_116201 C/T V396I minus 24494839 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.39 0.39 0 46 1 0.26 0.02 94 2 123 "by doubleHit,freq,cluster" Benign 0.697 8 conservative 606827 10p12.33 plexin domain containing 2 4048 rs3817672 TFRC 7037 3 197289121 NM_003234 NP_003225 A/G G142S minus 5586935 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.44 0.46 0.04 86 2 0.22 0.11 440 6 123 "by cluster,freq" Borderline 1.076 11 moderately conservative 190010 3q26.2-qter "transferrin receptor (p90, CD71)" 4049 rs3817672 TFRC 7037 3 197289121 NM_003234 NP_003225 A/G G142S minus 24608629 1371 PERLEGEN AFD_EUR_PANEL European American (24) 24 0.5 0.46 0.04 86 2 0.22 0.11 440 6 123 "by cluster,freq" Borderline 1.076 11 moderately conservative 190010 3q26.2-qter "transferrin receptor (p90, CD71)" 4050 rs3818511 INPP5A 3632 10 134309378 NM_005539 NP_005530 C/T K45R minus 5004926 1303 SEQUENOM CEPH CEPH (92) 92 0.14 0.17 0.07 138 2 0.28 0.03 1590 3 123 "by cluster,freq" Benign 0.675 8 Potentially intolerant 0.1 2.91 15 conservative 600106 10q26.3 "inositol polyphosphate-5-phosphatase, 40kDa" 4051 rs3818511 INPP5A 3632 10 134309378 NM_005539 NP_005530 C/T K45R minus 24090718 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.24 0.17 0.07 138 2 0.28 0.03 1590 3 123 "by cluster,freq" Benign 0.675 8 Potentially intolerant 0.1 2.91 15 conservative 600106 10q26.3 "inositol polyphosphate-5-phosphatase, 40kDa" 4052 rs3819946 CRYZ 1429 1 74887907 NM_001889 NP_001880 C/T I176V plus 23195090 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.3 0.19 71 2 123 "by doubleHit,freq,cluster" Benign 0.835 12 Tolerant 1 2.78 22 conservative 123691 1p31-p22 "crystallin, zeta (quinone reductase)" 4053 rs3820071 ELA2B 51032 1 15554073 NM_015849 NP_056933 A/G G79R plus 24220503 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.28 0.16 84 2 123 "by doubleHit,freq,cluster" Potentially damaging 1.4 83 moderately radical 1p36.13 pancreatic elastase IIB 4054 rs3821033 ZNF142 7701 2 219332807 XM_376172 XP_376172 C/T A1635T plus 23727423 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.04 0.04 0 46 1 0.11 0.03 1570 3 123 "by cluster,freq" moderately conservative 604083 2q34-q35 zinc finger protein 142 (clone pHZ-49) 4055 rs3821979 ShrmL 57619 4 77988604 NM_020859 NP_065910 A/T L146H minus 23909335 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.17 0 48 1 0.3 0.11 94 2 123 "by cluster,freq" moderately conservative 604570 4q21.22 Shroom-related protein 4056 rs3824419 DMRT2 10655 9 1046728 NM_181872 NP_870987 C/G A381P minus 24195860 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.35 0 48 1 0.49 0.05 1570 3 123 "HapMap,doubleHit,freq,cluster" conservative 604935 9p24.3 doublesex and mab-3 related transcription factor 2 4057 rs3824874 MTMR2 8898 11 95296759 NM_016156 NP_057240 G/T K3T plus 24511328 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.46 0 48 1 0.23 0.17 94 2 123 "by doubleHit,freq,cluster" moderately conservative 603557 11q22 myotubularin related protein 2 4058 rs3824886 HTATIP2 10553 11 20361189 NM_006410 NP_006401 G/T S197R plus 10691447 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.04 0.04 0 120 1 0.41 0.04 88 2 123 "HapMap,doubleHit,freq,cluster" Borderline 1.188 9 moderately radical 605628 11p15.1 "HIV-1 Tat interactive protein 2, 30kDa" 4059 rs3825549 MIA2 117153 14 38786559 NM_054024 NP_473365 A/G S344P minus 19303581 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.08 0.08 0 166 2 0.13 0.02 1580 3 123 "HapMap,freq,cluster" moderately conservative 608001 14q13.2 melanoma inhibitory activity 2 4060 rs3825549 MIA2 117153 14 38786559 NM_054024 NP_473365 A/G S344P minus 24579987 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 166 2 0.13 0.02 1580 3 123 "HapMap,freq,cluster" moderately conservative 608001 14q13.2 melanoma inhibitory activity 2 4061 rs3826007 BCL2A1 597 15 78050272 NM_004049 NP_004040 A/G G82D minus 5012488 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.25 0.22 0.06 166 2 0.22 0.04 1520 3 123 "HapMap,freq,cluster" Possibly damaging 1.806 7 Potentially intolerant 0.06 2.79 73 moderately conservative 601056 15q24.3 BCL2-related protein A1 4062 rs3826007 BCL2A1 597 15 78050272 NM_004049 NP_004040 A/G G82D minus 24064930 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.22 0.06 166 2 0.22 0.04 1520 3 123 "HapMap,freq,cluster" Possibly damaging 1.806 7 Potentially intolerant 0.06 2.79 73 moderately conservative 601056 15q24.3 BCL2-related protein A1 4063 rs3826942 MUM1 84939 19 1311575 NM_032853 NP_116242 C/T G220R minus 6636202 885 TSC-CSHL HapMap-CEPH-30-trios 114 0.28 0.24 0.08 160 2 0.36 0.12 90 2 123 "HapMap,freq,cluster" moderately radical 19p13.3 melanoma associated antigen (mutated) 1 4064 rs3826942 MUM1 84939 19 1311575 NM_032853 NP_116242 C/T G220R minus 24190653 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.15 0.24 0.08 160 2 0.36 0.12 90 2 123 "HapMap,freq,cluster" moderately radical 19p13.3 melanoma associated antigen (mutated) 1 4065 rs3827760 EDAR 10913 2 108972119 NM_022336 NP_071731 C/T V370A minus 23670642 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.02 0.02 0 46 1 0.21 0.05 1582 3 123 "by doubleHit,freq,cluster" Benign 0.463 11 moderately conservative 604095 2q11-q13 "ectodysplasin 1, anhidrotic receptor" 4066 rs3829037 MTSS1 9788 8 125634509 NM_014751 NP_055566 A/G T725A minus 5015539 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.26 0.26 0.01 168 2 0.15 0 94 2 123 "HapMap,freq" Borderline 1.045 9 moderately conservative 608486 8p22 metastasis suppressor 1 4067 rs3829037 MTSS1 9788 8 125634509 NM_014751 NP_055566 A/G T725A minus 24533147 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.26 0.01 168 2 0.15 0 94 2 123 "HapMap,freq" Borderline 1.045 9 moderately conservative 608486 8p22 metastasis suppressor 1 4068 rs3829078 CA9 768 9 35669251 NM_001216 NP_001207 A/G Q326R plus 5015580 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.11 0.11 0 120 1 107 "HapMap,freq" Tolerant 1 2.77 191 conservative 603179 9p13-p12 carbonic anhydrase IX 4069 rs3829462 LIPC 3990 15 56640371 NM_000236 NP_000227 G/T F356L minus 16334415 904 AFFY CEPH 10 0.4 0.09 0.21 56 2 0.09 0.06 150 4 123 by freq Probably damaging 2.001 8 conservative 151670 15q21-q23 "lipase, hepatic" 4070 rs3829462 LIPC 3990 15 56640371 NM_000236 NP_000227 G/T F356L minus 23811376 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.02 0.09 0.21 56 2 0.09 0.06 150 4 123 by freq Probably damaging 2.001 8 conservative 151670 15q21-q23 "lipase, hepatic" 4071 rs3829655 SIGLEC5 8778 19 56807457 NM_003830 NP_003821 C/G P499A minus 5016158 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.49 0.49 0 118 1 120 "HapMap,freq,cluster" conservative 604200 19q13.3 sialic acid binding Ig-like lectin 5 4072 rs3829659 SIGLEC8 27181 19 56649368 NM_014442 NP_055257 A/G R388G minus 14703015 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.23 0.23 0 120 1 0.32 0 752 1 119 "HapMap,doubleHit,freq,cluster" Probably damaging 2.27 14 moderately radical 605639 19q13.33-q13.41 sialic acid binding Ig-like lectin 8 4073 rs3829767 SYNE2 23224 14 63589208 NM_015180 NP_055995 A/G I2941V plus 5016271 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.14 0.13 0.03 168 2 0.31 0.08 94 2 123 "HapMap,doubleHit,freq,cluster" conservative 608442 14q23.2 "spectrin repeat containing, nuclear envelope 2" 4074 rs3829767 SYNE2 23224 14 63589208 NM_015180 NP_055995 A/G I2941V plus 23647972 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.13 0.03 168 2 0.31 0.08 94 2 123 "HapMap,doubleHit,freq,cluster" conservative 608442 14q23.2 "spectrin repeat containing, nuclear envelope 2" 4075 rs3859866 MYO18B 84700 22 24491454 NM_032608 NP_115997 C/G W547C plus 24114064 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.09 0.09 94 2 123 "by cluster,freq" Intolerant 0.02 2.81 98 radical 607295 22q11.2-q12.1 myosin XVIIIB 4076 rs3862618 ROBO3 64221 11 124247575 XM_370663 XP_370663 C/T R575H minus 5155031 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.09 0.09 0.01 168 2 0.11 0.13 90 2 123 "HapMap,doubleHit,freq,cluster" conservative 608630 11q24.2 "roundabout, axon guidance receptor, homolog 3 (Drosophila)" 4077 rs3862618 ROBO3 64221 11 124247575 XM_370663 XP_370663 C/T R575H minus 24124289 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.09 0.01 168 2 0.11 0.13 90 2 123 "HapMap,doubleHit,freq,cluster" conservative 608630 11q24.2 "roundabout, axon guidance receptor, homolog 3 (Drosophila)" 4078 rs3864017 FANCD2 2177 3 10081532 NM_033084 NP_149075 A/G P714L minus 5360912 1303 SEQUENOM CEPH CEPH (92) 92 0.48 0.48 0 92 1 123 by freq moderately conservative 227646 3p26 "Fanconi anemia, complementation group D2" 4079 rs3892221 UGT1A4 54657 2 234409497 NM_007120 NP_009051 C/T R11W plus 1292957 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.26 0 92 1 111 by freq Borderline 1.083 6 Borderline 0.19 3.02 78 moderately radical 606429 2q37 "UDP glycosyltransferase 1 family, polypeptide A4" 4080 rs3915806 ZNF142 7701 2 219328647 XM_376172 XP_376172 A/C T1984P minus 2393062 1303 SEQUENOM CEPH CEPH (92) 92 0.04 0.04 0 92 1 108 by freq conservative 604083 2q34-q35 zinc finger protein 142 (clone pHZ-49) 4081 rs3917594 PON1 5444 7 94582090 NM_000446 NP_000437 A/G W194X minus 5111675 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.02 0.02 0 110 2 121 "by cluster,freq" Probably damaging Intolerant radical 168820 7q21.3 paraoxonase 1 4082 rs3917594 PON1 5444 7 94582090 NM_000446 NP_000437 A/G W194X minus 16338590 1120 WIPGA POP-WIPGA-12-05-2003 CORIELL Mixed 64 0.02 0.02 0 110 2 121 "by cluster,freq" Probably damaging Intolerant radical 168820 7q21.3 paraoxonase 1 4083 rs3918021 CSF3R 1441 1 36601551 NM_156039 NP_724781 C/T R698C minus 5112180 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.04 0.04 0 92 2 123 by freq radical 138971 1p35-p34.3 colony stimulating factor 3 receptor (granulocyte) 4084 rs3918021 CSF3R 1441 1 36601551 NM_156039 NP_724781 C/T R698C minus 24253571 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.04 0.04 0 92 2 123 by freq radical 138971 1p35-p34.3 colony stimulating factor 3 receptor (granulocyte) 4085 rs3918234 NOS3 4846 7 150145683 NM_000603 NP_000594 A/T Q982L plus 5112449 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.02 0.02 0 92 2 0.01 0 94 1 123 "by cluster,freq" Possibly damaging 1.766 24 Tolerant 0.21 2.82 60 moderately radical 163729 7q36 nitric oxide synthase 3 (endothelial cell) 4086 rs3918234 NOS3 4846 7 150145683 NM_000603 NP_000594 A/T Q982L plus 24457964 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.02 0.02 0 92 2 0.01 0 94 1 123 "by cluster,freq" Possibly damaging 1.766 24 Tolerant 0.21 2.82 60 moderately radical 163729 7q36 nitric oxide synthase 3 (endothelial cell) 4087 rs3918248 MMP9 4318 20 44071031 NM_004994 NP_004985 C/T A20V plus 5112463 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.01 0 92 1 0.05 0 44 1 108 by freq Benign 0.367 16 Tolerant 0.51 2.78 44 moderately conservative 120361 20q11.2-q13.1 "matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)" 4088 rs3918252 MMP9 4318 20 44072538 NM_004994 NP_004985 C/G N127K plus 16338509 1120 WIPGA POP-WIPGA-12-05-2003 CORIELL Mixed 20 0.1 0.1 0 20 1 0.06 0.01 94 2 123 "by cluster,freq" Possibly damaging 1.832 18 Potentially intolerant 0.08 2.78 49 moderately conservative 120361 20q11.2-q13.1 "matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)" 4089 rs3923647 TLR1 7096 4 38622105 NM_003263 NP_003254 A/T H305L minus 7987553 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.05 0.04 0.01 88 2 0.08 0.01 94 2 123 "by doubleHit,freq,cluster" Probably damaging 2.551 14 Intolerant 0 2.78 32 moderately conservative 601194 4p14 toll-like receptor 1 4090 rs3923647 TLR1 7096 4 38622105 NM_003263 NP_003254 A/T H305L minus 23715763 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0.01 88 2 0.08 0.01 94 2 123 "by doubleHit,freq,cluster" Probably damaging 2.551 14 Intolerant 0 2.78 32 moderately conservative 601194 4p14 toll-like receptor 1 4091 rs3935209 OPLAH 26873 8 145185229 XM_291266 XP_291266 G/T S380R plus 5193200 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.07 0.07 0 120 1 120 "HapMap,doubleHit,freq,cluster" moderately radical 8q24.3 5-oxoprolinase (ATP-hydrolysing) 4092 rs3969860 RAB3D 9545 19 11308886 NM_004283 NP_004274 C/T V64I plus 23638766 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.1 0 42 1 123 "by cluster,freq" Benign 0.124 55 Tolerant 1 2.8 258 conservative 604350 19p13.2 "RAB3D, member RAS oncogene family" 4093 rs4012065 RANBP2 5903 2 108826951 NM_006267 NP_006258 A/G E580K plus 24819281 1303 SEQUENOM CEPH CEPH (92) 184 0.1 0.1 0 184 1 123 by freq moderately conservative 601181 2q12.3 RAN binding protein 2 4094 rs4015375 STEAP 26872 7 89434826 NM_012449 NP_036581 C/G H47Q plus 5352001 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.07 0.07 0 120 1 121 "HapMap,freq" Benign 0.882 7 conservative 604415 7q21 six transmembrane epithelial antigen of the prostate 4095 rs4027402 SYNE2 23224 14 63566502 NM_015180 NP_055995 C/T A2283V plus 5374587 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.13 0.13 0 120 1 120 "HapMap,doubleHit,freq,cluster" moderately conservative 608442 14q23.2 "spectrin repeat containing, nuclear envelope 2" 4096 rs4072111 IL16 3603 15 79365194 NM_172217 NP_757366 A/G P434S minus 5451276 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.16 0.16 0 120 1 120 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.8 5 Tolerant 0.49 2.8 151 moderately conservative 603035 15q26.3 interleukin 16 (lymphocyte chemoattractant factor) 4097 rs4134982 E2F3 1871 6 20598407 NM_001949 NP_001940 A/G D389N plus 5587215 693 EGP_SNPS PDR90 NIHPDR 168 0.01 0.01 0 168 1 108 by freq Benign 0.07 7 Tolerant 0.54 2.8 37 conservative 600427 6p22 E2F transcription factor 3 4098 rs4135012 CDC6 990 17 35703774 NM_001254 NP_001245 A/G D295N plus 5587248 693 EGP_SNPS PDR90 NIHPDR 178 0.01 0.01 0.01 226 2 123 by freq Potentially damaging 1.436 11 Potentially intolerant 0.09 2.77 16 conservative 602627 17q21.3 CDC6 cell division cycle 6 homolog (S. cerevisiae) 4099 rs4135012 CDC6 990 17 35703774 NM_001254 NP_001245 A/G D295N plus 24579095 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.01 0.01 226 2 123 by freq Potentially damaging 1.436 11 Potentially intolerant 0.09 2.77 16 conservative 602627 17q21.3 CDC6 cell division cycle 6 homolog (S. cerevisiae) 4100 rs4135016 CDC6 990 17 35705183 NM_001254 NP_001245 A/G R378H plus 5587252 693 EGP_SNPS PDR90 NIHPDR 168 0.01 0.01 0 168 1 108 HapMap Possibly damaging 1.582 11 Intolerant 0.02 2.77 16 conservative 602627 17q21.3 CDC6 cell division cycle 6 homolog (S. cerevisiae) 4101 rs4135113 TDG 6996 12 102879160 NM_003211 NP_003202 A/G G199S plus 5587376 693 EGP_SNPS PDR90 NIHPDR 176 0.09 0.07 0.04 296 2 120 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.581 9 moderately conservative 601423 12q24.1 thymine-DNA glycosylase 4102 rs4135113 TDG 6996 12 102879160 NM_003211 NP_003202 A/G G199S plus 5587376 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.03 0.07 0.04 296 2 120 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.581 9 moderately conservative 601423 12q24.1 thymine-DNA glycosylase 4103 rs4140446 MDN1 23195 6 90504813 NM_014611 NP_055426 C/T S1559N plus 24422483 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.23 0 48 1 0.2 0 46 1 123 "by cluster,freq" conservative 6q15 "MDN1, midasin homolog (yeast)" 4104 rs4144738 MLZE 56169 8 130830032 NM_031415 NP_113603 A/G M475T plus 6525061 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.38 0.38 0 120 1 120 "HapMap,doubleHit,freq,cluster" Intolerant 0.04 2.87 13 moderately conservative 608384 8q24.1-q24.2 "melanoma-derived leucine zipper, extra-nuclear factor" 4105 rs4145748 ITGA1 3672 5 52237479 NM_181501 NP_852478 C/T T480M plus 23982813 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.02 0.02 0 46 1 0.07 0.02 92 2 123 "by cluster,freq" Intolerant 0.04 2.76 17 moderately conservative 192968 5q11.2 "integrin, alpha 1" 4106 rs4145944 ATP10D 57205 4 47434211 NM_020453 NP_065186 C/G S1389T minus 23727027 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.31 0 48 1 0.3 0.22 94 2 123 "by doubleHit,freq,cluster" moderately conservative 4p12 "ATPase, Class V, type 10D" 4107 rs4148301 UGT2A1 10941 4 70642802 NM_006798 NP_006789 A/G G308R minus 14600403 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.13 0.13 0 120 1 120 "HapMap,doubleHit,freq,cluster" Probably damaging 2.492 69 Intolerant 0 2.85 127 moderately radical 604716 4q13 "UDP glycosyltransferase 2 family, polypeptide A1" 4108 rs4148880 TAP1 6890 6 32926752 NM_000593 NP_000584 A/G I393V minus 24169288 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.15 0.19 0.03 414 3 0.23 0.04 94 2 123 "by doubleHit,freq,cluster" Benign 0.33 27 Tolerant 0.42 2.8 74 conservative 170260 6p21.3 "transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)" 4109 rs4148880 TAP1 6890 6 32926752 NM_000593 NP_000584 A/G I393V minus 24796294 1303 SEQUENOM CEPH CEPH (92) 184 0.18 0.19 0.03 414 3 0.23 0.04 94 2 123 "by doubleHit,freq,cluster" Benign 0.33 27 Tolerant 0.42 2.8 74 conservative 170260 6p21.3 "transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)" 4110 rs4148880 TAP1 6890 6 32926752 NM_000593 NP_000584 A/G I393V minus 24818952 1303 SEQUENOM CEPH CEPH (92) 184 0.22 0.19 0.03 414 3 0.23 0.04 94 2 123 "by doubleHit,freq,cluster" Benign 0.33 27 Tolerant 0.42 2.8 74 conservative 170260 6p21.3 "transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)" 4111 rs4149584 TNFRSF1A 7132 12 6312904 NM_001065 NP_001056 A/G R121Q minus 5604300 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.04 0.03 0.01 166 2 0.02 0 44 1 110 "HapMap,freq" Potentially damaging 1.339 9 Tolerant 0.55 2.85 19 conservative 191190 12p13.2 "tumor necrosis factor receptor superfamily, member 1A" 4112 rs4149584 TNFRSF1A 7132 12 6312904 NM_001065 NP_001056 A/G R121Q minus 5604300 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.03 0.03 0.01 166 2 0.02 0 44 1 110 "HapMap,freq" Potentially damaging 1.339 9 Tolerant 0.55 2.85 19 conservative 191190 12p13.2 "tumor necrosis factor receptor superfamily, member 1A" 4113 rs4150313 ERCC5 2073 13 102311952 NM_000123 NP_000114 A/G Q256R plus 5605243 693 EGP_SNPS PDR90 NIHPDR 180 0.02 0.02 0 180 1 0.04 0.06 288 3 123 "by cluster,freq" Possibly damaging 1.696 7 Tolerant 0.64 2.9 8 conservative 133530 13q22 "excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))" 4114 rs4150342 ERCC5 2073 13 102318566 NM_000123 NP_000114 A/G N879S plus 5605277 693 EGP_SNPS PDR90 NIHPDR 168 0.01 0.01 0 168 1 110 by freq Potentially damaging 1.493 7 Tolerant 0.95 2.84 10 conservative 133530 13q22 "excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))" 4115 rs4150521 ERCC3 2071 2 127733208 NM_000122 NP_000113 C/T S704L minus 5605467 693 EGP_SNPS PDR90 NIHPDR 180 0.01 0.01 0 180 1 110 by freq Possibly damaging 1.599 32 Tolerant 0.36 3.02 30 moderately radical 133510 2q21 "excision repair cross-complementing rodent repair deficiency, complementation group 3 (xeroderma pigmentosum group B complementing)" 4116 rs4151030 RAG1 5896 11 36552336 NM_000448 NP_000439 A/C D302E plus 5606001 693 EGP_SNPS PDR90 NIHPDR 166 0.04 0.04 0 166 1 0.07 0 46 1 123 "by cluster,freq" Benign 0.965 331 conservative 179615 11p13 recombination activating gene 1 4117 rs4151033 RAG1 5896 11 36554068 NM_000448 NP_000439 A/G E880K plus 5606005 693 EGP_SNPS PDR90 NIHPDR 174 0.02 0.02 0 174 1 110 by freq Benign 0.926 334 moderately conservative 179615 11p13 recombination activating gene 1 4118 rs4151539 RB1 5925 13 47853459 NM_000321 NP_000312 C/G A525G plus 5606845 693 EGP_SNPS PDR90 NIHPDR 158 0.02 0.02 0 158 1 0.11 0 46 1 123 by freq Potentially damaging 1.438 11 Intolerant 0.03 2.8 26 moderately conservative 180200 13q14.2 retinoblastoma 1 (including osteosarcoma) 4119 rs4151651 BF 629 6 32023593 NM_001710 NP_001701 A/G G252S plus 5606989 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.04 0.04 0 46 1 0.02 0 48 1 110 by freq Tolerant 0.71 2.94 18 moderately conservative 138470 6p21.3 "B-factor, properdin" 4120 rs4151667 BF 629 6 32022003 NM_001710 NP_001701 A/T L9H plus 5607016 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 28 0.07 0.08 0.01 74 2 119 "by cluster,freq" moderately conservative 138470 6p21.3 "B-factor, properdin" 4121 rs4151667 BF 629 6 32022003 NM_001710 NP_001701 A/T L9H plus 12674498 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.09 0.08 0.01 74 2 119 "by cluster,freq" moderately conservative 138470 6p21.3 "B-factor, properdin" 4122 rs4236480 TRPV5 56302 7 142143386 NM_019841 NP_062815 A/G R154H minus 5608314 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.28 0.28 0 46 1 0.44 0 48 1 120 "by doubleHit,freq,cluster" Intolerant 0.01 2.79 66 conservative 606679 7q35 "transient receptor potential cation channel, subfamily V, member 5" 4123 rs4238001 SCARB1 949 12 123873143 NM_005505 NP_005496 C/T G2S plus 14660124 1073 ELEVY MQFCEPOP_DS49 French Canadian Caucasians and European Caucasians 36 0.08 0.08 0 36 1 0.09 0.04 124 3 120 "by doubleHit,freq" Possibly damaging 1.581 15 moderately conservative 601040 12q24.31 "scavenger receptor class B, member 1" 4124 rs4251545 IRAK4 51135 12 42466562 NM_016123 NP_057207 A/G A428T plus 5607207 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 42 0.1 0.1 0 90 2 0.24 0.13 136 3 123 "by doubleHit,freq,cluster" Benign 0.859 6 Tolerant 0.27 2.81 159 moderately conservative 606883 12q12 interleukin-1 receptor-associated kinase 4 4125 rs4251545 IRAK4 51135 12 42466562 NM_016123 NP_057207 A/G A428T plus 23465789 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 90 2 0.24 0.13 136 3 123 "by doubleHit,freq,cluster" Benign 0.859 6 Tolerant 0.27 2.81 159 moderately conservative 606883 12q12 interleukin-1 receptor-associated kinase 4 4126 rs4252125 PLG 5340 6 161122651 NM_000301 NP_000292 A/G D472N plus 5607943 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 42 0.26 0.25 0.01 90 2 0.19 0.01 94 2 123 "by doubleHit,freq,cluster" Borderline 1.157 15 Tolerant 0.81 3.14 26 conservative 173350 6q26 plasminogen 4127 rs4252125 PLG 5340 6 161122651 NM_000301 NP_000292 A/G D472N plus 24471664 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.25 0.01 90 2 0.19 0.01 94 2 123 "by doubleHit,freq,cluster" Borderline 1.157 15 Tolerant 0.81 3.14 26 conservative 173350 6q26 plasminogen 4128 rs4252233 TAF9 6880 5 68697304 NM_003187 NP_003178 C/T T6M minus 5608071 693 EGP_SNPS PDR90 NIHPDR 174 0.01 0.02 0.01 294 2 111 "HapMap,freq" Probably damaging 2.163 6 moderately conservative 600822 5q11.2-q13.1 "TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 32kDa" 4129 rs4252233 TAF9 6880 5 68697304 NM_003187 NP_003178 C/T T6M minus 5608071 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.03 0.02 0.01 294 2 111 "HapMap,freq" Probably damaging 2.163 6 moderately conservative 600822 5q11.2-q13.1 "TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 32kDa" 4130 rs4252272 IL10RA 3587 11 117369273 NM_001558 NP_001549 A/G S159G plus 5608113 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.28 0.29 0.01 94 2 0.02 0 94 2 123 "by cluster,freq" moderately conservative 146933 11q23 "interleukin 10 receptor, alpha" 4131 rs4252272 IL10RA 3587 11 117369273 NM_001558 NP_001549 A/G S159G plus 24565466 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.29 0.01 94 2 0.02 0 94 2 123 "by cluster,freq" moderately conservative 146933 11q23 "interleukin 10 receptor, alpha" 4132 rs4252303 IL10RA 3587 11 117365515 NM_001558 NP_001549 A/G V113I plus 5608153 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.04 0.04 0 46 1 111 by freq conservative 146933 11q23 "interleukin 10 receptor, alpha" 4133 rs4252589 HSPB2 3316 11 111289611 NM_001541 NP_001532 A/G G111S plus 5608512 693 EGP_SNPS PDR90 NIHPDR 172 0.01 0.01 0 172 1 111 by freq Intolerant 0 2.92 103 moderately conservative 602179 11q22-q23 heat shock 27kDa protein 2 4134 rs4252716 MDM4 4194 1 201243581 NM_002393 NP_002384 C/T I175T plus 5608655 693 EGP_SNPS PDR90 NIHPDR 174 0.04 0.04 0 174 1 0.02 0 46 1 123 "by cluster,freq" Tolerant 0.59 2.98 25 moderately conservative 602704 1q32 "Mdm4, transformed 3T3 cell double minute 4, p53 binding protein (mouse)" 4135 rs4253047 ERCC6 2074 10 50402145 NM_000124 NP_000115 A/G G446D minus 5609014 693 EGP_SNPS PDR90 NIHPDR 166 0.01 0.01 0 166 1 111 by freq Tolerant 0.58 2.9 75 moderately conservative 133540 10q11 "excision repair cross-complementing rodent repair deficiency, complementation group 6" 4136 rs4253199 ERCC6 2074 10 50350965 NM_000124 NP_000115 C/T T942M minus 5609179 693 EGP_SNPS PDR90 NIHPDR 180 0.02 0.02 0 180 1 111 by freq Potentially intolerant 0.1 2.89 187 moderately conservative 133540 10q11 "excision repair cross-complementing rodent repair deficiency, complementation group 6" 4137 rs4253211 ERCC6 2074 10 50348323 NM_000124 NP_000115 C/G R1230P minus 5609194 693 EGP_SNPS PDR90 NIHPDR 168 0.08 0.07 0.02 216 2 0.08 0 48 1 123 by freq moderately radical 133540 10q11 "excision repair cross-complementing rodent repair deficiency, complementation group 6" 4138 rs4253211 ERCC6 2074 10 50348323 NM_000124 NP_000115 C/G R1230P minus 24205469 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.07 0.02 216 2 0.08 0 48 1 123 by freq moderately radical 133540 10q11 "excision repair cross-complementing rodent repair deficiency, complementation group 6" 4139 rs4253219 ERCC6 2074 10 50339422 NM_000124 NP_000115 G/T G1322V minus 5609203 693 EGP_SNPS PDR90 NIHPDR 178 0.01 0.01 0 178 1 111 by freq moderately radical 133540 10q11 "excision repair cross-complementing rodent repair deficiency, complementation group 6" 4140 rs4253230 ERCC6 2074 10 50337027 NM_000124 NP_000115 C/T T1441I minus 5609217 693 EGP_SNPS PDR90 NIHPDR 180 0.01 0.01 0 180 1 0.07 0 46 1 123 "by doubleHit,freq,cluster" moderately conservative 133540 10q11 "excision repair cross-complementing rodent repair deficiency, complementation group 6" 4141 rs4253301 KLKB1 3818 4 187548161 NM_000892 NP_000883 G/T S381A plus 5609308 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.04 0.05 0.01 94 2 0.08 0.02 138 3 123 "by cluster,freq" Borderline 1.217 12 Tolerant 0.48 2.91 206 moderately conservative 229000 4q34-q35 "kallikrein B, plasma (Fletcher factor) 1" 4142 rs4253301 KLKB1 3818 4 187548161 NM_000892 NP_000883 G/T S381A plus 23275024 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.05 0.01 94 2 0.08 0.02 138 3 123 "by cluster,freq" Borderline 1.217 12 Tolerant 0.48 2.91 206 moderately conservative 229000 4q34-q35 "kallikrein B, plasma (Fletcher factor) 1" 4143 rs4253325 KLKB1 3818 4 187553622 NM_000892 NP_000883 A/G R560Q plus 5609337 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.09 0.08 0.01 94 2 0.23 0.05 138 3 123 "by doubleHit,freq,cluster" Potentially damaging 1.365 12 Tolerant 0.58 2.92 398 conservative 229000 4q34-q35 "kallikrein B, plasma (Fletcher factor) 1" 4144 rs4253325 KLKB1 3818 4 187553622 NM_000892 NP_000883 A/G R560Q plus 24179513 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0.01 94 2 0.23 0.05 138 3 123 "by doubleHit,freq,cluster" Potentially damaging 1.365 12 Tolerant 0.58 2.92 398 conservative 229000 4q34-q35 "kallikrein B, plasma (Fletcher factor) 1" 4145 rs4301822 APOF 319 12 55041325 NM_001638 NP_001629 C/T I311T minus 16361197 693 EGP_SNPS PDR90 NIHPDR 178 0.13 0.13 0 178 1 120 "by cluster,freq" moderately conservative 107760 12q13.13 apolipoprotein F 4146 rs4358188 BPI 671 20 36380262 NM_001725 NP_001716 A/G E216K plus 7987430 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.45 0.47 0.02 91 3 0.38 0.11 140 3 123 "by doubleHit,freq,cluster" Benign 0.48 7 moderately conservative 109195 20q11.23-q12 bactericidal/permeability-increasing protein 4147 rs4358188 BPI 671 20 36380262 NM_001725 NP_001716 A/G E216K plus 7987430 848 IIPGA-WEISS-MARTINEZ E-1 CEPH 3 0.5 0.47 0.02 91 3 0.38 0.11 140 3 123 "by doubleHit,freq,cluster" Benign 0.48 7 moderately conservative 109195 20q11.23-q12 bactericidal/permeability-increasing protein 4148 rs4358188 BPI 671 20 36380262 NM_001725 NP_001716 A/G E216K plus 24694557 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.47 0.02 91 3 0.38 0.11 140 3 123 "by doubleHit,freq,cluster" Benign 0.48 7 moderately conservative 109195 20q11.23-q12 bactericidal/permeability-increasing protein 4149 rs4371716 CDH12 1010 5 22114341 NM_004061 NP_004052 C/T V68M plus 7930772 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.22 0.23 0.03 168 2 0.26 0.1 94 2 123 "HapMap,doubleHit,freq,cluster" Probably damaging 2.083 50 Tolerant 0.37 2.86 57 conservative 600562 5p14-p13 "cadherin 12, type 2 (N-cadherin 2)" 4150 rs4371716 CDH12 1010 5 22114341 NM_004061 NP_004052 C/T V68M plus 23164497 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.23 0.03 168 2 0.26 0.1 94 2 123 "HapMap,doubleHit,freq,cluster" Probably damaging 2.083 50 Tolerant 0.37 2.86 57 conservative 600562 5p14-p13 "cadherin 12, type 2 (N-cadherin 2)" 4151 rs4426527 AGXT 189 2 241537506 NM_000030 NP_000021 A/G I340M plus 7853995 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.18 0.19 0.02 168 2 0.03 0.01 94 2 123 "HapMap,doubleHit,freq,cluster" Borderline 1.12 17 Tolerant 0.96 2.8 36 conservative 604285 2q36-q37 alanine-glyoxylate aminotransferase (oxalosis I; hyperoxaluria I; glycolicaciduria; serine-pyruvate aminotransferase) 4152 rs4426527 AGXT 189 2 241537506 NM_000030 NP_000021 A/G I340M plus 24260964 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.19 0.02 168 2 0.03 0.01 94 2 123 "HapMap,doubleHit,freq,cluster" Borderline 1.12 17 Tolerant 0.96 2.8 36 conservative 604285 2q36-q37 alanine-glyoxylate aminotransferase (oxalosis I; hyperoxaluria I; glycolicaciduria; serine-pyruvate aminotransferase) 4153 rs4430553 HELB 92797 12 64985162 NM_033647 NP_387467 C/T L191P plus 24705888 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.42 0 48 1 0.29 0.01 94 2 123 "by doubleHit,freq,cluster" moderately conservative 12q14.2 helicase (DNA) B 4154 rs4438413 ZNF525 170958 19 58576224 XM_375646 XP_375646 A/G D140N plus 5949365 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.33 0.33 0 120 1 121 "HapMap,doubleHit,freq" Possibly damaging 1.646 28 Potentially intolerant 0.07 2.79 136 conservative 19q13.42 zinc finger protein 525 4155 rs4452075 ZNF527 84503 19 42571429 XM_030378 XP_030378 A/G H213R plus 5973879 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.16 0.16 0 118 1 116 "HapMap,doubleHit,freq,cluster" Intolerant 0.02 2.79 34 conservative 19q13.1 zinc finger protein 527 4156 rs4459610 ACE 1636 17 58938452 NM_152831 NP_690044 A/T K715N plus 5987275 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.42 0.42 0 118 1 121 "HapMap,doubleHit,freq,cluster" moderately conservative 106180 17q23 angiotensin I converting enzyme (peptidyl-dipeptidase A) 1 4157 rs4479748 ENPP6 133121 4 185387547 NM_153343 NP_699174 C/T S419G plus 24661524 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.44 0 48 1 0.41 0.05 94 2 123 "by doubleHit,freq,cluster" Tolerant 0.5 2.9 16 moderately conservative 4q35.1 ectonucleotide pyrophosphatase/phosphodiesterase 6 4158 rs4514875 CD8B1 926 2 86981089 NM_172099 NP_742097 C/T M230I plus 7978240 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.28 0.28 0 120 1 120 "HapMap,freq,cluster" conservative 186730 2p12 "CD8 antigen, beta polypeptide 1 (p37)" 4159 rs4645959 MYC 4609 8 128819722 NM_002467 NP_002458 A/G N11S plus 6310760 693 EGP_SNPS PDR90 NIHPDR 172 0.02 0.03 0.04 220 2 123 "by cluster,freq" Possibly damaging 1.699 21 Intolerant 0 2.93 72 conservative 190080 8q24.12-q24.13 v-myc myelocytomatosis viral oncogene homolog (avian) 4160 rs4645959 MYC 4609 8 128819722 NM_002467 NP_002458 A/G N11S plus 24506255 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.03 0.04 220 2 123 "by cluster,freq" Possibly damaging 1.699 21 Intolerant 0 2.93 72 conservative 190080 8q24.12-q24.13 v-myc myelocytomatosis viral oncogene homolog (avian) 4161 rs4645960 MYC 4609 8 128820168 NM_002467 NP_002458 G/T G160C plus 6310761 693 EGP_SNPS PDR90 NIHPDR 166 0.01 0.01 0 166 1 111 by freq Potentially damaging 1.463 22 Intolerant 0.03 2.86 94 radical 190080 8q24.12-q24.13 v-myc myelocytomatosis viral oncogene homolog (avian) 4162 rs4645961 MYC 4609 8 128820198 NM_002467 NP_002458 A/G V170I plus 6310762 693 EGP_SNPS PDR90 NIHPDR 164 0.02 0.02 0 164 1 0.02 0 46 1 123 "by cluster,freq" Benign 0.857 19 Tolerant 0.24 2.95 89 conservative 190080 8q24.12-q24.13 v-myc myelocytomatosis viral oncogene homolog (avian) 4163 rs4645968 MYC 4609 8 128822031 NM_002467 NP_002458 C/T A322V plus 6310770 693 EGP_SNPS PDR90 NIHPDR 176 0.01 0.01 0 176 1 111 by freq Benign 0.163 20 Tolerant 0.29 2.81 350 moderately conservative 190080 8q24.12-q24.13 v-myc myelocytomatosis viral oncogene homolog (avian) 4164 rs4646487 CYP4B1 1580 1 46991195 NM_000779 NP_000770 C/T R173W plus 23160462 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 0.23 0.01 94 2 123 "by doubleHit,freq,cluster" Possibly damaging 1.718 45 Intolerant 0.01 2.8 88 moderately radical 124075 1p34-p12 "cytochrome P450, family 4, subfamily B, polypeptide 1" 4165 rs4646491 CYP4B1 1580 1 46992904 NM_000779 NP_000770 C/T R340C plus 23843598 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.14 0.1 94 2 123 "by doubleHit,freq" Probably damaging 2.128 45 Intolerant 0 2.8 89 radical 124075 1p34-p12 "cytochrome P450, family 4, subfamily B, polypeptide 1" 4166 rs4646750 FTHFD 10840 3 127308701 NM_012190 NP_036322 A/G I812V minus 12674967 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.07 0.07 0 60 1 0.13 0.05 344 4 118 "by cluster,freq" Benign 0.427 17 Tolerant 0.58 2.99 397 conservative 600249 3q21.2 formyltetrahydrofolate dehydrogenase 4167 rs4647338 CASP2 835 7 142518963 NM_032982 NP_116764 C/G R441G plus 6313054 693 EGP_SNPS PDR90 NIHPDR 172 0.02 0.02 0 172 1 111 by freq Probably damaging 2.027 8 Intolerant 0.01 2.92 17 moderately radical 600639 7q34-q35 "caspase 2, apoptosis-related cysteine protease (neural precursor cell expressed, developmentally down-regulated 2)" 4168 rs4647932 FGFRL1 53834 4 1008841 NM_021923 NP_068742 C/T P464L plus 6313860 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.08 0.08 0 120 1 0.08 0 40 1 111 "HapMap,freq" Possibly damaging 1.744 10 moderately conservative 605830 4p16 fibroblast growth factor receptor-like 1 4169 rs4648072 NFKB1 4790 4 103875893 NM_003998 NP_003989 A/G M507V plus 6395926 693 EGP_SNPS PDR90 NIHPDR 176 0.01 0.01 0.01 224 2 0.05 0 44 1 123 "by cluster,freq" Possibly damaging 1.838 9 Borderline 0.15 2.99 17 conservative 164011 4q24 nuclear factor of kappa light polypeptide gene enhancer in B-cells 1 (p105) 4170 rs4648072 NFKB1 4790 4 103875893 NM_003998 NP_003989 A/G M507V plus 23394935 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.01 0.01 224 2 0.05 0 44 1 123 "by cluster,freq" Possibly damaging 1.838 9 Borderline 0.15 2.99 17 conservative 164011 4q24 nuclear factor of kappa light polypeptide gene enhancer in B-cells 1 (p105) 4171 rs4648099 NFKB1 4790 4 103886010 NM_003998 NP_003989 G/T H712Q plus 6395957 693 EGP_SNPS PDR90 NIHPDR 176 0.02 0.02 0 176 1 0.07 0 46 1 123 "by cluster,freq" Possibly damaging 1.932 9 Potentially intolerant 0.1 2.97 19 conservative 164011 4q24 nuclear factor of kappa light polypeptide gene enhancer in B-cells 1 (p105) 4172 rs4667591 LRP2 4036 2 169828939 NM_004525 NP_004516 G/T I4210L plus 23903166 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.23 0 48 1 0.3 0.18 94 2 123 "by doubleHit,freq,cluster" Intolerant 0.02 2.76 21 conservative 600073 2q24-q31 low density lipoprotein-related protein 2 4173 rs4668123 LRP2 4036 2 169879012 NM_004525 NP_004516 C/T A2872T plus 23903504 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.33 0 48 1 0.34 0.08 94 2 123 "by doubleHit,freq,cluster" Tolerant 0.36 2.94 13 moderately conservative 600073 2q24-q31 low density lipoprotein-related protein 2 4174 rs4698803 EGF 1950 4 111272031 NM_001963 NP_001954 A/T E920V plus 16340424 693 EGP_SNPS PDR90 NIHPDR 176 0.1 0.13 0.08 224 2 123 "by doubleHit,freq,cluster" Potentially damaging 1.253 10 moderately radical 131530 4q25 epidermal growth factor (beta-urogastrone) 4175 rs4698803 EGF 1950 4 111272031 NM_001963 NP_001954 A/T E920V plus 24326010 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.13 0.08 224 2 123 "by doubleHit,freq,cluster" Potentially damaging 1.253 10 moderately radical 131530 4q25 epidermal growth factor (beta-urogastrone) 4176 rs4707358 GJB7 375519 6 88051291 NM_198568 NP_940970 A/G T20I plus 24388166 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.44 0 48 1 0.27 0.25 94 2 123 "by cluster,freq" Possibly damaging 1.625 28 Tolerant 1 2.81 140 moderately conservative 6q15 "gap junction protein, beta 7" 4177 rs4707569 MDN1 23195 6 90554310 NM_014611 NP_055426 A/C F440V plus 24016989 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.17 0 48 1 0.15 0.06 94 2 123 "by doubleHit,freq,cluster" conservative 6q15 "MDN1, midasin homolog (yeast)" 4178 rs4715227 PKHD1 5314 6 51599843 NM_138694 NP_619639 C/T Q3899R plus 23771066 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.48 0 48 1 0.45 0.05 70 2 123 "by doubleHit,freq,cluster" conservative 606702 6p12.2 polycystic kidney and hepatic disease 1 (autosomal recessive) 4179 rs4723010 INMT 11185 7 30565088 NM_006774 NP_006765 A/G D28N plus 24495168 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.42 0 48 1 0.41 0 46 1 123 by freq Benign 0.948 7 Tolerant 0.86 2.78 17 conservative 604854 7p15.3-p15.2 indolethylamine N-methyltransferase 4180 rs4725617 EPHA1 2041 7 142613937 NM_005232 NP_005223 A/G V160A plus 23768517 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.1 0.1 0 42 1 0.13 0 38 1 123 "by doubleHit,freq,cluster" Borderline 1.099 10 moderately conservative 179610 7q34 EphA1 4181 rs4728712 SRCRB4D 136853 7 75674346 NM_080744 NP_542782 C/T R128H plus 6517550 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.27 0.27 0 120 1 120 "HapMap,doubleHit,freq,cluster" Tolerant 0.26 2.83 52 conservative 607639 7q11.23 "scavenger receptor cysteine rich domain containing, group B (4 domains)" 4182 rs4730283 LAMB1 3912 7 107187940 NM_002291 NP_002282 C/T Q1022R plus 24451746 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.32 0.32 0 44 1 0.23 0.08 86 2 123 "by doubleHit,freq" Benign 0.396 13 conservative 150240 7q22 "laminin, beta 1" 4183 rs4735133 PKHD1L1 93035 8 110506560 NM_177531 NP_803875 A/G H923R plus 24083586 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.31 0 48 1 0.34 0.2 94 2 123 "by doubleHit,freq,cluster" conservative 607843 8q23.2 polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1 4184 rs4738070 NCOA2 10499 8 71201672 NM_006540 NP_006531 C/G M1282I plus 6531880 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.04 0.06 0.04 192 3 0.12 0.1 150 4 123 "HapMap,doubleHit,freq,cluster" Benign 0.557 6 Tolerant 0.33 3.06 14 conservative 601993 8q13.2 nuclear receptor coactivator 2 4185 rs4738070 NCOA2 10499 8 71201672 NM_006540 NP_006531 C/G M1282I plus 14898624 902 AFFY Caucasian 24 0.13 0.06 0.04 192 3 0.12 0.1 150 4 123 "HapMap,doubleHit,freq,cluster" Benign 0.557 6 Tolerant 0.33 3.06 14 conservative 601993 8q13.2 nuclear receptor coactivator 2 4186 rs4738070 NCOA2 10499 8 71201672 NM_006540 NP_006531 C/G M1282I plus 24036929 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.06 0.04 192 3 0.12 0.1 150 4 123 "HapMap,doubleHit,freq,cluster" Benign 0.557 6 Tolerant 0.33 3.06 14 conservative 601993 8q13.2 nuclear receptor coactivator 2 4187 rs4740412 LAMC3 10319 9 130992562 NM_006059 NP_006050 A/G R1459Q plus 6535329 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.25 0.25 0.01 166 2 0.04 0 94 2 123 "HapMap,doubleHit,freq" Tolerant 0.6 2.87 14 conservative 604349 9q31-q34 "laminin, gamma 3" 4188 rs4740412 LAMC3 10319 9 130992562 NM_006059 NP_006050 A/G R1459Q plus 24555579 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.24 0.25 0.01 166 2 0.04 0 94 2 123 "HapMap,doubleHit,freq" Tolerant 0.6 2.87 14 conservative 604349 9q31-q34 "laminin, gamma 3" 4189 rs4742754 COL15A1 1306 9 98827911 NM_001855 NP_001846 A/G M204V plus 24496377 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.38 0 48 1 0.28 0.05 94 2 123 "by doubleHit,freq,cluster" conservative 120325 9q21-q22 "collagen, type XV, alpha 1" 4190 rs4752904 PTPRJ 5795 11 48122843 NM_002843 NP_002834 C/G E872D plus 24698066 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.46 0 48 1 0.26 0.2 92 2 123 by freq conservative 600925 11p11.2 "protein tyrosine phosphatase, receptor type, J" 4191 rs4758443 PCDH16 8642 11 6605000 NM_003737 NP_003728 A/G T1949M plus 6563207 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.38 0.38 0 120 1 120 "HapMap,doubleHit,freq" Tolerant 0.22 2.8 15 moderately conservative 603057 11p15.4 protocadherin 16 dachsous-like (Drosophila) 4192 rs4767884 PXN 5829 12 119124697 NM_002859 NP_002850 C/T S73G plus 24452475 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.17 0 48 1 0.05 0 42 1 123 "by cluster,freq" Benign 0.041 8 moderately conservative 602505 12q24.31 paxillin 4193 rs4777035 ITGA11 22801 15 66392223 NM_012211 NP_036343 A/G P972L plus 23411071 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.27 0 48 1 0.22 0.26 94 2 123 "by doubleHit,freq,cluster" Borderline 1.164 6 Borderline 0.13 2.76 16 moderately conservative 604789 15q22.3-q23 "integrin, alpha 11" 4194 rs4780144 RYR3 6263 15 31741944 NM_001036 NP_001027 C/T R1641C plus 23661938 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.3 0.17 92 2 123 "by doubleHit,freq,cluster" Possibly damaging 1.754 9 radical 180903 15q14-q15 ryanodine receptor 3 4195 rs4785963 DNAJA3 9093 16 4424397 NM_005147 NP_005138 A/T N75Y plus 24403455 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.27 0 48 1 0.19 0.09 94 2 123 "by doubleHit,freq,cluster" Probably damaging 2.131 11 moderately radical 608382 16p13.3 "DnaJ (Hsp40) homolog, subfamily A, member 3" 4196 rs4791641 PFAS 5198 17 8101874 NM_012393 NP_036525 C/T P367L plus 6612289 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.47 0.47 0 120 1 121 "HapMap,doubleHit,freq" Tolerant 0.66 2.81 16 moderately conservative 602133 17p13.1 phosphoribosylformylglycinamidine synthase (FGAR amidotransferase) 4197 rs4792147 ALOX15B 247 17 7892544 NM_001141 NP_001132 A/G Q656R plus 24004299 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.35 0.35 0 46 1 0.25 0.13 86 2 123 "by doubleHit,freq,cluster" Benign 0.394 8 conservative 603697 17p13.1 "arachidonate 15-lipoxygenase, second type" 4198 rs4801478 ZNF548 147694 19 62601684 NM_152909 NP_690873 A/G A73T plus 6627127 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.04 0.04 0 120 1 121 "HapMap,doubleHit,freq,cluster" moderately conservative 19q13.43 zinc finger protein 548 4199 rs4802584 RYR1 6261 19 43717206 NM_000540 NP_000531 C/G Q3756E plus 6628761 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.02 0.02 0 120 1 111 "HapMap,doubleHit,freq" Benign 0.019 16 Tolerant 1 3.17 38 conservative 180901 19q13.1 ryanodine receptor 1 (skeletal) 4200 rs4804773 FCER2 2208 19 7669248 NM_002002 NP_001993 A/G R62W plus 23398440 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.13 0.1 94 2 123 "by doubleHit,freq,cluster" Benign 0.675 8 Intolerant 0.01 2.94 28 moderately radical 151445 19p13.3 "Fc fragment of IgE, low affinity II, receptor for (CD23A)" 4201 rs4819522 TBX1 6899 22 18141336 NM_080646 NP_542377 C/T T350M plus 23788861 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 0.11 0.03 92 2 123 "by doubleHit,freq,cluster" Borderline 0.14 2.95 26 moderately conservative 602054 22q11.21 T-box 1 4202 rs4820853 SEC14L3 266629 22 29189164 NM_174975 NP_777635 A/G I103T plus 24118524 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.25 0 48 1 0.46 0 94 2 123 "by doubleHit,freq,cluster" Possibly damaging 1.793 16 Potentially intolerant 0.09 2.82 30 moderately conservative 22q12.2 SEC14-like 3 (S. cerevisiae) 4203 rs4822063 SREBF2 6721 22 40601242 NM_004599 NP_004590 C/G G595A plus 8298620 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.26 0.28 0.04 168 2 0.4 0.14 78 2 123 "HapMap,doubleHit,freq,cluster" Borderline 1.096 8 Tolerant 0.64 2.78 24 moderately conservative 600481 22q13 sterol regulatory element binding transcription factor 2 4204 rs4822063 SREBF2 6721 22 40601242 NM_004599 NP_004590 C/G G595A plus 23575094 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.28 0.04 168 2 0.4 0.14 78 2 123 "HapMap,doubleHit,freq,cluster" Borderline 1.096 8 Tolerant 0.64 2.78 24 moderately conservative 600481 22q13 sterol regulatory element binding transcription factor 2 4205 rs4832524 KCNS3 3790 2 18035251 NM_002252 NP_002243 A/G T450A plus 24634569 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.38 0 48 1 0.13 0.16 94 2 123 "by doubleHit,freq,cluster" Benign 0 8 Tolerant 0.63 3.01 34 moderately conservative 603888 2p24 "potassium voltage-gated channel, delayed-rectifier, subfamily S, member 3" 4206 rs4833095 TLR1 7096 4 38622276 NM_003263 NP_003254 C/T N248S plus 7987552 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.2 0.2 0.01 94 3 0.34 0.01 140 3 123 "by doubleHit,freq,cluster" Possibly damaging 1.699 14 Tolerant 0.36 2.8 31 conservative 601194 4p14 toll-like receptor 1 4207 rs4833095 TLR1 7096 4 38622276 NM_003263 NP_003254 C/T N248S plus 7987552 848 IIPGA-WEISS-MARTINEZ E-1 CEPH 6 0.17 0.2 0.01 94 3 0.34 0.01 140 3 123 "by doubleHit,freq,cluster" Possibly damaging 1.699 14 Tolerant 0.36 2.8 31 conservative 601194 4p14 toll-like receptor 1 4208 rs4833095 TLR1 7096 4 38622276 NM_003263 NP_003254 C/T N248S plus 23715766 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.2 0.01 94 3 0.34 0.01 140 3 123 "by doubleHit,freq,cluster" Possibly damaging 1.699 14 Tolerant 0.36 2.8 31 conservative 601194 4p14 toll-like receptor 1 4209 rs4839469 VANGL1 81839 1 115918465 NM_138959 NP_620409 A/G A116T plus 24260545 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 0.04 0.04 94 2 123 by freq moderately conservative 1p11-p13.1 "vang-like 1 (van gogh, Drosophila)" 4210 rs4844658 PLXNA2 5362 1 204778557 NM_025179 NP_079455 C/T E369G plus 24248006 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 123 "by doubleHit,freq" Possibly damaging 1.759 12 moderately conservative 601054 1q32.2 plexin A2 4211 rs4859571 ASAHL 27163 4 77214488 NM_014435 NP_055250 C/T V151I plus 24165355 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.26 0.26 0 42 1 0.26 0.21 90 2 123 "by doubleHit,freq,cluster" Benign 0.33 7 Tolerant 0.35 2.89 27 conservative 607469 4q21.1 N-acylsphingosine amidohydrolase (acid ceramidase)-like 4212 rs4867440 ZFR 51663 5 32439103 NM_016107 NP_057191 C/T V461I plus 14684148 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.04 0.05 0.01 168 2 0.07 0.04 94 2 123 "HapMap,freq,cluster" conservative 5p13.3 zinc finger RNA binding protein 4213 rs4867440 ZFR 51663 5 32439103 NM_016107 NP_057191 C/T V461I plus 24009996 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.05 0.01 168 2 0.07 0.04 94 2 123 "HapMap,freq,cluster" conservative 5p13.3 zinc finger RNA binding protein 4214 rs4871827 DEPDC6 64798 8 121131060 NM_022783 NP_073620 A/G S389N plus 23976041 1371 PERLEGEN AFD_EUR_PANEL European American (24) 40 0.33 0.33 0 40 1 0.25 0.18 80 2 123 "by doubleHit,freq,cluster" conservative 8q24.12 DEP domain containing 6 4215 rs4871857 TNFRSF10A 8797 8 23115269 NM_003844 NP_003835 C/G R209T plus 6731796 1303 SEQUENOM CEPH CEPH (92) 92 0.18 0.32 0.17 192 3 0.37 0.15 370 5 123 "by doubleHit,freq,cluster" Tolerant 0.52 2.84 17 moderately conservative 603611 8p21 "tumor necrosis factor receptor superfamily, member 10a" 4216 rs4871857 TNFRSF10A 8797 8 23115269 NM_003844 NP_003835 C/G R209T plus 12675180 775 SNP500CANCER CAUC1 Caucasian (31) 52 0.46 0.32 0.17 192 3 0.37 0.15 370 5 123 "by doubleHit,freq,cluster" Tolerant 0.52 2.84 17 moderately conservative 603611 8p21 "tumor necrosis factor receptor superfamily, member 10a" 4217 rs4871857 TNFRSF10A 8797 8 23115269 NM_003844 NP_003835 C/G R209T plus 24491984 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.32 0.17 192 3 0.37 0.15 370 5 123 "by doubleHit,freq,cluster" Tolerant 0.52 2.84 17 moderately conservative 603611 8p21 "tumor necrosis factor receptor superfamily, member 10a" 4218 rs4874147 ZC3HDC3 23144 8 144691326 NM_015117 NP_055932 C/T S452G plus 6734706 1303 SEQUENOM CEPH CEPH (92) 92 0.37 0.35 0.05 138 2 0.16 0.12 92 2 123 "by doubleHit,freq,cluster" moderately conservative 8q24.3 zinc finger CCCH type domain containing 3 4219 rs4874147 ZC3HDC3 23144 8 144691326 NM_015117 NP_055932 C/T S452G plus 24398124 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.3 0.35 0.05 138 2 0.16 0.12 92 2 123 "by doubleHit,freq,cluster" moderately conservative 8q24.3 zinc finger CCCH type domain containing 3 4220 rs4878199 ALDH1B1 219 9 38386502 NM_000692 NP_000683 A/G V253M plus 6740188 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.05 0.05 0.01 168 2 0.02 0 42 1 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.812 129 Tolerant 0.41 2.83 146 conservative 100670 9p11.1 "aldehyde dehydrogenase 1 family, member B1" 4221 rs4878199 ALDH1B1 219 9 38386502 NM_000692 NP_000683 A/G V253M plus 24555214 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.05 0.01 168 2 0.02 0 42 1 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.812 129 Tolerant 0.41 2.83 146 conservative 100670 9p11.1 "aldehyde dehydrogenase 1 family, member B1" 4222 rs4884021 LMO7 4008 13 75295732 NM_005358 NP_005349 A/G V609I plus 12231043 885 TSC-CSHL HapMap-CEPH-30-trios 110 0.16 0.16 0 110 1 121 "HapMap,doubleHit,freq,cluster" conservative 604362 13q21.33 LIM domain only 7 4223 rs4895943 VNN3 55350 6 133094309 NM_078625 NP_523239 C/T C132Y plus 24477691 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.48 0 48 1 0.27 0.16 94 2 123 "by doubleHit,freq,cluster" radical 606592 6q23-q24 vanin 3 4224 rs4902176 KCNH5 27133 14 62244713 NM_139318 NP_647479 C/T A745T plus 24616820 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.33 0 48 1 0.19 0.06 94 2 123 "by doubleHit,freq,cluster" Borderline 1.227 6 Tolerant 0.38 2.92 38 moderately conservative 605716 14q23.1 "potassium voltage-gated channel, subfamily H (eag-related), member 5" 4225 rs4902264 SYNE2 23224 14 63561448 NM_015180 NP_055995 C/T M1968T plus 6774754 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.14 0.14 0 120 1 121 "HapMap,doubleHit,freq,cluster" moderately conservative 608442 14q23.2 "spectrin repeat containing, nuclear envelope 2" 4226 rs4935502 PCDH15 65217 10 55625450 NM_033056 NP_149045 G/T D435A plus 23479696 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.09 0.08 94 2 123 "by doubleHit,freq,cluster" Benign 0.379 5 Tolerant 0.81 2.88 29 moderately radical 605514 10p11.2-q21 protocadherin 15 4227 rs4938016 ANKK1 255239 11 112775225 NM_178510 NP_848605 C/G G442R plus 24101853 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.35 0 48 1 0.42 0.04 92 2 123 "by doubleHit,freq,cluster" Tolerant 0.45 2.76 28 moderately radical 608774 11q23.2 ankyrin repeat and kinase domain containing 1 4228 rs4941543 LCP1 3936 13 45606292 NM_002298 NP_002289 C/T K533E plus 24666681 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.19 0 48 1 0.11 0.1 90 2 123 "by doubleHit,freq,cluster" Borderline 1.041 30 moderately conservative 153430 13q14.3 lymphocyte cytosolic protein 1 (L-plastin) 4229 rs4942848 RCBTB1 55213 13 49039346 NM_018191 NP_060661 A/G A24V plus 24001656 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.26 0.26 0 46 1 0.32 0.02 94 2 123 "by doubleHit,freq,cluster" Benign 0.367 14 Tolerant 0.51 2.79 54 moderately conservative 607867 13q14 regulator of chromosome condensation (RCC1) and BTB (POZ) domain containing protein 1 4230 rs4950394 CHD1L 9557 1 143991965 NM_004284 NP_004275 G/T A885S plus 14883473 902 AFFY Caucasian 24 0.08 0.05 0.03 72 2 0.05 0.04 92 2 123 "by cluster,freq" moderately conservative 1q12 chromodomain helicase DNA binding protein 1-like 4231 rs4950394 CHD1L 9557 1 143991965 NM_004284 NP_004275 G/T A885S plus 24236777 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.05 0.03 72 2 0.05 0.04 92 2 123 "by cluster,freq" moderately conservative 1q12 chromodomain helicase DNA binding protein 1-like 4232 rs4956145 HADHSC 3033 4 109288643 NM_005327 NP_005318 C/T L86P plus 10158514 1303 SEQUENOM CEPH CEPH (92) 92 0.05 0.08 0.05 140 2 0.33 0 46 1 123 "by doubleHit,freq,cluster" Probably damaging 2.293 16 moderately conservative 601609 4q22-q26 "L-3-hydroxyacyl-Coenzyme A dehydrogenase, short chain" 4233 rs4956145 HADHSC 3033 4 109288643 NM_005327 NP_005318 C/T L86P plus 23719514 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.08 0.05 140 2 0.33 0 46 1 123 "by doubleHit,freq,cluster" Probably damaging 2.293 16 moderately conservative 601609 4q22-q26 "L-3-hydroxyacyl-Coenzyme A dehydrogenase, short chain" 4234 rs4958531 NMUR2 56923 5 151752031 NM_020167 NP_064552 C/T M388V plus 24458014 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.19 0 48 1 0.06 0.04 94 2 123 "by doubleHit,freq" Benign 0.131 5 conservative 605108 5q33.1 neuromedin U receptor 2 4235 rs4958535 NMUR2 56923 5 151755257 NM_020167 NP_064552 C/G S298T plus 24458129 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.19 0 48 1 0.06 0.04 94 2 123 "by doubleHit,freq" Potentially damaging 1.261 5 Tolerant 0.93 2.87 30 moderately conservative 605108 5q33.1 neuromedin U receptor 2 4236 rs4968281 WNT9B 7484 17 42305121 NM_003396 NP_003387 C/T M106T plus 6876304 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.33 0.28 0.11 164 2 0.28 0.26 94 2 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.515 12 Tolerant 0.67 2.79 80 moderately conservative 602864 17q21 "wingless-type MMTV integration site family, member 9B" 4237 rs4968281 WNT9B 7484 17 42305121 NM_003396 NP_003387 C/T M106T plus 24110061 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.15 0.28 0.11 164 2 0.28 0.26 94 2 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.515 12 Tolerant 0.67 2.79 80 moderately conservative 602864 17q21 "wingless-type MMTV integration site family, member 9B" 4238 rs4986761 ATM 472 11 107629971 NM_000051 NP_000042 C/T S707P plus 5586263 775 SNP500CANCER CAUC1 Caucasian (31) 58 0.02 0.01 0.01 226 2 0.01 0 198 1 113 "by cluster,freq" Benign 0.102 5 moderately conservative 607585 11q22-q23 "ataxia telangiectasia mutated (includes complementation groups A, C and D)" 4239 rs4986761 ATM 472 11 107629971 NM_000051 NP_000042 C/T S707P plus 6904864 693 EGP_SNPS PDR90 NIHPDR 168 0.01 0.01 0.01 226 2 0.01 0 198 1 113 "by cluster,freq" Benign 0.102 5 moderately conservative 607585 11q22-q23 "ataxia telangiectasia mutated (includes complementation groups A, C and D)" 4240 rs4986764 BRIP1 83990 17 57118129 NM_032043 NP_114432 C/T S919P minus 5586323 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.37 0.38 0.02 110 2 0.32 0.09 556 7 123 "by doubleHit,freq,cluster" moderately conservative 605882 17q22-q24 BRCA1 interacting protein C-terminal helicase 1 4241 rs4986764 BRIP1 83990 17 57118129 NM_032043 NP_114432 C/T S919P minus 24454918 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.38 0.02 110 2 0.32 0.09 556 7 123 "by doubleHit,freq,cluster" moderately conservative 605882 17q22-q24 BRCA1 interacting protein C-terminal helicase 1 4242 rs4986771 ZNF350 59348 19 57160104 NM_021632 NP_067645 C/T S472P minus 5586997 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.02 0.02 0 110 2 0.01 0.01 298 3 123 "by cluster,freq" Intolerant 0.02 2.79 33 moderately conservative 605422 19q13.41 zinc finger protein 350 4243 rs4986771 ZNF350 59348 19 57160104 NM_021632 NP_067645 C/T S472P minus 24692813 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 110 2 0.01 0.01 298 3 123 "by cluster,freq" Intolerant 0.02 2.79 33 moderately conservative 605422 19q13.41 zinc finger protein 350 4244 rs4986783 NAT1 9 8 18124476 NM_000662 NP_000653 G/T S214A plus 6903885 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.03 0.03 0 62 1 0.01 0.01 250 2 123 "by cluster,freq" Benign 0.183 42 Tolerant 0.36 2.88 41 moderately conservative 108345 8p23.1-p21.3 N-acetyltransferase 1 (arylamine N-acetyltransferase) 4245 rs4986860 BRCA2 675 13 31827309 NM_000059 NP_000050 A/G H2440R plus 16355877 693 EGP_SNPS PDR90 NIHPDR 154 0.01 0.01 0 154 1 0.01 0.01 248 2 120 "by cluster,freq" Probably damaging 2.33 9 conservative 600185 13q12.3 "breast cancer 2, early onset" 4246 rs4986910 CYP3A4 1576 7 99003175 NM_017460 NP_059488 C/T M445T minus 5586459 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.03 0.03 0 62 1 0.01 0 202 1 113 "HapMap,freq" Probably damaging 3.043 59 Intolerant 0.01 2.84 65 moderately conservative 124010 7q21.1 "cytochrome P450, family 3, subfamily A, polypeptide 4" 4247 rs4986941 FCGR2A 2212 1 158292718 NM_021642 NP_067674 A/G M138V plus 5586538 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.02 0.02 0 62 1 0.01 0.01 298 3 113 by freq Benign 0.702 24 conservative 146790 1q23 "Fc fragment of IgG, low affinity IIa, receptor for (CD32)" 4248 rs4986948 GSTP1 2950 11 67109281 NM_000852 NP_000843 C/G T110S plus 5586575 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.02 0.02 0 62 1 0.01 0 202 1 113 by freq Borderline 1.159 26 Tolerant 0.4 2.8 37 moderately conservative 134660 11q13 glutathione S-transferase pi 4249 rs4986952 HSD3B1 3283 1 119766234 NM_000862 NP_000853 G/T R71I plus 5586594 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.03 0.03 0 62 1 0.01 0 200 1 113 by freq Probably damaging 2.548 29 Intolerant 0.02 2.84 40 moderately conservative 109715 1p13.1 "hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1" 4250 rs4986958 IFNGR2 3460 21 33709164 NM_005534 NP_005525 C/G T58R plus 5586620 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.02 0.02 0 110 2 0.08 0.06 338 4 123 "HapMap,freq,cluster" Tolerant 0.25 2.88 11 moderately conservative 147569 21q22.11 interferon gamma receptor 2 (interferon gamma transducer 1) 4251 rs4986958 IFNGR2 3460 21 33709164 NM_005534 NP_005525 C/G T58R plus 23626410 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 110 2 0.08 0.06 338 4 123 "HapMap,freq,cluster" Tolerant 0.25 2.88 11 moderately conservative 147569 21q22.11 interferon gamma receptor 2 (interferon gamma transducer 1) 4252 rs4986970 LCAT 3931 16 66533821 NM_000229 NP_000220 A/T S232T minus 5586722 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.03 0.04 0.02 110 2 0.02 0 248 2 123 by freq Benign 0.364 15 Tolerant 0.22 2.78 37 moderately conservative 606967 16q22.1 lecithin-cholesterol acyltransferase 4253 rs4986970 LCAT 3931 16 66533821 NM_000229 NP_000220 A/T S232T minus 24680369 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.04 0.02 110 2 0.02 0 248 2 123 by freq Benign 0.364 15 Tolerant 0.22 2.78 37 moderately conservative 606967 16q22.1 lecithin-cholesterol acyltransferase 4254 rs4986997 NAT2 10 8 18302204 NM_000015 NP_000006 A/T L137F plus 5586802 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.02 0.02 0 62 1 0.01 0 202 1 113 by freq Possibly damaging 1.568 34 Intolerant 0.02 2.85 40 conservative 243400 8p22 N-acetyltransferase 2 (arylamine N-acetyltransferase) 4255 rs4986998 NQO1 1728 16 68306370 NM_000903 NP_000894 C/T R139W minus 5586809 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.03 0.03 0 60 1 0.02 0.01 246 2 120 "by cluster,freq" Benign 0.675 7 Intolerant 0.01 2.82 35 moderately radical 125860 16q22.1 "NAD(P)H dehydrogenase, quinone 1" 4256 rs4987047 BRCA2 675 13 31851529 NM_000059 NP_000050 A/T I2944F plus 5606242 1303 SEQUENOM CEPH CEPH (92) 92 0.05 0.02 0.03 262 2 0.03 0.03 294 3 123 "by cluster,freq" Possibly damaging 1.635 9 conservative 600185 13q12.3 "breast cancer 2, early onset" 4257 rs4987047 BRCA2 675 13 31851529 NM_000059 NP_000050 A/T I2944F plus 16355964 693 EGP_SNPS PDR90 NIHPDR 170 0.01 0.02 0.03 262 2 0.03 0.03 294 3 123 "by cluster,freq" Possibly damaging 1.635 9 conservative 600185 13q12.3 "breast cancer 2, early onset" 4258 rs4987068 LIG1 3978 19 53332619 NM_000234 NP_000225 A/G R409H minus 5606321 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.03 0.02 0.01 154 2 0.01 0 202 1 113 by freq Potentially damaging 1.487 6 Borderline 0.14 2.8 25 conservative 126391 19q13.2-q13.3 "ligase I, DNA, ATP-dependent" 4259 rs4987068 LIG1 3978 19 53332619 NM_000234 NP_000225 A/G R409H minus 5606321 1303 SEQUENOM CEPH CEPH (92) 92 0.01 0.02 0.01 154 2 0.01 0 202 1 113 by freq Potentially damaging 1.487 6 Borderline 0.14 2.8 25 conservative 126391 19q13.2-q13.3 "ligase I, DNA, ATP-dependent" 4260 rs4987076 NAT1 9 8 18124281 NM_000662 NP_000653 A/G V149I plus 5606338 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.03 0.03 0 62 1 0.01 0.01 252 2 123 by freq Benign 0.609 42 Tolerant 1 2.88 41 conservative 108345 8p23.1-p21.3 N-acetyltransferase 1 (arylamine N-acetyltransferase) 4261 rs4987115 BAK1 578 6 33651671 NM_001188 NP_001179 C/T A28V minus 7990000 693 EGP_SNPS PDR90 NIHPDR 176 0.01 0.01 0 176 1 0.02 0.01 300 3 123 "by cluster,freq" Borderline 1.227 5 moderately conservative 600516 6p21.3 BCL2-antagonist/killer 1 4262 rs4987117 BRCA2 675 13 31812236 NM_000059 NP_000050 C/T T1915M plus 6903687 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.07 0.03 0.04 200 2 0.04 0 296 3 120 "by cluster,freq" Borderline 1.133 9 moderately conservative 600185 13q12.3 "breast cancer 2, early onset" 4263 rs4987117 BRCA2 675 13 31812236 NM_000059 NP_000050 C/T T1915M plus 16355811 693 EGP_SNPS PDR90 NIHPDR 140 0.01 0.03 0.04 200 2 0.04 0 296 3 120 "by cluster,freq" Borderline 1.133 9 moderately conservative 600185 13q12.3 "breast cancer 2, early onset" 4264 rs4987161 CYP3A4 1576 7 99010732 NM_017460 NP_059488 C/T F189S minus 6903778 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.02 0.02 0 60 1 0.01 0 200 1 113 HapMap Probably damaging 2.771 60 Intolerant 0 2.84 65 radical 124010 7q21.1 "cytochrome P450, family 3, subfamily A, polypeptide 4" 4265 rs4987188 MSH2 4436 2 47555108 NM_000251 NP_000242 A/G G322D plus 6903873 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.03 0.03 0 182 2 0.01 0 204 1 113 "HapMap,freq" Potentially damaging 1.435 13 Tolerant 0.36 2.78 21 moderately conservative 120435 2p22-p21 "mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)" 4266 rs4987188 MSH2 4436 2 47555108 NM_000251 NP_000242 A/G G322D plus 6903873 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.03 0.03 0 182 2 0.01 0 204 1 113 "HapMap,freq" Potentially damaging 1.435 13 Tolerant 0.36 2.78 21 moderately conservative 120435 2p22-p21 "mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)" 4267 rs4987202 RAD23A 5886 19 12920626 NM_005053 NP_005044 C/T T200M plus 6903907 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.01 0.01 0.01 168 2 0.01 0.01 250 2 123 "HapMap,freq" Benign 0.284 15 Borderline 0.2 2.76 31 moderately conservative 600061 19p13.2 RAD23 homolog A (S. cerevisiae) 4268 rs4987202 RAD23A 5886 19 12920626 NM_005053 NP_005044 C/T T200M plus 24683069 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.01 0.01 168 2 0.01 0.01 250 2 123 "HapMap,freq" Benign 0.284 15 Borderline 0.2 2.76 31 moderately conservative 600061 19p13.2 RAD23 homolog A (S. cerevisiae) 4269 rs4987236 WRN 7486 8 31041477 NM_000553 NP_000544 A/G V114I plus 6903976 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.02 0.06 0.03 278 3 0.07 0.05 390 5 123 "by cluster,freq" Benign 0.711 6 conservative 604611 8p12-p11.2 Werner syndrome 4270 rs4987236 WRN 7486 8 31041477 NM_000553 NP_000544 A/G V114I plus 16359348 693 EGP_SNPS PDR90 NIHPDR 170 0.08 0.06 0.03 278 3 0.07 0.05 390 5 123 "by cluster,freq" Benign 0.711 6 conservative 604611 8p12-p11.2 Werner syndrome 4271 rs4987236 WRN 7486 8 31041477 NM_000553 NP_000544 A/G V114I plus 23471979 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0.03 278 3 0.07 0.05 390 5 123 "by cluster,freq" Benign 0.711 6 conservative 604611 8p12-p11.2 Werner syndrome 4272 rs4987310 SELL 6402 1 166405496 NM_000655 NP_000646 C/T P213S minus 6904144 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.07 0.06 0.01 94 2 0.31 0.03 140 3 123 "by cluster,freq" Benign 0.739 10 Borderline 0.19 2.88 142 moderately conservative 153240 1q23-q25 selectin L (lymphocyte adhesion molecule 1) 4273 rs4987310 SELL 6402 1 166405496 NM_000655 NP_000646 C/T P213S minus 23189336 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0.01 94 2 0.31 0.03 140 3 123 "by cluster,freq" Benign 0.739 10 Borderline 0.19 2.88 142 moderately conservative 153240 1q23-q25 selectin L (lymphocyte adhesion molecule 1) 4274 rs4987657 TRPV6 55503 7 142091750 NM_018646 NP_061116 C/T C157R minus 6904509 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 42 0.02 0.02 0 42 1 0.48 0 46 1 116 "by doubleHit,freq,cluster" Benign 0.702 13 Tolerant 0.3 2.8 59 radical 606680 7q33-q34 "transient receptor potential cation channel, subfamily V, member 6" 4275 rs4987667 TRPV6 55503 7 142089745 NM_018646 NP_061116 A/G M378V minus 6904519 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.02 0.02 0 94 2 0.32 0.25 140 3 123 "by doubleHit,freq,cluster" Benign 0.239 14 Tolerant 0.51 2.92 39 conservative 606680 7q33-q34 "transient receptor potential cation channel, subfamily V, member 6" 4276 rs4987667 TRPV6 55503 7 142089745 NM_018646 NP_061116 A/G M378V minus 23768032 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 94 2 0.32 0.25 140 3 123 "by doubleHit,freq,cluster" Benign 0.239 14 Tolerant 0.51 2.92 39 conservative 606680 7q33-q34 "transient receptor potential cation channel, subfamily V, member 6" 4277 rs4987682 TRPV6 55503 7 142086433 NM_018646 NP_061116 C/T M681T minus 6904534 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 44 0.02 0.02 0 92 2 0.27 0.28 93 3 123 "by cluster,freq" Benign 0.397 12 Tolerant 0.29 3.07 29 moderately conservative 606680 7q33-q34 "transient receptor potential cation channel, subfamily V, member 6" 4278 rs4987682 TRPV6 55503 7 142086433 NM_018646 NP_061116 C/T M681T minus 23768012 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 92 2 0.27 0.28 93 3 123 "by cluster,freq" Benign 0.397 12 Tolerant 0.29 3.07 29 moderately conservative 606680 7q33-q34 "transient receptor potential cation channel, subfamily V, member 6" 4279 rs4987945 ATM 472 11 107627802 NM_000051 NP_000042 C/G L546V plus 6904854 693 EGP_SNPS PDR90 NIHPDR 174 0.01 0.01 0 174 1 0.09 0 46 1 123 "by cluster,freq" Borderline 1.03 5 conservative 607585 11q22-q23 "ataxia telangiectasia mutated (includes complementation groups A, C and D)" 4280 rs4988492 GHRH 2691 20 35316112 NM_021081 NP_066567 A/G L75F plus 8318871 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.02 0.02 0 118 1 0.09 0 46 1 123 "HapMap,doubleHit,freq,cluster" Benign 0.209 6 Tolerant 0.29 3.23 59 conservative 139190 20q11.2 growth hormone releasing hormone 4281 rs4988498 GHRHR 2692 7 30782816 NM_000823 NP_000814 G/T E121D plus 14148490 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.06 0.06 0 118 1 120 "HapMap,freq,cluster" Benign 0.197 16 Tolerant 0.75 2.75 59 conservative 139191 7p14 growth hormone releasing hormone receptor 4282 rs5029942 TNFAIP3 7128 6 138237759 NM_006290 NP_006281 G/T F127C plus 7984949 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.02 0.02 0 94 2 0.25 0.2 140 3 123 "by doubleHit,freq,cluster" Benign 0.571 5 radical 191163 6q23 "tumor necrosis factor, alpha-induced protein 3" 4283 rs5029942 TNFAIP3 7128 6 138237759 NM_006290 NP_006281 G/T F127C plus 23371171 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 94 2 0.25 0.2 140 3 123 "by doubleHit,freq,cluster" Benign 0.571 5 radical 191163 6q23 "tumor necrosis factor, alpha-induced protein 3" 4284 rs5030878 FPR1 2357 19 56942028 NM_002029 NP_002020 C/T I11T minus 23767446 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.23 0 48 1 0.19 0.17 92 2 123 "by doubleHit,freq,cluster" Borderline 1.094 27 moderately conservative 136537 19q13.4 formyl peptide receptor 1 4285 rs5741804 BPI 671 20 36385756 NM_001725 NP_001716 C/T A280V plus 7987435 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.05 0.03 0.02 206 3 0.19 0.07 140 3 123 "HapMap,freq,cluster" Benign 0.899 7 Borderline 0.2 2.87 17 moderately conservative 109195 20q11.23-q12 bactericidal/permeability-increasing protein 4286 rs5741804 BPI 671 20 36385756 NM_001725 NP_001716 C/T A280V plus 8424264 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.02 0.03 0.02 206 3 0.19 0.07 140 3 123 "HapMap,freq,cluster" Benign 0.899 7 Borderline 0.2 2.87 17 moderately conservative 109195 20q11.23-q12 bactericidal/permeability-increasing protein 4287 rs5741804 BPI 671 20 36385756 NM_001725 NP_001716 C/T A280V plus 24205110 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.03 0.02 206 3 0.19 0.07 140 3 123 "HapMap,freq,cluster" Benign 0.899 7 Borderline 0.2 2.87 17 moderately conservative 109195 20q11.23-q12 bactericidal/permeability-increasing protein 4288 rs5742915 PML 5371 15 72123686 NM_033238 NP_150241 C/T F645L plus 7986650 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.45 0.45 0 116 1 0.47 0 95 1 120 "HapMap,freq" conservative 102578 15q22 promyelocytic leukemia 4289 rs5743291 CARD15 64127 16 49314777 NM_022162 NP_071445 A/G V955I plus 7987116 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.05 0.07 0.06 46 2 114 by freq Benign 0.07 18 Potentially intolerant 0.06 2.84 31 conservative 605956 16p12-q21 "caspase recruitment domain family, member 15" 4290 rs5743291 CARD15 64127 16 49314777 NM_022162 NP_071445 A/G V955I plus 7987116 848 IIPGA-WEISS-MARTINEZ E-1 CEPH 6 0.17 0.07 0.06 46 2 114 by freq Benign 0.07 18 Potentially intolerant 0.06 2.84 31 conservative 605956 16p12-q21 "caspase recruitment domain family, member 15" 4291 rs5743509 BPI 671 20 36373728 NM_001725 NP_001716 C/T A196V plus 7987428 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 38 0.08 0.09 0.03 92 3 0.04 0.02 136 3 123 by freq Benign 0.945 7 Tolerant 0.25 2.87 19 moderately conservative 109195 20q11.23-q12 bactericidal/permeability-increasing protein 4292 rs5743509 BPI 671 20 36373728 NM_001725 NP_001716 C/T A196V plus 7987428 848 IIPGA-WEISS-MARTINEZ E-1 CEPH 6 0.17 0.09 0.03 92 3 0.04 0.02 136 3 123 by freq Benign 0.945 7 Tolerant 0.25 2.87 19 moderately conservative 109195 20q11.23-q12 bactericidal/permeability-increasing protein 4293 rs5743509 BPI 671 20 36373728 NM_001725 NP_001716 C/T A196V plus 24694542 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.09 0.03 92 3 0.04 0.02 136 3 123 by freq Benign 0.945 7 Tolerant 0.25 2.87 19 moderately conservative 109195 20q11.23-q12 bactericidal/permeability-increasing protein 4294 rs5743611 TLR1 7096 4 38622780 NM_003263 NP_003254 C/G R80T minus 7987550 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 36 0.06 0.05 0.01 84 2 0.04 0 94 2 123 "by cluster,freq" Probably damaging 2.045 14 Tolerant 0.54 2.78 32 moderately conservative 601194 4p14 toll-like receptor 1 4295 rs5743611 TLR1 7096 4 38622780 NM_003263 NP_003254 C/G R80T minus 23715774 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.05 0.01 84 2 0.04 0 94 2 123 "by cluster,freq" Probably damaging 2.045 14 Tolerant 0.54 2.78 32 moderately conservative 601194 4p14 toll-like receptor 1 4296 rs5743618 TLR1 7096 4 38621214 NM_003263 NP_003254 G/T S602I minus 7987559 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.25 0.24 0.04 46 2 0.25 0 48 1 119 "by doubleHit,freq,cluster" Possibly damaging 1.668 14 Tolerant 0.4 2.78 29 moderately radical 601194 4p14 toll-like receptor 1 4297 rs5743618 TLR1 7096 4 38621214 NM_003263 NP_003254 G/T S602I minus 7987559 848 IIPGA-WEISS-MARTINEZ E-1 CEPH 6 0.17 0.24 0.04 46 2 0.25 0 48 1 119 "by doubleHit,freq,cluster" Possibly damaging 1.668 14 Tolerant 0.4 2.78 29 moderately radical 601194 4p14 toll-like receptor 1 4298 rs5743704 TLR2 7097 4 154983556 NM_003264 NP_003255 A/C P631H plus 7987689 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 36 0.03 0.05 0.07 42 2 0.02 0 44 1 114 by freq Probably damaging 2.621 14 Intolerant 0 2.8 22 moderately conservative 603028 4q32 toll-like receptor 2 4299 rs5743704 TLR2 7097 4 154983556 NM_003264 NP_003255 A/C P631H plus 7987689 848 IIPGA-WEISS-MARTINEZ E-1 CEPH 6 0.17 0.05 0.07 42 2 0.02 0 44 1 114 by freq Probably damaging 2.621 14 Intolerant 0 2.8 22 moderately conservative 603028 4q32 toll-like receptor 2 4300 rs5743810 TLR6 10333 4 38652916 NM_006068 NP_006059 C/T S249P minus 7987824 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.45 0.44 0.02 89 3 0.11 0.02 86 2 123 by freq Possibly damaging 1.783 17 Borderline 0.17 2.78 32 moderately conservative 605403 4p14 toll-like receptor 6 4301 rs5743810 TLR6 10333 4 38652916 NM_006068 NP_006059 C/T S249P minus 7987824 848 IIPGA-WEISS-MARTINEZ E-1 CEPH 3 0.5 0.44 0.02 89 3 0.11 0.02 86 2 123 by freq Possibly damaging 1.783 17 Borderline 0.17 2.78 32 moderately conservative 605403 4p14 toll-like receptor 6 4302 rs5743810 TLR6 10333 4 38652916 NM_006068 NP_006059 C/T S249P minus 24650952 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.43 0.44 0.02 89 3 0.11 0.02 86 2 123 by freq Possibly damaging 1.783 17 Borderline 0.17 2.78 32 moderately conservative 605403 4p14 toll-like receptor 6 4303 rs5743813 TLR6 10333 4 38652628 NM_006068 NP_006059 C/T H345Y minus 7987827 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.03 0.02 0.01 160 2 114 "HapMap,freq" Probably damaging 2.082 17 Borderline 0.15 2.78 32 moderately conservative 605403 4p14 toll-like receptor 6 4304 rs5743813 TLR6 10333 4 38652628 NM_006068 NP_006059 C/T H345Y minus 7987827 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.01 0.02 0.01 160 2 114 "HapMap,freq" Probably damaging 2.082 17 Borderline 0.15 2.78 32 moderately conservative 605403 4p14 toll-like receptor 6 4305 rs5743815 TLR6 10333 4 38652381 NM_006068 NP_006059 C/T V427A minus 7987831 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.05 0.06 0.03 94 3 0.04 0.04 92 2 123 "by cluster,freq" Benign 0.093 17 Tolerant 0.59 2.79 31 moderately conservative 605403 4p14 toll-like receptor 6 4306 rs5743815 TLR6 10333 4 38652381 NM_006068 NP_006059 C/T V427A minus 7987831 848 IIPGA-WEISS-MARTINEZ E-1 CEPH 6 0.17 0.06 0.03 94 3 0.04 0.04 92 2 123 "by cluster,freq" Benign 0.093 17 Tolerant 0.59 2.79 31 moderately conservative 605403 4p14 toll-like receptor 6 4307 rs5743815 TLR6 10333 4 38652381 NM_006068 NP_006059 C/T V427A minus 23715866 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0.03 94 3 0.04 0.04 92 2 123 "by cluster,freq" Benign 0.093 17 Tolerant 0.59 2.79 31 moderately conservative 605403 4p14 toll-like receptor 6 4308 rs5744015 TOLLIP 54472 11 1255006 NM_019009 NP_061882 G/T A222S minus 7988051 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.13 0.14 0.02 46 2 114 by freq Borderline 1.002 8 moderately conservative 606277 11p toll interacting protein 4309 rs5744015 TOLLIP 54472 11 1255006 NM_019009 NP_061882 G/T A222S minus 7988051 848 IIPGA-WEISS-MARTINEZ E-1 CEPH 6 0.17 0.14 0.02 46 2 114 by freq Borderline 1.002 8 moderately conservative 606277 11p toll interacting protein 4310 rs5744168 TLR5 7100 1 2900559 NM_003268 NP_003259 C/T R392X minus 7988260 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.08 0.08 0 40 1 0.06 0 48 1 114 by freq Probably damaging Intolerant radical 603031 1q41-q42 toll-like receptor 5 4311 rs5744174 TLR5 7100 1 2899887 NM_003268 NP_003259 C/T F616L minus 7988267 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.38 0.36 0.06 88 3 0.19 0.07 124 3 123 by freq Tolerant 1 2.82 10 conservative 603031 1q41-q42 toll-like receptor 5 4312 rs5744174 TLR5 7100 1 2899887 NM_003268 NP_003259 C/T F616L minus 7988267 848 IIPGA-WEISS-MARTINEZ E-1 CEPH 6 0.17 0.36 0.06 88 3 0.19 0.07 124 3 123 by freq Tolerant 1 2.82 10 conservative 603031 1q41-q42 toll-like receptor 5 4313 rs5744174 TLR5 7100 1 2899887 NM_003268 NP_003259 C/T F616L minus 24600729 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.36 0.36 0.06 88 3 0.19 0.07 124 3 123 by freq Tolerant 1 2.82 10 conservative 603031 1q41-q42 toll-like receptor 5 4314 rs5744204 LBP 3929 20 36416225 NM_004139 NP_004130 A/G V166M plus 7988324 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 38 0.03 0.03 0 74 2 0.21 0 96 2 120 "by cluster,freq" Benign 0.717 5 Intolerant 0.02 2.88 19 conservative 151990 20q11.23-q12 lipopolysaccharide binding protein 4315 rs5744204 LBP 3929 20 36416225 NM_004139 NP_004130 A/G V166M plus 16215301 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 36 0.03 0.03 0 74 2 0.21 0 96 2 120 "by cluster,freq" Benign 0.717 5 Intolerant 0.02 2.88 19 conservative 151990 20q11.23-q12 lipopolysaccharide binding protein 4316 rs5744212 LBP 3929 20 36431086 NM_004139 NP_004130 C/T L339F plus 7988356 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.08 0.06 0.04 80 2 120 "by cluster,freq" Borderline 1.242 5 Intolerant 0.01 2.89 17 conservative 151990 20q11.23-q12 lipopolysaccharide binding protein 4317 rs5744212 LBP 3929 20 36431086 NM_004139 NP_004130 C/T L339F plus 16215378 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.03 0.06 0.04 80 2 120 "by cluster,freq" Borderline 1.242 5 Intolerant 0.01 2.89 17 conservative 151990 20q11.23-q12 lipopolysaccharide binding protein 4318 rs5744463 LY64 4064 5 66528168 NM_005582 NP_005573 C/G V20L minus 7988729 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.15 0.13 0.03 86 2 0.02 0 92 2 123 by freq Tolerant 0.41 3.23 16 conservative 602226 5q12 "lymphocyte antigen 64 homolog, radioprotective 105kDa (mouse)" 4319 rs5744463 LY64 4064 5 66528168 NM_005582 NP_005573 C/G V20L minus 24322566 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.11 0.13 0.03 86 2 0.02 0 92 2 123 by freq Tolerant 0.41 3.23 16 conservative 602226 5q12 "lymphocyte antigen 64 homolog, radioprotective 105kDa (mouse)" 4320 rs5744751 POLE 5426 12 131864345 NM_006231 NP_006222 C/T A252V minus 7989040 693 EGP_SNPS PDR90 NIHPDR 174 0.05 0.05 0 174 1 120 "by doubleHit,freq,cluster" Benign 0.08 8 Tolerant 0.63 2.87 12 moderately conservative 174762 12q24.3 "polymerase (DNA directed), epsilon" 4321 rs5744760 POLE 5426 12 131863043 NM_006231 NP_006222 A/G N336S minus 7989050 693 EGP_SNPS PDR90 NIHPDR 180 0.01 0.01 0 180 1 0.04 0 46 1 123 by freq Potentially damaging 1.494 8 Intolerant 0 2.81 15 conservative 174762 12q24.3 "polymerase (DNA directed), epsilon" 4322 rs5744799 POLE 5426 12 131855382 NM_006231 NP_006222 A/T F695I minus 7989091 693 EGP_SNPS PDR90 NIHPDR 176 0.02 0.02 0 176 1 114 by freq Possibly damaging 1.775 9 Intolerant 0.02 2.88 14 conservative 174762 12q24.3 "polymerase (DNA directed), epsilon" 4323 rs5744933 POLE 5426 12 131830879 NM_006231 NP_006222 A/G Y1395C minus 7989234 693 EGP_SNPS PDR90 NIHPDR 180 0.01 0.01 0 180 1 0.02 0 46 1 123 by freq Probably damaging 2.37 9 Borderline 0.17 2.88 14 radical 174762 12q24.3 "polymerase (DNA directed), epsilon" 4324 rs5744934 POLE 5426 12 131830876 NM_006231 NP_006222 A/G N1396S minus 7989235 693 EGP_SNPS PDR90 NIHPDR 180 0.13 0.13 0 228 2 0.22 0 46 1 123 by freq Possibly damaging 1.584 9 Tolerant 0.23 2.96 13 conservative 174762 12q24.3 "polymerase (DNA directed), epsilon" 4325 rs5744934 POLE 5426 12 131830876 NM_006231 NP_006222 A/G N1396S minus 23500549 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 228 2 0.22 0 46 1 123 by freq Possibly damaging 1.584 9 Tolerant 0.23 2.96 13 conservative 174762 12q24.3 "polymerase (DNA directed), epsilon" 4326 rs5744935 POLE 5426 12 131830868 NM_006231 NP_006222 C/G E1399Q minus 7989236 693 EGP_SNPS PDR90 NIHPDR 180 0.01 0.01 0 180 1 114 by freq Benign 0.233 9 Borderline 0.18 2.88 14 conservative 174762 12q24.3 "polymerase (DNA directed), epsilon" 4327 rs5745021 POLE 5426 12 131819617 NM_006231 NP_006222 C/T A2040V minus 7989329 693 EGP_SNPS PDR90 NIHPDR 166 0.01 0.01 0 166 1 114 by freq Tolerant 0.27 2.9 13 moderately conservative 174762 12q24.3 "polymerase (DNA directed), epsilon" 4328 rs5745068 POLE 5426 12 131813090 NM_006231 NP_006222 A/G R2165H minus 7989377 693 EGP_SNPS PDR90 NIHPDR 174 0.01 0.01 0 174 1 114 by freq Borderline 0.16 2.88 14 conservative 174762 12q24.3 "polymerase (DNA directed), epsilon" 4329 rs5745324 MSH4 4438 1 75981460 NM_002440 NP_002431 A/G A90T plus 7989700 693 EGP_SNPS PDR90 NIHPDR 176 0.02 0.02 0 176 1 114 by freq Benign 0 5 moderately conservative 602105 1p31 mutS homolog 4 (E. coli) 4330 rs5745325 MSH4 4438 1 75981481 NM_002440 NP_002431 A/G A97T plus 7989701 693 EGP_SNPS PDR90 NIHPDR 176 0.19 0.22 0.07 224 2 0.13 0.13 94 2 123 "by doubleHit,freq,cluster" Benign 0.9 5 moderately conservative 602105 1p31 mutS homolog 4 (E. coli) 4331 rs5745325 MSH4 4438 1 75981481 NM_002440 NP_002431 A/G A97T plus 24274892 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.22 0.07 224 2 0.13 0.13 94 2 123 "by doubleHit,freq,cluster" Benign 0.9 5 moderately conservative 602105 1p31 mutS homolog 4 (E. coli) 4332 rs5745549 MSH4 4438 1 76090523 NM_002440 NP_002431 A/G S914N plus 7989953 693 EGP_SNPS PDR90 NIHPDR 180 0.03 0.04 0.03 228 2 0.12 0.14 94 2 123 "by cluster,freq" Benign 0.929 6 Tolerant 0.69 2.95 11 conservative 602105 1p31 mutS homolog 4 (E. coli) 4333 rs5745549 MSH4 4438 1 76090523 NM_002440 NP_002431 A/G S914N plus 23202526 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.04 0.03 228 2 0.12 0.14 94 2 123 "by cluster,freq" Benign 0.929 6 Tolerant 0.69 2.95 11 conservative 602105 1p31 mutS homolog 4 (E. coli) 4334 rs5745687 HGF 3082 7 81003702 NM_000601 NP_000592 A/G E304K minus 7990318 693 EGP_SNPS PDR90 NIHPDR 158 0.02 0.02 0 158 1 114 by freq Borderline 1.184 14 Tolerant 0.56 2.81 38 moderately conservative 142409 7q21.1 hepatocyte growth factor (hepapoietin A; scatter factor) 4335 rs5746025 TNFRSF1B 7133 1 12187193 NM_001066 NP_001057 A/G V187M plus 7990726 693 EGP_SNPS PDR90 NIHPDR 172 0.02 0.02 0 172 1 0.02 0 46 1 123 "by cluster,freq" Benign 0.952 10 Tolerant 0.21 2.77 81 conservative 191191 1p36.3-p36.2 "tumor necrosis factor receptor superfamily, member 1B" 4336 rs5746026 TNFRSF1B 7133 1 12187328 NM_001066 NP_001057 A/G E232K plus 7990728 693 EGP_SNPS PDR90 NIHPDR 174 0.02 0.02 0.01 222 2 0.04 0 46 1 123 by freq Potentially damaging 1.267 10 Tolerant 0.23 2.97 13 moderately conservative 191191 1p36.3-p36.2 "tumor necrosis factor receptor superfamily, member 1B" 4337 rs5746026 TNFRSF1B 7133 1 12187328 NM_001066 NP_001057 A/G E232K plus 23845247 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.02 0.01 222 2 0.04 0 46 1 123 by freq Potentially damaging 1.267 10 Tolerant 0.23 2.97 13 moderately conservative 191191 1p36.3-p36.2 "tumor necrosis factor receptor superfamily, member 1B" 4338 rs5746129 SOD2 6648 6 160076354 NM_000636 NP_000627 C/T R156W minus 7990860 693 EGP_SNPS PDR90 NIHPDR 180 0.01 0.01 0 180 1 114 by freq Borderline 1.131 101 Intolerant 0.02 2.81 114 moderately radical 147460 6q25.3 "superoxide dismutase 2, mitochondrial" 4339 rs5761268 MYO18B 84700 22 24564404 NM_032608 NP_115997 A/C H1119Q plus 8014665 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.3 0.3 0.01 168 2 0.43 0 44 1 123 "HapMap,doubleHit,freq,cluster" Tolerant 1 2.8 124 conservative 607295 22q11.2-q12.1 myosin XVIIIB 4340 rs5761268 MYO18B 84700 22 24564404 NM_032608 NP_115997 A/C H1119Q plus 23623194 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.3 0.01 168 2 0.43 0 44 1 123 "HapMap,doubleHit,freq,cluster" Tolerant 1 2.8 124 conservative 607295 22q11.2-q12.1 myosin XVIIIB 4341 rs5764698 SMC1L2 27127 22 44070520 NM_148674 NP_683515 G/T L1051M plus 24571168 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.35 0 48 1 0.2 0.16 92 2 123 "by doubleHit,freq" Benign 0.073 14 conservative 608685 22q13.31 SMC1 structural maintenance of chromosomes 1-like 2 (yeast) 4342 rs6004901 MYO18B 84700 22 24747678 NM_032608 NP_115997 C/G G2395A plus 23557104 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 0.12 0.14 94 2 123 "by cluster,freq" moderately conservative 607295 22q11.2-q12.1 myosin XVIIIB 4343 rs6037651 SN 6614 20 3634436 NM_023068 NP_075556 C/T V221M plus 24497154 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.42 0 48 1 0.31 0.01 94 2 123 "by doubleHit,freq" Benign 0.049 5 Borderline 0.18 2.83 10 conservative 600751 20p13 sialoadhesin 4344 rs6048760 ZNF336 64412 20 23293844 NM_022482 NP_071927 A/C Q275P plus 24690495 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.48 0 48 1 0.13 0.06 92 2 123 "by doubleHit,freq,cluster" Benign 0.353 7 Tolerant 0.42 2.78 269 moderately conservative 20p12.3-p11.21 zinc finger protein 336 4345 rs6050249 ACAS2L 84532 20 24942289 NM_032501 NP_115890 C/T V488M plus 23665053 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.13 0.13 0 46 1 0.14 0.11 82 2 123 "by doubleHit,freq,cluster" Benign 0.647 23 Intolerant 0.04 2.81 136 conservative 20p11.23-p11.21 acetyl-Coenzyme A synthetase 2 (AMP forming)-like 4346 rs6063377 DDX27 55661 20 47292624 NM_017895 NP_060365 A/G G766S plus 8379349 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.31 0.33 0.05 202 4 0.19 0.11 160 5 123 "HapMap,doubleHit,freq,cluster" Benign 0.39 9 moderately conservative 20q13.13 DEAD (Asp-Glu-Ala-Asp) box polypeptide 27 4347 rs6063377 DDX27 55661 20 47292624 NM_017895 NP_060365 A/G G766S plus 14871695 902 AFFY Caucasian 24 0.46 0.33 0.05 202 4 0.19 0.11 160 5 123 "HapMap,doubleHit,freq,cluster" Benign 0.39 9 moderately conservative 20q13.13 DEAD (Asp-Glu-Ala-Asp) box polypeptide 27 4348 rs6063377 DDX27 55661 20 47292624 NM_017895 NP_060365 A/G G766S plus 14871695 904 AFFY CEPH 12 0.33 0.33 0.05 202 4 0.19 0.11 160 5 123 "HapMap,doubleHit,freq,cluster" Benign 0.39 9 moderately conservative 20q13.13 DEAD (Asp-Glu-Ala-Asp) box polypeptide 27 4349 rs6063377 DDX27 55661 20 47292624 NM_017895 NP_060365 A/G G766S plus 24696222 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.33 0.05 202 4 0.19 0.11 160 5 123 "HapMap,doubleHit,freq,cluster" Benign 0.39 9 moderately conservative 20q13.13 DEAD (Asp-Glu-Ala-Asp) box polypeptide 27 4350 rs6063966 ZNF217 7764 20 51626495 NM_006526 NP_006517 C/T V739I plus 23588126 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.06 0.06 94 2 123 by freq conservative 602967 20q13.2 zinc finger protein 217 4351 rs6080719 BFSP1 631 20 17425592 NM_001195 NP_001186 C/T G345S plus 8401763 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.19 0.19 0 118 1 114 "HapMap,doubleHit,freq" Benign 0.007 12 Tolerant 1 2.78 75 moderately conservative 603307 20p11.23-p12.1 "beaded filament structural protein 1, filensin" 4352 rs6088066 BPIL1 80341 20 31060133 NM_025227 NP_079503 A/T K31M plus 8411129 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.34 0.26 0.19 156 2 0.02 0 46 1 123 "HapMap,freq" Potentially damaging 1.35 5 Intolerant 0.05 2.77 10 moderately conservative 20q11.22 bactericidal/permeability-increasing protein-like 1 4353 rs6088066 BPIL1 80341 20 31060133 NM_025227 NP_079503 A/T K31M plus 24533707 1371 PERLEGEN AFD_EUR_PANEL European American (24) 38 0.03 0.26 0.19 156 2 0.02 0 46 1 123 "HapMap,freq" Potentially damaging 1.35 5 Intolerant 0.05 2.77 10 moderately conservative 20q11.22 bactericidal/permeability-increasing protein-like 1 4354 rs6138482 VSX1 30813 20 25007442 NM_199425 NP_955457 C/T R217H plus 8470331 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.21 0.21 0 118 1 114 "HapMap,doubleHit,freq" Intolerant 0 2.72 287 conservative 605020 20p11.23-p11.22 "visual system homeobox 1 homolog, CHX10-like (zebrafish)" 4355 rs6151415 ARSA 410 22 49355505 NM_000487 NP_000478 G/T W193C minus 8485016 693 EGP_SNPS PDR90 NIHPDR 174 0.03 0.03 0 174 1 114 by freq Probably damaging 2.636 7 Potentially intolerant 0.09 2.75 21 radical 607574 22q13.33 arylsulfatase A 4356 rs6151428 ARSA 410 22 49353754 NM_000487 NP_000478 A/G R496H minus 8485036 693 EGP_SNPS PDR90 NIHPDR 174 0.03 0.03 0 294 2 114 "HapMap,freq" Benign 0.517 7 Tolerant 0.58 2.8 17 conservative 607574 22q13.33 arylsulfatase A 4357 rs6151428 ARSA 410 22 49353754 NM_000487 NP_000478 A/G R496H minus 8485036 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.03 0.03 0 294 2 114 "HapMap,freq" Benign 0.517 7 Tolerant 0.58 2.8 17 conservative 607574 22q13.33 arylsulfatase A 4358 rs6413413 ADH1B 125 4 100596462 NM_000668 NP_000659 A/T T60S minus 5586190 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.05 0.05 0 62 1 0.02 0 200 1 117 "by cluster,freq" Benign 0.279 241 Tolerant 0.37 2.79 360 moderately conservative 103720 4q21-q23 "alcohol dehydrogenase IB (class I), beta polypeptide" 4359 rs6413419 CYP2E1 1571 10 135234556 NM_000773 NP_000764 A/G V179I plus 23588573 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.08 0.09 340 4 123 "by doubleHit,freq,cluster" Potentially damaging 1.274 108 Tolerant 0.36 2.78 161 conservative 124040 10q24.3-qter "cytochrome P450, family 2, subfamily E, polypeptide 1" 4360 rs6413491 IGF2R 3482 6 160438720 NM_000876 NP_000867 A/G A724T plus 12585801 693 EGP_SNPS PDR90 NIHPDR 176 0.01 0.01 0 176 1 0.02 0.04 290 3 123 "by cluster,freq" Borderline 1.212 17 Tolerant 0.26 2.78 37 moderately conservative 147280 6q26 insulin-like growth factor 2 receptor 4361 rs6413508 NBS1 4683 8 91027599 NM_002485 NP_002476 C/T P672L minus 8819821 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.02 0.02 0 60 1 0.01 0 202 1 116 by freq Benign 0.512 6 moderately conservative 602667 8q21 Nijmegen breakage syndrome 1 (nibrin) 4362 rs6425977 THRAP3 9967 1 36421526 NM_005119 NP_005110 C/T A201V plus 9893643 1303 SEQUENOM CEPH CEPH (92) 92 0.07 0.07 0 92 1 123 "by doubleHit,freq,cluster" moderately conservative 603809 1p34.3 thyroid hormone receptor associated protein 3 4363 rs6427504 ATP1A4 480 1 156937948 NM_144699 NP_653300 A/G G83D plus 14883599 902 AFFY Caucasian 22 0.36 0.37 0.06 78 3 0.31 0.04 156 5 123 "by doubleHit,freq,cluster" Probably damaging 2.113 136 moderately conservative 607321 1q21-q23 "ATPase, Na+/K+ transporting, alpha 4 polypeptide" 4364 rs6427504 ATP1A4 480 1 156937948 NM_144699 NP_653300 A/G G83D plus 14883599 904 AFFY CEPH 8 0.25 0.37 0.06 78 3 0.31 0.04 156 5 123 "by doubleHit,freq,cluster" Probably damaging 2.113 136 moderately conservative 607321 1q21-q23 "ATPase, Na+/K+ transporting, alpha 4 polypeptide" 4365 rs6427504 ATP1A4 480 1 156937948 NM_144699 NP_653300 A/G G83D plus 24239001 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.37 0.06 78 3 0.31 0.04 156 5 123 "by doubleHit,freq,cluster" Probably damaging 2.113 136 moderately conservative 607321 1q21-q23 "ATPase, Na+/K+ transporting, alpha 4 polypeptide" 4366 rs6429757 AGMAT 79814 1 15655156 NM_024758 NP_079034 C/G G105R plus 9837663 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.49 0.49 0 120 1 121 "HapMap,doubleHit,freq,cluster" Benign 0.752 15 Tolerant 0.86 2.76 29 moderately radical 1p36.13 agmatine ureohydrolase (agmatinase) 4367 rs6446261 GPX1 2876 3 49369857 NM_000581 NP_000572 C/T A194T plus 12568571 693 EGP_SNPS PDR90 NIHPDR 180 0.02 0.02 0 180 1 117 "HapMap,doubleHit,freq,cluster" Benign 0.038 31 Tolerant 0.36 2.77 84 moderately conservative 138320 3p21.3 glutathione peroxidase 1 4368 rs6456811 PGBD1 84547 6 28378026 NM_032507 NP_115896 C/G H806D plus 10288276 885 TSC-CSHL HapMap-CEPH-30-trios 112 0.07 0.08 0.02 160 2 0.24 0.26 94 2 123 "HapMap,doubleHit,freq,cluster" moderately conservative 6p21.33 piggyBac transposable element derived 1 4369 rs6456811 PGBD1 84547 6 28378026 NM_032507 NP_115896 C/G H806D plus 23290764 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.08 0.02 160 2 0.24 0.26 94 2 123 "HapMap,doubleHit,freq,cluster" moderately conservative 6p21.33 piggyBac transposable element derived 1 4370 rs6456880 ZNF311 282890 6 29071227 XM_212581 XP_212581 G/T K718Q plus 24338016 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.4 0 48 1 0.24 0.16 94 2 123 "by doubleHit,freq,cluster" Potentially intolerant 0.09 3.05 398 moderately conservative 6p21.33 zinc finger protein 311 4371 rs6458687 MUT 4594 6 49511241 NM_000255 NP_000246 C/T I671V plus 10313461 1303 SEQUENOM CEPH CEPH (92) 92 0.26 0.26 0 92 1 119 "by doubleHit,freq,cluster" Benign 0.302 57 conservative 251000 6p21 methylmalonyl Coenzyme A mutase 4372 rs6459166 DST 667 6 56590760 NM_001723 NP_001714 C/G V2011L plus 24379600 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.38 0 48 1 0.34 0.03 74 2 123 "by doubleHit,freq,cluster" conservative 113810 6p12-p11 "bullous pemphigoid antigen 1, 230/240kDa" 4373 rs6485702 LRP4 4038 11 46855347 XM_035037 XP_035037 C/T I1056V plus 24207566 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.25 0 48 1 0.3 0.08 94 2 123 "by doubleHit,freq,cluster" Benign 0.3 5 Tolerant 0.66 2.85 27 conservative 604270 11p11.2-p12 low density lipoprotein receptor-related protein 4 4374 rs6489795 P2RX7 5027 12 120077851 NM_002562 NP_002553 C/G T357S plus 23933360 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.22 0.02 94 2 123 "by doubleHit,freq,cluster" Benign 0.9 5 Tolerant 0.59 2.99 58 moderately conservative 602566 12q24 "purinergic receptor P2X, ligand-gated ion channel, 7" 4375 rs6495228 RYR3 6263 15 31803566 NM_001036 NP_001027 A/G G2270E plus 23661970 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.09 0.11 94 2 123 "by cluster,freq" Possibly damaging 1.586 9 moderately conservative 180903 15q14-q15 ryanodine receptor 3 4376 rs6497759 TNRC6 27327 16 24709238 NM_014494 NP_055309 A/G A339T plus 23382113 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 0.09 0.05 94 2 123 "by doubleHit,freq,cluster" moderately conservative 16p11.2 trinucleotide repeat containing 6 4377 rs6500437 ZFP276 92822 16 88317399 NM_152287 NP_689500 C/T W188R plus 10811248 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.4 0.4 0 116 1 116 "HapMap,doubleHit,freq,cluster" moderately radical 608460 16q24.3 zinc finger protein 276 homolog (mouse) 4378 rs6504649 XYLT2 64132 17 45792455 NM_022167 NP_071450 C/G T801R plus 24594979 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.4 0.4 0 42 1 0.13 0.13 92 2 123 "by doubleHit,freq,cluster" Potentially damaging 1.26 16 Intolerant 0.03 3.13 24 moderately conservative 608125 17q21.3-17q22 xylosyltransferase II 4379 rs6509138 ZNF223 7766 19 49262233 NM_013361 NP_037493 A/C L138I plus 10917856 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.36 0.36 0 120 1 116 "HapMap,doubleHit,freq,cluster" Benign 0.985 21 conservative 19q13.2 zinc finger protein 223 4380 rs6510057 ZNF543 125919 19 62529830 NM_213598 NP_998763 C/G P55A plus 24534001 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.48 0 48 1 0.38 0.07 92 2 123 "by doubleHit,freq,cluster" Tolerant 0.33 2.83 23 conservative 19q13.43 zinc finger protein 543 4381 rs6510130 ZNF544 27300 19 63464391 NM_014480 NP_055295 C/G H203D plus 23563149 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.13 0 46 1 123 "by doubleHit,freq,cluster" Potentially intolerant 0.07 2.81 26 moderately conservative 19q13.43 zinc finger protein 544 4382 rs6518291 PCNT2 5116 21 46646016 NM_006031 NP_006022 A/G I1639V plus 23558338 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.3 0.3 0 46 1 0.33 0.21 94 2 123 "by doubleHit,freq,cluster" conservative 605925 21q22.3 pericentrin 2 (kendrin) 4383 rs6557634 TNFRSF10A 8797 8 23116201 NM_003844 NP_003835 C/T H141R plus 10474821 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.41 0.41 0 120 1 116 "HapMap,doubleHit,freq,cluster" Tolerant 0.52 2.83 18 conservative 603611 8p21 "tumor necrosis factor receptor superfamily, member 10a" 4384 rs6569605 LAMA2 3908 6 129849322 NM_000426 NP_000417 C/T A2587V plus 23966188 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.29 0 48 1 0.46 0.04 94 2 123 "by doubleHit,freq,cluster" moderately conservative 156225 6q22-q23 "laminin, alpha 2 (merosin, congenital muscular dystrophy)" 4385 rs6580942 ESPL1 9700 12 51948891 NM_012291 NP_036423 A/C A25D plus 24392178 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.35 0 48 1 0.09 0 46 1 123 "by cluster,freq" moderately radical 604143 8 extra spindle poles like 1 (S. cerevisiae) 4386 rs6586145 LIPF 8513 10 90423325 NM_004190 NP_004181 A/T F224I plus 23569735 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.2 0.05 94 2 123 "by doubleHit,freq,cluster" Benign 0.162 44 Tolerant 0.48 2.79 38 conservative 601980 10q23.31 "lipase, gastric" 4387 rs6586179 LIPA 3988 10 90997319 NM_000235 NP_000226 C/T G23R plus 10604742 1303 SEQUENOM CEPH CEPH (92) 92 0.15 0.17 0.04 134 2 0.11 0.13 90 2 123 "by doubleHit,freq,cluster" Benign 0.074 32 Tolerant 0.7 2.97 23 moderately radical 278000 10q23.2-q23.3 "lipase A, lysosomal acid, cholesterol esterase (Wolman disease)" 4388 rs6586179 LIPA 3988 10 90997319 NM_000235 NP_000226 C/T G23R plus 24546497 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.21 0.17 0.04 134 2 0.11 0.13 90 2 123 "by doubleHit,freq,cluster" Benign 0.074 32 Tolerant 0.7 2.97 23 moderately radical 278000 10q23.2-q23.3 "lipase A, lysosomal acid, cholesterol esterase (Wolman disease)" 4389 rs6586239 RIPK4 54101 21 42060236 NM_020639 NP_065690 C/G A12G plus 23652015 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.17 0.17 0 46 1 0.2 0 46 1 123 "by doubleHit,freq,cluster" Benign 0.7 7 moderately conservative 605706 21q22.3 ankyrin repeat domain 3 4390 rs6595908 ADAMTS19 171019 5 128891370 NM_133638 NP_598377 A/G S367G plus 10202455 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.02 0.02 0 168 2 0.02 0 46 1 123 "HapMap,freq,cluster" moderately conservative 607513 5q31 "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19" 4391 rs6595908 ADAMTS19 171019 5 128891370 NM_133638 NP_598377 A/G S367G plus 23758401 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 168 2 0.02 0 46 1 123 "HapMap,freq,cluster" moderately conservative 607513 5q31 "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19" 4392 rs6597801 LHPP 64077 10 126162853 NM_022126 NP_071409 A/G Q94R plus 24580172 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.23 0 48 1 0.03 0.01 94 2 123 "by cluster,freq" conservative 10q26.2 phospholysine phosphohistidine inorganic pyrophosphate phosphatase 4393 rs6650971 FAT2 2196 5 150881454 NM_001447 NP_001438 C/T M3631I plus 23767398 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.21 0 48 1 0.22 0.27 68 2 123 "by doubleHit,freq,cluster" Tolerant 1 2.9 11 conservative 604269 5q32-q33 FAT tumor suppressor homolog 2 (Drosophila) 4394 rs6667260 ITPKB 3707 1 223230673 NM_002221 NP_002212 A/C S408A plus 28460842 549 KYUGEN CP CEPH (78) 156 0.46 0.46 0 156 1 0.33 0 200 1 123 "by doubleHit,freq,cluster" Benign 0.234 5 moderately conservative 147522 1q42.13 "inositol 1,4,5-trisphosphate 3-kinase B" 4395 rs6671421 EVI5 7813 1 92881430 XM_496372 XP_496372 A/G S137P plus 9839005 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.08 0.08 0 120 1 121 "HapMap,freq,cluster" moderately conservative 602942 1p22 ecotropic viral integration site 5 4396 rs6674775 HBXIP 10542 1 110662481 NM_006402 NP_006393 C/T S17N plus 9845789 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.47 0.46 0.02 168 2 0.3 0.11 92 2 123 "HapMap,doubleHit,freq,cluster" conservative 608521 1p13.2 hepatitis B virus x interacting protein 4397 rs6674775 HBXIP 10542 1 110662481 NM_006402 NP_006393 C/T S17N plus 24279415 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.46 0.02 168 2 0.3 0.11 92 2 123 "HapMap,doubleHit,freq,cluster" conservative 608521 1p13.2 hepatitis B virus x interacting protein 4398 rs6688832 H6PD 9563 1 9258176 NM_004285 NP_004276 A/G R453Q plus 24220458 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.31 0 48 1 0.49 0.01 70 2 123 "by doubleHit,freq" Benign 0.961 6 Tolerant 0.38 2.77 259 conservative 138090 1p36 hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase) 4399 rs6698159 HBXIP 10542 1 110662319 NM_006402 NP_006393 A/G P71L plus 23208636 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.13 0.13 0 46 1 0.1 0.08 90 2 123 "by doubleHit,freq,cluster" moderately conservative 608521 1p13.2 hepatitis B virus x interacting protein 4400 rs6704505 TDRD5 163589 1 176331658 NM_173533 NP_775804 A/G K358E plus 24631065 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.1 0.01 94 2 123 "by doubleHit,freq" moderately conservative 1q24.3-q25.1 tudor domain containing 5 4401 rs6710480 UPP2 151531 2 158784113 NM_173355 NP_775491 G/T R10S plus 23714369 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.02 0.02 0 46 1 0.24 0.16 94 2 123 "by doubleHit,freq,cluster" Benign 0.237 5 moderately radical 2q24.2 uridine phosphorylase 2 4402 rs6719500 DNAH7 56171 2 196650908 NM_018897 NP_061720 C/T K825E plus 9933808 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.14 0.14 0 120 1 116 "HapMap,doubleHit,freq" Benign 0.03 5 Tolerant 0.93 2.86 19 moderately conservative 2q33.1 "dynein, axonemal, heavy polypeptide 7" 4403 rs6720173 ABCG5 64240 2 43952052 NM_022436 NP_071881 C/G Q604E plus 24650850 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.21 0 48 1 0.16 0.05 94 2 123 "by doubleHit,freq" Borderline 1.166 5 Tolerant 1 2.78 13 conservative 605459 2p21 "ATP-binding cassette, sub-family G (WHITE), member 5 (sterolin 1)" 4404 rs6729801 DNAJC10 54431 2 183410261 NM_018981 NP_061854 A/G D76N plus 24151107 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.33 0.33 0 46 1 0.24 0.21 94 2 123 "by cluster,freq" Benign 0.106 8 conservative 607987 2q32.1 "DnaJ (Hsp40) homolog, subfamily C, member 10" 4405 rs6737156 DGUOK 1716 2 74071389 NM_080915 NP_550437 C/T L51P plus 23221307 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.11 0 46 1 123 "by doubleHit,freq,cluster" moderately conservative 601465 2p13 deoxyguanosine kinase 4406 rs6755571 UGT1A4 54657 2 234409536 NM_007120 NP_009051 A/C P24T plus 9999931 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.05 0.05 0 120 1 116 "HapMap,freq" Benign 0.635 20 Tolerant 0.39 2.81 142 conservative 606429 2q37 "UDP glycosyltransferase 1 family, polypeptide A4" 4407 rs6759356 GALNT5 11227 2 157966314 NM_014568 NP_055383 C/G Q489H plus 23268342 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.43 0 46 1 123 "by doubleHit,freq,cluster" conservative 2q24.2 UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 5 (GalNAc-T5) 4408 rs6759892 UGT1A6 54578 2 234383669 NM_001072 NP_001063 G/T S7A plus 10007811 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.38 0.4 0.04 168 2 0.26 0.16 92 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.143 18 moderately conservative 606431 2q37 "UDP glycosyltransferase 1 family, polypeptide A6" 4409 rs6759892 UGT1A6 54578 2 234383669 NM_001072 NP_001063 G/T S7A plus 24278533 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.4 0.04 168 2 0.26 0.16 92 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.143 18 moderately conservative 606431 2q37 "UDP glycosyltransferase 1 family, polypeptide A6" 4410 rs6761637 MARCO 8685 2 119455293 NM_006770 NP_006761 C/T F282S plus 23251087 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.21 0.06 94 2 123 "by doubleHit,freq,cluster" radical 604870 2q12-q13 macrophage receptor with collagenous structure 4411 rs6761641 PASK 23178 2 241766775 NM_015148 NP_055963 A/C F1266C plus 10010980 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.13 0.14 0.01 258 3 0.44 0.06 88 2 123 "HapMap,doubleHit,freq,cluster" radical 607505 2q37.3 PAS domain containing serine/threonine kinase 4412 rs6761641 PASK 23178 2 241766775 NM_015148 NP_055963 A/C F1266C plus 10010980 1303 SEQUENOM CEPH CEPH (92) 92 0.14 0.14 0.01 258 3 0.44 0.06 88 2 123 "HapMap,doubleHit,freq,cluster" radical 607505 2q37.3 PAS domain containing serine/threonine kinase 4413 rs6761641 PASK 23178 2 241766775 NM_015148 NP_055963 A/C F1266C plus 23922873 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.15 0.14 0.01 258 3 0.44 0.06 88 2 123 "HapMap,doubleHit,freq,cluster" radical 607505 2q37.3 PAS domain containing serine/threonine kinase 4414 rs6807963 HCLS1 3059 3 122835944 NM_005335 NP_005326 C/T T235A plus 23322875 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.21 0 48 1 0.19 0.13 94 2 123 "by doubleHit,freq,cluster" moderately conservative 601306 3q13 hematopoietic cell-specific Lyn substrate 1 4415 rs6897932 IL7R 3575 5 35910332 NM_002185 NP_002176 C/T T244I plus 16336732 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.33 0.33 0 46 1 0.11 0 46 1 120 "by doubleHit,freq,cluster" Possibly damaging 1.533 5 Tolerant 0.45 2.81 49 moderately conservative 146661 5p13 interleukin 7 receptor 4416 rs6907125 GPR111 222611 6 47754801 NM_153839 NP_722581 A/G Q148R plus 10283844 885 TSC-CSHL HapMap-CEPH-30-trios 112 0.36 0.35 0.03 160 2 0.35 0.08 94 2 123 "HapMap,doubleHit,freq,cluster" Borderline 0.17 2.95 15 conservative 6p12.3 G protein-coupled receptor 111 4417 rs6907125 GPR111 222611 6 47754801 NM_153839 NP_722581 A/G Q148R plus 23334435 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.35 0.03 160 2 0.35 0.08 94 2 123 "HapMap,doubleHit,freq,cluster" Borderline 0.17 2.95 15 conservative 6p12.3 G protein-coupled receptor 111 4418 rs6925178 ZNF311 282890 6 29081194 XM_212581 XP_212581 A/C D203Y plus 23294545 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.27 0 48 1 0.28 0.18 94 2 123 "by doubleHit,freq,cluster" radical 6p21.33 zinc finger protein 311 4419 rs6926570 ENPP5 59084 6 46243448 NM_021572 NP_067547 C/T I171V plus 24000776 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.44 0 48 1 0.27 0.23 70 2 123 "by doubleHit,freq,cluster" Potentially intolerant 0.07 2.77 34 conservative 6p21.1-p11.2 ectonucleotide pyrophosphatase/phosphodiesterase 5 (putative function) 4420 rs6926628 HLA-DMA 3108 6 33025476 NM_006120 NP_006111 C/G G181A plus 24169457 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.04 0 48 1 123 by freq Possibly damaging 1.552 19 Intolerant 0 2.84 266 moderately conservative 142855 6p21.3 "major histocompatibility complex, class II, DM alpha" 4421 rs6927706 PBOV1 59351 6 138581008 NM_021635 NP_067648 A/G I73T plus 24030357 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 0.25 0.11 94 2 123 "by doubleHit,freq,cluster" moderately conservative 605669 6q23-q24 prostate and breast cancer overexpressed 1 4422 rs6934603 GJB7 375519 6 88050734 NM_198568 NP_940970 A/G F206L plus 23956395 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.37 0.37 0 46 1 0.4 0.06 90 2 123 "by doubleHit,freq,cluster" Benign 0.351 13 Tolerant 0.49 2.77 115 conservative 6q15 "gap junction protein, beta 7" 4423 rs6941583 POLH 5429 6 43690069 NM_006502 NP_006493 A/T M647L plus 12709528 693 EGP_SNPS PDR90 NIHPDR 178 0.08 0.08 0 178 1 119 "by doubleHit,freq,cluster" Borderline 1.005 5 conservative 603968 6p21.1 "polymerase (DNA directed), eta" 4424 rs6954345 PON2 5445 7 94679426 NM_000305 NP_000296 C/G S311C plus 10371805 1303 SEQUENOM CEPH CEPH (92) 92 0.23 0.22 0.03 140 2 0.18 0.08 94 2 123 "by cluster,freq" Benign 0.106 50 Potentially intolerant 0.07 2.79 31 moderately radical 602447 7q21.3 paraoxonase 2 4425 rs6954345 PON2 5445 7 94679426 NM_000305 NP_000296 C/G S311C plus 23760919 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.22 0.03 140 2 0.18 0.08 94 2 123 "by cluster,freq" Benign 0.106 50 Potentially intolerant 0.07 2.79 31 moderately radical 602447 7q21.3 paraoxonase 2 4426 rs6958498 NRCAM 4897 7 107428564 NM_005010 NP_005001 C/G P539A plus 10379607 1303 SEQUENOM CEPH CEPH (92) 92 0.17 0.17 0 92 1 121 "by doubleHit,freq,cluster" Probably damaging 2.274 25 Tolerant 0.56 2.82 46 conservative 601581 7q31.1-q31.2 neuronal cell adhesion molecule 4427 rs7017102 OPLAH 26873 8 145190636 XM_291266 XP_291266 A/G W64R plus 10487748 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.07 0.07 0 120 1 116 "HapMap,doubleHit,freq" moderately radical 8q24.3 5-oxoprolinase (ATP-hydrolysing) 4428 rs7017776 ChGn 55790 8 19407048 NM_018371 NP_060841 C/T S193N plus 10489004 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.18 0.19 0.03 166 2 0.28 0.16 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.5 13 conservative 8p21.3 "chondroitin beta1,4 N-acetylgalactosaminyltransferase" 4429 rs7017776 ChGn 55790 8 19407048 NM_018371 NP_060841 C/T S193N plus 23711507 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.19 0.03 166 2 0.28 0.16 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.5 13 conservative 8p21.3 "chondroitin beta1,4 N-acetylgalactosaminyltransferase" 4430 rs7021366 CTNNAL1 8727 9 108807225 NM_003798 NP_003789 C/G E527Q plus 14910990 902 AFFY Caucasian 22 0.27 0.35 0.07 80 3 0.2 0.16 162 5 123 "by cluster,freq" Borderline 1.042 5 Intolerant 0.03 2.8 37 conservative 604785 9q31.2 "catenin (cadherin-associated protein), alpha-like 1" 4431 rs7021366 CTNNAL1 8727 9 108807225 NM_003798 NP_003789 C/G E527Q plus 14910990 904 AFFY CEPH 10 0.3 0.35 0.07 80 3 0.2 0.16 162 5 123 "by cluster,freq" Borderline 1.042 5 Intolerant 0.03 2.8 37 conservative 604785 9q31.2 "catenin (cadherin-associated protein), alpha-like 1" 4432 rs7021366 CTNNAL1 8727 9 108807225 NM_003798 NP_003789 C/G E527Q plus 24698582 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.35 0.07 80 3 0.2 0.16 162 5 123 "by cluster,freq" Borderline 1.042 5 Intolerant 0.03 2.8 37 conservative 604785 9q31.2 "catenin (cadherin-associated protein), alpha-like 1" 4433 rs7023954 MTAP 4507 9 21806758 NM_002451 NP_002442 A/G V56I plus 24692235 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.48 0 48 1 0.46 0.03 94 2 123 "by doubleHit,freq,cluster" Benign 0.835 8 Borderline 0.11 2.75 32 conservative 156540 9p21 methylthioadenosine phosphorylase 4434 rs7036635 CER1 9350 9 14710357 NM_005454 NP_005445 C/T V179I plus 23542758 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.2 0 46 1 123 "by cluster,freq" Tolerant 0.31 3.08 67 conservative 603777 9p23-p22 "cerberus 1 homolog, cysteine knot superfamily (Xenopus laevis)" 4435 rs7083622 MKI67 4288 10 129793084 NM_002417 NP_002408 G/T T2337N plus 10611413 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.03 0.03 0 120 1 120 "HapMap,doubleHit,freq,cluster" Tolerant 0.33 2.89 9 moderately conservative 176741 10q25-qter antigen identified by monoclonal antibody Ki-67 4436 rs7103126 MYEOV 26579 11 68819969 NM_138768 NP_620123 C/T V159A plus 10648994 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.16 0.17 0.03 168 2 0.39 0.11 68 2 123 "HapMap,doubleHit,freq" moderately conservative 605625 11q13 myeloma overexpressed gene (in a subset of t(11;14) positive multiple myelomas) 4437 rs7103126 MYEOV 26579 11 68819969 NM_138768 NP_620123 C/T V159A plus 24175952 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.17 0.03 168 2 0.39 0.11 68 2 123 "HapMap,doubleHit,freq" moderately conservative 605625 11q13 myeloma overexpressed gene (in a subset of t(11;14) positive multiple myelomas) 4438 rs7110845 POU2F3 25833 11 119680959 NM_014352 NP_055167 A/G H152R plus 10664391 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.38 0.38 0 120 1 121 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.712 18 Tolerant 1 2.78 55 conservative 607394 11q23.3 "POU domain, class 2, transcription factor 3" 4439 rs7116130 PSMD13 5719 11 234129 NM_175932 NP_787128 A/G R35W minus 24117440 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.17 0 48 1 0.19 0.08 94 2 123 "by cluster,freq" moderately radical 603481 11p15.5 "proteasome (prosome, macropain) 26S subunit, non-ATPase, 13" 4440 rs7128029 PSMD13 5719 11 234141 NM_175932 NP_787128 C/T A39T minus 24117442 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.17 0 48 1 0.19 0.08 94 2 123 "by cluster,freq" moderately conservative 603481 11p15.5 "proteasome (prosome, macropain) 26S subunit, non-ATPase, 13" 4441 rs7131283 NYD-SP21 84689 11 59939546 XM_495876 XP_495876 A/T N177Y plus 23605058 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.27 0 48 1 0.37 0.06 94 2 123 "by doubleHit,freq,cluster" moderately radical 11q12.2 testes development-related NYD-SP21 4442 rs7144658 FOXA1 3169 14 37131493 NM_004496 NP_004487 C/T A83T plus 10730203 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.38 0.38 0 120 1 121 "HapMap,doubleHit,freq,cluster" Potentially damaging 1.398 14 Tolerant 0.25 2.92 32 moderately conservative 602294 14q12-q13 forkhead box A1 4443 rs7146310 IPO4 79711 14 23723794 NM_024658 NP_078934 A/G A513V plus 24217272 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.25 0 48 1 0.37 0.09 90 2 123 by freq moderately conservative 14q11.2 importin 4 4444 rs7149586 NFATC4 4776 14 23915681 NM_004554 NP_004545 C/T S800P plus 23799260 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.23 0 48 1 0.18 0.17 94 2 123 "by doubleHit,freq,cluster" Tolerant 0.35 2.97 10 moderately conservative 602699 14q11.2 "nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4" 4445 rs7161563 CDKL1 8814 14 49868876 NM_004196 NP_004187 C/G Q275E plus 16342974 693 EGP_SNPS PDR90 NIHPDR 162 0.44 0.44 0.01 210 2 0.38 0.07 94 2 123 "by doubleHit,freq,cluster" Borderline 1.028 10 Tolerant 0.5 2.78 186 conservative 603441 14q22.1 cyclin-dependent kinase-like 1 (CDC2-related kinase) 4446 rs7161563 CDKL1 8814 14 49868876 NM_004196 NP_004187 C/G Q275E plus 23640535 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.44 0.01 210 2 0.38 0.07 94 2 123 "by doubleHit,freq,cluster" Borderline 1.028 10 Tolerant 0.5 2.78 186 conservative 603441 14q22.1 cyclin-dependent kinase-like 1 (CDC2-related kinase) 4447 rs7162473 HERC1 8925 15 61724262 NM_003922 NP_003913 C/G E3722D plus 10763447 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.04 0.05 0.01 168 2 0.24 0 46 1 123 "HapMap,doubleHit,freq,cluster" conservative 605109 15q22 hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1 4448 rs7162473 HERC1 8925 15 61724262 NM_003922 NP_003913 C/G E3722D plus 23518142 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.05 0.01 168 2 0.24 0 46 1 123 "HapMap,doubleHit,freq,cluster" conservative 605109 15q22 hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1 4449 rs7188856 NAGPA 51172 16 5015634 NM_016256 NP_057340 A/G T465I plus 24483406 1371 PERLEGEN AFD_EUR_PANEL European American (24) 38 0.32 0.32 0 38 1 0.13 0 78 2 123 "by doubleHit,freq,cluster" moderately conservative 607985 16p13.3 N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase 4450 rs7190823 FANCA 2175 16 88393544 NM_000135 NP_000126 C/T T266A plus 14268354 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.43 0.42 0.03 168 2 0.08 0.09 94 2 123 "HapMap,doubleHit,freq,cluster" moderately conservative 607139 16q24.3 "Fanconi anemia, complementation group A" 4451 rs7190823 FANCA 2175 16 88393544 NM_000135 NP_000126 C/T T266A plus 24487952 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.42 0.03 168 2 0.08 0.09 94 2 123 "HapMap,doubleHit,freq,cluster" moderately conservative 607139 16q24.3 "Fanconi anemia, complementation group A" 4452 rs7193955 ABCC12 94160 16 46680083 NM_033226 NP_150229 A/G R1117C plus 10822374 885 TSC-CSHL HapMap-CEPH-30-trios 114 0.18 0.18 0 114 1 121 "HapMap,doubleHit,freq,cluster" radical 607041 16q12.1 "ATP-binding cassette, sub-family C (CFTR/MRP), member 12" 4453 rs7195066 FANCA 2175 16 88363824 NM_000135 NP_000126 C/T G809D plus 14270147 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.3 0.3 0 116 1 121 "HapMap,doubleHit,freq,cluster" moderately conservative 607139 16q24.3 "Fanconi anemia, complementation group A" 4454 rs7198458 RRAD 6236 16 65516387 NM_004165 NP_004156 G/T Q66P plus 10830636 1303 SEQUENOM CEPH CEPH (92) 92 0.1 0.1 0 92 1 119 "by doubleHit,freq,cluster" Potentially damaging 1.429 10 Tolerant 0.22 3.08 18 moderately conservative 179503 16q22 Ras-related associated with diabetes 4455 rs7201448 ITGAM 3684 16 31244389 NM_000632 NP_000623 C/T A858V plus 23450038 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 0.08 0.09 94 2 123 "by doubleHit,freq,cluster" Benign 0.007 10 Borderline 0.18 2.83 18 moderately conservative 120980 16p11.2 "integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide)" 4456 rs7208693 MPO 4353 17 53712817 NM_000250 NP_000241 A/C V53F plus 16338617 1120 WIPGA POP-WIPGA-12-05-2003 CORIELL Mixed 80 0.11 0.11 0 80 1 120 "by cluster,freq" Borderline 1.193 11 Tolerant 0.51 2.98 23 conservative 606989 17q23.1 myeloperoxidase 4457 rs7212483 KRT20 54474 17 36294578 NM_019010 NP_061883 C/T S129N plus 23594533 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.08 0.08 92 2 123 "by doubleHit,freq,cluster" Benign 0.28 14 Tolerant 1 2.72 138 conservative 608218 17q21.2 keratin 20 4458 rs7212506 ABCA6 23460 17 64613313 NM_080284 NP_525023 C/T M875I plus 23634168 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.29 0.14 94 2 123 "by doubleHit,freq,cluster" Benign 0.872 15 Tolerant 0.38 3.17 15 conservative 17q24.3 "ATP-binding cassette, sub-family A (ABC1), member 6" 4459 rs7224723 ZNF287 57336 17 16397339 NM_020653 NP_065704 G/T K274T plus 10878053 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.05 0.05 0.01 168 2 0.37 0 46 1 123 "HapMap,doubleHit,freq,cluster" Tolerant 0.67 2.83 96 moderately conservative 17p11.2 zinc finger protein 287 4460 rs7224723 ZNF287 57336 17 16397339 NM_020653 NP_065704 G/T K274T plus 23640398 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.05 0.01 168 2 0.37 0 46 1 123 "HapMap,doubleHit,freq,cluster" Tolerant 0.67 2.83 96 moderately conservative 17p11.2 zinc finger protein 287 4461 rs7225107 ALOX15B 247 17 7892603 NM_001141 NP_001132 A/G I676V plus 10878732 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.01 0.01 0.01 168 2 0.15 0.07 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.96 8 Intolerant 0 2.76 29 conservative 603697 17p13.1 "arachidonate 15-lipoxygenase, second type" 4462 rs7225107 ALOX15B 247 17 7892603 NM_001141 NP_001132 A/G I676V plus 23438017 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.01 0.01 168 2 0.15 0.07 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.96 8 Intolerant 0 2.76 29 conservative 603697 17p13.1 "arachidonate 15-lipoxygenase, second type" 4463 rs7247284 RNASEH2A 10535 19 12782186 NM_006397 NP_006388 C/T L202S plus 10921045 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.03 0.03 0 120 1 116 "HapMap,doubleHit,freq" Potentially damaging 1.468 8 Tolerant 0.65 2.87 20 moderately radical 606034 19p13.2 "ribonuclease H2, large subunit" 4464 rs7250872 ATP8B3 148229 19 1762603 NM_138813 NP_620168 C/T G45R plus 23755358 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.25 0 48 1 0.44 0.01 92 2 123 "by doubleHit,freq,cluster" moderately radical 605866 19p13.3 "ATPase, Class I, type 8B, member 3" 4465 rs7258368 ZNF625 90589 19 12117912 NM_145233 NP_660276 C/T V41M plus 10940970 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.15 0.15 0 120 1 116 "HapMap,freq" Borderline 1.155 43 Intolerant 0.03 2.92 400 conservative 19p13.2 zinc finger protein 625 4466 rs7273698 TNFRSF5 958 20 44190230 NM_152854 NP_690593 C/T R182W plus 16340751 693 EGP_SNPS PDR90 NIHPDR 176 0.01 0.01 0 176 1 120 "by cluster,freq" Intolerant 0.05 2.78 15 moderately radical 109535 20q12-q13.2 "tumor necrosis factor receptor superfamily, member 5" 4467 rs7277175 PCNT2 5116 21 46666369 NM_006031 NP_006022 A/G Q2361R plus 10978373 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.09 0.08 0.03 164 2 0.43 0 44 1 123 "HapMap,doubleHit,freq,cluster" conservative 605925 21q22.3 pericentrin 2 (kendrin) 4468 rs7277175 PCNT2 5116 21 46666369 NM_006031 NP_006022 A/G Q2361R plus 23558538 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.04 0.08 0.03 164 2 0.43 0 44 1 123 "HapMap,doubleHit,freq,cluster" conservative 605925 21q22.3 pericentrin 2 (kendrin) 4469 rs7288201 GGTLA1 2687 22 22945847 NM_004121 NP_004112 C/T I475V plus 11002305 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.04 0.03 0.01 164 2 0.02 0 44 1 123 "HapMap,doubleHit,freq,cluster" Intolerant 0.03 2.82 21 conservative 137168 22q11.23 gamma-glutamyltransferase-like activity 1 4470 rs7288201 GGTLA1 2687 22 22945847 NM_004121 NP_004112 C/T I475V plus 23610262 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.02 0.03 0.01 164 2 0.02 0 44 1 123 "HapMap,doubleHit,freq,cluster" Intolerant 0.03 2.82 21 conservative 137168 22q11.23 gamma-glutamyltransferase-like activity 1 4471 rs7302230 CLSTN3 9746 12 7179699 NM_014718 NP_055533 A/G S209G plus 24697852 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 123 by freq Benign 0.023 17 Tolerant 0.56 2.87 391 moderately conservative 12p13.31 calsyntenin 3 4472 rs7302981 LASS5 91012 12 48824082 NM_147190 NP_671723 A/G C75R plus 24419989 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.4 0 48 1 0.12 0.11 94 2 123 "by doubleHit,freq,cluster" Possibly damaging 1.644 13 Tolerant 0.38 2.82 24 radical 12q13.12 LAG1 longevity assurance homolog 5 (S. cerevisiae) 4473 rs7312857 BIN2 51411 12 49993893 NM_016293 NP_057377 C/T S48N plus 11048789 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.18 0.21 0.06 168 2 0.17 0 94 2 123 "HapMap,doubleHit,freq" Potentially intolerant 0.09 2.83 22 conservative 605936 12q13 bridging integrator 2 4474 rs7312857 BIN2 51411 12 49993893 NM_016293 NP_057377 C/T S48N plus 24423322 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.21 0.06 168 2 0.17 0 94 2 123 "HapMap,doubleHit,freq" Potentially intolerant 0.09 2.83 22 conservative 605936 12q13 bridging integrator 2 4475 rs7313020 BCAT1 586 12 24877007 NM_005504 NP_005495 C/T E321K plus 11049057 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.01 0.01 0.01 166 2 123 "HapMap,doubleHit,freq" Potentially damaging 1.388 23 Tolerant 0.68 2.79 40 moderately conservative 113520 12pter-q12 "branched chain aminotransferase 1, cytosolic" 4476 rs7313020 BCAT1 586 12 24877007 NM_005504 NP_005495 C/T E321K plus 24433944 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.01 0.01 166 2 123 "HapMap,doubleHit,freq" Potentially damaging 1.388 23 Tolerant 0.68 2.79 40 moderately conservative 113520 12pter-q12 "branched chain aminotransferase 1, cytosolic" 4477 rs7373165 LMLN 89782 3 199190223 NM_033029 NP_149018 G/T E106D plus 23707271 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.09 0.09 0 46 1 0.46 0 46 1 123 "by doubleHit,freq,cluster" Tolerant 0.7 2.89 17 conservative 3q29 leishmanolysin-like (metallopeptidase M8 family) 4478 rs7406910 HOXB7 3217 17 44043255 NM_004502 NP_004493 C/T T9A plus 11190642 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.12 0.12 0 120 1 123 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.542 15 moderately conservative 142962 17q21.3 homeo box B7 4479 rs7410919 LAMC1 3915 1 179826204 NM_002293 NP_002284 C/T L888P plus 23853076 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.35 0 48 1 0.44 0.06 70 2 123 "by doubleHit,freq,cluster" Probably damaging 2.55 6 moderately conservative 150290 1q31 "laminin, gamma 1 (formerly LAMB2)" 4480 rs7422339 CPS1 1373 2 211366013 NM_001875 NP_001866 A/C T1406N plus 11212944 1303 SEQUENOM CEPH CEPH (92) 92 0.22 0.22 0 92 1 123 "by doubleHit,freq,cluster" Possibly damaging 1.592 8 Tolerant 0.44 2.83 134 moderately conservative 608307 2q35 "carbamoyl-phosphate synthetase 1, mitochondrial" 4481 rs7439869 SMARCAD1 56916 4 95530957 NM_020159 NP_064544 C/T V301A plus 23915574 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.38 0 48 1 0.3 0.21 82 2 123 "by doubleHit,freq,cluster" Benign 0.079 7 moderately conservative 4q22-q23 "SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1" 4482 rs7503034 SGSH 6448 17 75798988 NM_000199 NP_000190 C/T R456H plus 24073464 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.17 0 48 1 0.36 0.06 92 2 123 "by doubleHit,freq,cluster" Borderline 1.087 10 Borderline 0.12 2.83 17 conservative 605270 17q25.3 N-sulfoglucosamine sulfohydrolase (sulfamidase) 4483 rs7516919 SIPA1L2 57568 1 228871032 NM_020808 NP_065859 A/T M1200L plus 24307620 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.23 0 48 1 0.04 0 46 1 123 by freq Potentially damaging 1.398 14 conservative 1q42.2 signal-induced proliferation-associated 1 like 2 4484 rs7527017 ROR1 4919 1 64355298 NM_005012 NP_005003 C/T T518M plus 24629260 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.35 0 48 1 0.19 0.17 94 2 123 by freq Benign 0.29 10 moderately conservative 602336 1p32-p31 receptor tyrosine kinase-like orphan receptor 1 4485 rs7528153 VAV3 10451 1 108019769 NM_006113 NP_006104 A/T T298S plus 23179921 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.19 0 48 1 0.44 0.06 94 2 123 "by doubleHit,freq,cluster" Benign 0.255 22 moderately conservative 605541 1p13.3 vav 3 oncogene 4486 rs7530511 IL23R 149233 1 67397408 NM_144701 NP_653302 C/T L310P plus 15355771 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.18 0.18 0 40 1 0.23 0 48 1 121 "by doubleHit,freq,cluster" Tolerant 0.68 2.91 305 moderately conservative 607562 1p31.3-p31.2 interleukin-23 receptor 4487 rs7535533 RGSL1 353299 1 179228486 NM_181572 NP_853550 A/G I107V plus 23856127 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.48 0.48 0 46 1 0.39 0.13 94 2 123 "by doubleHit,freq,cluster" conservative 1q25 regulator of G-protein signalling like 1 4488 rs7536561 LHX4 89884 1 176975181 NM_033343 NP_203129 A/G N328S plus 11391290 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.48 0.48 0 168 2 0.38 0.04 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.212 22 Tolerant 1 2.9 35 conservative 602146 1q25.1 LIM homeobox 4 4489 rs7536561 LHX4 89884 1 176975181 NM_033343 NP_203129 A/G N328S plus 24631758 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.48 0 168 2 0.38 0.04 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.212 22 Tolerant 1 2.9 35 conservative 602146 1q25.1 LIM homeobox 4 4490 rs7537203 CLSPN 63967 1 35895041 NM_022111 NP_071394 C/T N525S plus 11392680 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.13 0.13 0 120 1 119 "HapMap,doubleHit,freq,cluster" conservative 605434 1p34.2 claspin homolog (Xenopus laevis) 4491 rs7556132 LAMC1 3915 1 179817412 NM_002293 NP_002284 A/G I458V plus 11431206 1303 SEQUENOM CEPH CEPH (92) 92 0.31 0.32 0.03 140 2 0.44 0.06 70 2 123 "by doubleHit,freq,cluster" Benign 0.773 7 conservative 150290 1q31 "laminin, gamma 1 (formerly LAMB2)" 4492 rs7556132 LAMC1 3915 1 179817412 NM_002293 NP_002284 A/G I458V plus 23852981 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.32 0.03 140 2 0.44 0.06 70 2 123 "by doubleHit,freq,cluster" Benign 0.773 7 conservative 150290 1q31 "laminin, gamma 1 (formerly LAMB2)" 4493 rs7558074 EIF5B 9669 2 99451340 NM_015904 NP_056988 A/C K522T plus 11434921 885 TSC-CSHL HapMap-CEPH-30-trios 60 0.5 0.5 0 60 1 119 "HapMap,doubleHit,freq,cluster" moderately conservative 606086 2p11.1-q11.1 eukaryotic translation initiation factor 5B 4494 rs7565893 CD8B1 926 2 86990216 NM_172100 NP_742098 G/T P168Q plus 11449148 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.26 0.26 0 116 1 121 "HapMap,freq,cluster" moderately conservative 186730 2p12 "CD8 antigen, beta polypeptide 1 (p37)" 4495 rs7594497 PNPT1 87178 2 55784189 NM_033109 NP_149100 C/T N590D plus 23239344 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.25 0.25 94 2 123 "by doubleHit,freq,cluster" Benign 0.119 8 Tolerant 0.6 2.8 93 conservative 2p15 polyribonucleotide nucleotidyltransferase 1 4496 rs7598922 DHX57 90957 2 38993995 NM_198963 NP_945314 C/T N587S plus 24650482 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.48 0.48 0 46 1 0.23 0.13 84 2 123 "by doubleHit,freq" Benign 0.272 9 Tolerant 0.77 2.81 69 conservative 2p22.3 DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57 4497 rs7604639 MERTK 10461 2 112468159 NM_006343 NP_006334 A/G R466K plus 24311085 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.44 0 48 1 0.27 0.11 94 2 123 "by doubleHit,freq,cluster" Tolerant 0.97 2.76 38 conservative 604705 2q14.1 c-mer proto-oncogene tyrosine kinase 4498 rs7632885 CLSTN2 64084 3 141661183 NM_022131 NP_071414 A/G V366I plus 23297518 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.38 0 48 1 0.43 0.07 92 2 123 "by doubleHit,freq,cluster" Benign 0.119 18 conservative 3q23-q24 calsyntenin 2 4499 rs7640654 ZNF502 91392 3 44738041 NM_033210 NP_149987 A/C E243A plus 11586991 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.47 0.47 0 120 1 119 "HapMap,doubleHit,freq,cluster" Intolerant 0.02 2.75 97 moderately radical 3p21.32 zinc finger protein 502 4500 rs7675987 SCFD2 152579 4 53852454 NM_152540 NP_689753 A/G L512S plus 24383719 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.27 0 48 1 0.2 0.05 92 2 123 "by doubleHit,freq,cluster" moderately radical 4q12 sec1 family domain containing 2 4501 rs7698628 SPARCL1 8404 4 88773367 NM_004684 NP_004675 G/T A49D plus 11692482 1303 SEQUENOM CEPH CEPH (92) 92 0.31 0.34 0.06 140 2 0.39 0.07 92 2 123 "by doubleHit,freq,cluster" Potentially damaging 1.35 5 moderately radical 606041 4q22.1 "SPARC-like 1 (mast9, hevin)" 4502 rs7698628 SPARCL1 8404 4 88773367 NM_004684 NP_004675 G/T A49D plus 23881474 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.34 0.06 140 2 0.39 0.07 92 2 123 "by doubleHit,freq,cluster" Potentially damaging 1.35 5 moderately radical 606041 4q22.1 "SPARC-like 1 (mast9, hevin)" 4503 rs7699006 HERC5 51191 4 89754269 NM_016323 NP_057407 A/G M498V plus 23238101 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.21 0 48 1 0.18 0.11 94 2 123 "by doubleHit,freq,cluster" conservative 608242 4q22.1-q23 hect domain and RLD 5 4504 rs7700833 PCDHB8 56128 5 140538764 NM_019120 NP_061993 C/T A322V plus 23351129 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.15 0 46 1 123 "by doubleHit,freq,cluster" Possibly damaging 1.809 100 Intolerant 0.04 2.77 132 moderately conservative 606334 5q31 protocadherin beta 8 4505 rs7718054 FAT2 2196 5 150889005 NM_001447 NP_001438 C/T R3318Q plus 23296184 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.07 0.07 0 42 1 0.05 0.05 94 2 123 "by doubleHit,freq,cluster" Tolerant 0.61 2.82 16 conservative 604269 5q32-q33 FAT tumor suppressor homolog 2 (Drosophila) 4506 rs7732671 PPARGC1B 133522 5 149192436 NM_133263 NP_573570 C/G A203P plus 24658264 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 0.08 0.04 94 2 123 "by doubleHit,freq" conservative 608886 5q33.1 "peroxisome proliferative activated receptor, gamma, coactivator 1, beta" 4507 rs7761137 CAPN11 11131 6 44259468 NM_007058 NP_008989 A/G S691N plus 11813519 885 TSC-CSHL HapMap-CEPH-30-trios 112 0.23 0.23 0 112 1 116 "HapMap,doubleHit,freq" Benign 0.577 58 Tolerant 1 2.91 75 conservative 604822 6p12 calpain 11 4508 rs7761731 CYP39A1 51302 6 46671776 NM_016593 NP_057677 A/T N324K plus 23353458 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.27 0 48 1 0.29 0.01 94 2 123 "by doubleHit,freq,cluster" Tolerant 0.76 2.75 19 moderately conservative 605994 6p21.1-p11.2 "cytochrome P450, family 39, subfamily A, polypeptide 1" 4509 rs7785206 CROT 54677 7 86665674 NM_021151 NP_066974 C/G V474L plus 23472360 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.08 0.09 94 2 123 "by cluster,freq" Benign 0.747 8 Tolerant 0.3 2.77 12 conservative 606090 7q21.1 carnitine O-octanoyltransferase 4510 rs7871785 PSMB7 5695 9 124256715 NM_002799 NP_002790 A/G V39A plus 12017785 1303 SEQUENOM CEPH CEPH (92) 92 0.44 0.45 0.03 140 2 0.38 0.01 94 2 123 "by doubleHit,freq,cluster" Potentially damaging 1.477 46 Tolerant 0.63 2.81 48 moderately conservative 604030 9q34.11-q34.12 "proteasome (prosome, macropain) subunit, beta type, 7" 4511 rs7871785 PSMB7 5695 9 124256715 NM_002799 NP_002790 A/G V39A plus 24524743 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.45 0.03 140 2 0.38 0.01 94 2 123 "by doubleHit,freq,cluster" Potentially damaging 1.477 46 Tolerant 0.63 2.81 48 moderately conservative 604030 9q34.11-q34.12 "proteasome (prosome, macropain) subunit, beta type, 7" 4512 rs7900194 CYP2C9 1559 10 96692056 NM_000771 NP_000762 A/G R150H plus 12588497 693 EGP_SNPS PDR90 NIHPDR 180 0.02 0.02 0 180 1 119 "by cluster,freq" Benign 0.274 152 Tolerant 0.36 2.79 164 conservative 601130 10q24 "cytochrome P450, family 2, subfamily C, polypeptide 9" 4513 rs7901604 ECHS1 1892 10 135073007 NM_004092 NP_004083 A/G T75I plus 12074823 1303 SEQUENOM CEPH CEPH (92) 92 0.16 0.16 0 92 1 123 "by doubleHit,freq,cluster" Benign 0.278 33 moderately conservative 602292 10q26.2-q26.3 "enoyl Coenzyme A hydratase, short chain, 1, mitochondrial" 4514 rs7903344 CHUK 1147 10 101967873 NM_001278 NP_001269 C/T V268I plus 24035549 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.42 0 48 1 0.4 0.06 90 2 123 "by doubleHit,freq,cluster" Benign 0.971 12 conservative 600664 10q24-q25 conserved helix-loop-helix ubiquitous kinase 4515 rs7948666 XLKD1 10894 11 10537260 NM_006691 NP_006682 C/T V315M plus 23564140 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.04 0 46 1 123 "by cluster,freq" conservative 605702 11p15 extracellular link domain containing 1 4516 rs7955866 FGF23 8074 12 4349810 NM_020638 NP_065689 A/G T239M plus 22969966 693 EGP_SNPS PDR90 NIHPDR 180 0.17 0.16 0.02 228 2 0.1 0.01 94 2 123 "by doubleHit,freq,cluster" moderately conservative 605380 12p13.3 fibroblast growth factor 23 4517 rs7955866 FGF23 8074 12 4349810 NM_020638 NP_065689 A/G T239M plus 24694339 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.16 0.02 228 2 0.1 0.01 94 2 123 "by doubleHit,freq,cluster" moderately conservative 605380 12p13.3 fibroblast growth factor 23 4518 rs7958311 P2RX7 5027 12 120068075 NM_002562 NP_002553 A/G R270H plus 24009654 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.31 0 48 1 0.37 0.02 94 2 123 "by cluster,freq" Potentially damaging 1.312 5 Tolerant 0.55 2.92 84 conservative 602566 12q24 "purinergic receptor P2X, ligand-gated ion channel, 7" 4519 rs7986131 LMO7 4008 13 75321249 NM_005358 NP_005349 C/T M1113T plus 23954179 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.23 0 48 1 0.32 0.19 70 2 123 "by doubleHit,freq,cluster" moderately conservative 604362 13q21.33 LIM domain only 7 4520 rs7988661 LMO7 4008 13 75325348 NM_005358 NP_005349 A/C P1213Q plus 23355857 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.17 0 48 1 0.2 0 46 1 123 "by doubleHit,freq,cluster" moderately conservative 604362 13q21.33 LIM domain only 7 4521 rs7995033 MTMR6 9107 13 24729888 NM_004685 NP_004676 C/T I319V plus 24007111 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.15 0.15 0 46 1 0.36 0.11 94 2 123 "by doubleHit,freq,cluster" Benign 0.136 15 conservative 603561 13q12 myotubularin related protein 6 4522 rs7998427 SETDB2 83852 13 48948621 NM_031915 NP_114121 A/G E117G plus 23439415 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.19 0 48 1 0.28 0.11 92 2 123 "by doubleHit,freq,cluster" moderately conservative 607865 13q14 "SET domain, bifurcated 2" 4523 rs8002697 LNX2 222484 13 27041229 NM_153371 NP_699202 A/G S198P plus 23966822 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.3 0.3 0 44 1 0.4 0.06 88 2 123 "by doubleHit,freq,cluster" Probably damaging 2.1 5 Tolerant 0.32 2.9 30 moderately conservative 13q12.2 ligand of numb-protein X 2 4524 rs8010699 SYNE2 23224 14 63592596 NM_015180 NP_055995 A/G H3308R plus 12284130 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.14 0.13 0.03 166 2 0.36 0.16 94 2 123 "HapMap,doubleHit,freq,cluster" conservative 608442 14q23.2 "spectrin repeat containing, nuclear envelope 2" 4525 rs8010699 SYNE2 23224 14 63592596 NM_015180 NP_055995 A/G H3308R plus 23647994 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.09 0.13 0.03 166 2 0.36 0.16 94 2 123 "HapMap,doubleHit,freq,cluster" conservative 608442 14q23.2 "spectrin repeat containing, nuclear envelope 2" 4526 rs8010911 SYNE2 23224 14 63592427 NM_015180 NP_055995 C/G D3252H plus 23647990 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.09 0.09 0 46 1 0.36 0.16 94 2 123 "by doubleHit,freq,cluster" moderately conservative 608442 14q23.2 "spectrin repeat containing, nuclear envelope 2" 4527 rs8014538 TRIP11 9321 14 91510819 NM_004239 NP_004230 C/T G1827S plus 12291419 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.35 0.38 0.05 260 3 0.32 0.01 94 2 123 "HapMap,doubleHit,freq,cluster" moderately conservative 604505 14q31-q32 thyroid hormone receptor interactor 11 4528 rs8014538 TRIP11 9321 14 91510819 NM_004239 NP_004230 C/T G1827S plus 12291419 1303 SEQUENOM CEPH CEPH (92) 92 0.37 0.38 0.05 260 3 0.32 0.01 94 2 123 "HapMap,doubleHit,freq,cluster" moderately conservative 604505 14q31-q32 thyroid hormone receptor interactor 11 4529 rs8014538 TRIP11 9321 14 91510819 NM_004239 NP_004230 C/T G1827S plus 24599389 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.38 0.05 260 3 0.32 0.01 94 2 123 "HapMap,doubleHit,freq,cluster" moderately conservative 604505 14q31-q32 thyroid hormone receptor interactor 11 4530 rs8018720 SEC23A 10484 14 38625936 NM_006364 NP_006355 C/G L211V plus 12299296 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.13 0.12 0.02 168 2 0.22 0.13 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.442 33 Tolerant 0.38 2.9 42 conservative 14q13.3 Sec23 homolog A (S. cerevisiae) 4531 rs8018720 SEC23A 10484 14 38625936 NM_006364 NP_006355 C/G L211V plus 24118853 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.12 0.02 168 2 0.22 0.13 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.442 33 Tolerant 0.38 2.9 42 conservative 14q13.3 Sec23 homolog A (S. cerevisiae) 4532 rs8050871 ZNF19 7567 16 70067297 NM_006961 NP_008892 C/G Q218H plus 23414322 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.4 0 48 1 0.43 0.04 94 2 123 "by doubleHit,freq,cluster" Intolerant 0.04 2.77 57 conservative 194525 16q22 zinc finger protein 19 (KOX 12) 4533 rs8065506 ZNF624 57547 17 16468520 NM_020787 NP_065838 A/C K135N plus 12386386 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.28 0.27 0.01 166 2 0.42 0.06 94 2 123 "HapMap,doubleHit,freq,cluster" moderately conservative 17p11.2 zinc finger protein 624 4534 rs8065506 ZNF624 57547 17 16468520 NM_020787 NP_065838 A/C K135N plus 24008833 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.26 0.27 0.01 166 2 0.42 0.06 94 2 123 "HapMap,doubleHit,freq,cluster" moderately conservative 17p11.2 zinc finger protein 624 4535 rs8069315 DHX33 56919 17 5307671 NM_020162 NP_064547 A/G R118C plus 23625827 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.09 0.09 0 46 1 0.09 0.09 90 2 123 "by doubleHit,freq,cluster" Probably damaging 2.257 5 Intolerant 0.02 2.77 98 radical 17p13.3 DEAH (Asp-Glu-Ala-His) box polypeptide 33 4536 rs8069344 GUCY2D 3000 17 7858004 NM_000180 NP_000171 A/T L782H plus 12393066 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.13 0.13 0 120 1 116 "HapMap,doubleHit,freq" Probably damaging 2.559 20 Tolerant 0.25 2.77 33 moderately conservative 600179 17p13.1 "guanylate cyclase 2D, membrane (retina-specific)" 4537 rs8074498 ASPSCR1 79058 17 77547833 NM_024083 NP_076988 A/T L252Q plus 12402152 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.43 0.43 0 120 1 120 "HapMap,freq,cluster" Tolerant 0.25 3.01 9 moderately radical 606236 17q25 "alveolar soft part sarcoma chromosome region, candidate 1" 4538 rs8077302 COX10 1352 17 13921075 NM_001303 NP_001294 A/G R159Q plus 12407037 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.38 0.39 0.03 168 2 0.34 0.16 92 2 123 "HapMap,doubleHit,freq,cluster" Tolerant 1 2.8 18 conservative 602125 17p12-17p11.2 "COX10 homolog, cytochrome c oxidase assembly protein, heme A: farnesyltransferase (yeast)" 4539 rs8077302 COX10 1352 17 13921075 NM_001303 NP_001294 A/G R159Q plus 23618057 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.39 0.03 168 2 0.34 0.16 92 2 123 "HapMap,doubleHit,freq,cluster" Tolerant 1 2.8 18 conservative 602125 17p12-17p11.2 "COX10 homolog, cytochrome c oxidase assembly protein, heme A: farnesyltransferase (yeast)" 4540 rs8080100 HELZ 9931 17 62642504 XM_375485 XP_375485 C/T V74M plus 12411961 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.16 0.14 0.04 190 3 0.25 0.1 157 5 123 "HapMap,freq,cluster" conservative 606699 17q24.3 helicase with zinc finger domain 4541 rs8080100 HELZ 9931 17 62642504 XM_375485 XP_375485 C/T V74M plus 14911206 902 AFFY Caucasian 22 0.05 0.14 0.04 190 3 0.25 0.1 157 5 123 "HapMap,freq,cluster" conservative 606699 17q24.3 helicase with zinc finger domain 4542 rs8080100 HELZ 9931 17 62642504 XM_375485 XP_375485 C/T V74M plus 23627554 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.14 0.04 190 3 0.25 0.1 157 5 123 "HapMap,freq,cluster" conservative 606699 17q24.3 helicase with zinc finger domain 4543 rs8082898 EPB41L3 23136 18 5406160 NM_012307 NP_036439 C/T Y575C plus 24546024 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 0.06 0.01 92 2 123 by freq radical 605331 18p11.32 erythrocyte membrane protein band 4.1-like 3 4544 rs8091003 DSG1 1828 18 27173777 NM_001942 NP_001933 A/C N493T plus 23766610 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.25 0.25 94 2 123 "by doubleHit,freq,cluster" Benign 0.509 10 Tolerant 0.44 2.8 28 moderately conservative 125670 18q12.1 desmoglein 1 4545 rs8091117 DSG1 1828 18 27173792 NM_001942 NP_001933 A/C T498N plus 23766614 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.23 0.22 94 2 123 "by doubleHit,freq,cluster" Potentially damaging 1.344 10 Tolerant 0.33 2.81 26 moderately conservative 125670 18q12.1 desmoglein 1 4546 rs8097425 SERPINB10 5273 18 59733847 NM_005024 NP_005015 A/G I41M plus 24058571 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.19 0 48 1 0.34 0.11 94 2 123 "by doubleHit,freq,cluster" Tolerant 1 2.76 59 conservative 602058 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10" 4547 rs8100856 ATP8B3 148229 19 1747166 NM_138813 NP_620168 C/T V618I plus 12451295 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.2 0.2 0.01 162 2 0.24 0.12 84 2 123 "HapMap,doubleHit,freq,cluster" Tolerant 0.63 2.83 24 conservative 605866 19p13.3 "ATPase, Class I, type 8B, member 3" 4548 rs8100856 ATP8B3 148229 19 1747166 NM_138813 NP_620168 C/T V618I plus 24123665 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.21 0.2 0.01 162 2 0.24 0.12 84 2 123 "HapMap,doubleHit,freq,cluster" Tolerant 0.63 2.83 24 conservative 605866 19p13.3 "ATPase, Class I, type 8B, member 3" 4549 rs8104890 ZNF614 80110 19 57211420 NM_025040 NP_079316 C/T V415I plus 12458406 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.24 0.24 0.01 162 2 0.32 0.02 94 2 123 "HapMap,doubleHit,freq" Benign 0.315 6 Tolerant 1 2.73 45 conservative 19q13.41 zinc finger protein 614 4550 rs8104890 ZNF614 80110 19 57211420 NM_025040 NP_079316 C/T V415I plus 24199238 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.23 0.24 0.01 162 2 0.32 0.02 94 2 123 "HapMap,doubleHit,freq" Benign 0.315 6 Tolerant 1 2.73 45 conservative 19q13.41 zinc finger protein 614 4551 rs8110220 DHRS10 51171 19 54030910 NM_016246 NP_057330 C/T N31D plus 23812929 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.34 0.34 0 44 1 0.28 0.11 90 2 123 "by doubleHit,freq,cluster" Tolerant 0.66 2.78 14 conservative 19q13.33 dehydrogenase/reductase (SDR family) member 10 4552 rs8110904 CEACAM1 634 19 47723209 NM_001712 NP_001703 A/G A83V plus 12469171 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.01 0.01 0 120 1 123 "HapMap,doubleHit,cluster" Benign 0.643 25 Tolerant 1 2.81 70 moderately conservative 109770 19q13.2 carcinoembryonic antigen-related cell adhesion molecule 1 (biliary glycoprotein) 4553 rs8128440 NDUFV3 4731 21 43197434 NM_021075 NP_066553 A/G D398N plus 12504022 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.32 0.34 0.06 162 2 0.2 0 90 2 123 "HapMap,doubleHit,freq,cluster" conservative 602184 21q22.3 "NADH dehydrogenase (ubiquinone) flavoprotein 3, 10kDa" 4554 rs8128440 NDUFV3 4731 21 43197434 NM_021075 NP_066553 A/G D398N plus 24605489 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.41 0.34 0.06 162 2 0.2 0 90 2 123 "HapMap,doubleHit,freq,cluster" conservative 602184 21q22.3 "NADH dehydrogenase (ubiquinone) flavoprotein 3, 10kDa" 4555 rs8133052 CBR3 874 21 36429371 NM_001236 NP_001227 A/G C4Y plus 24219547 1371 PERLEGEN AFD_EUR_PANEL European American (24) 36 0.36 0.36 0 36 1 0.37 0.15 84 2 123 "by doubleHit,freq,cluster" Borderline 1.178 21 Tolerant 0.57 3.06 20 radical 603608 21q22.2 carbonyl reductase 3 4556 rs8176344 CYP27B1 1594 12 56445440 NM_000785 NP_000776 C/G V166L minus 8486489 693 EGP_SNPS PDR90 NIHPDR 160 0.02 0.02 0 160 1 117 by freq Borderline 1.047 7 Tolerant 0.26 2.76 20 conservative 264700 12q13.1-q13.3 "cytochrome P450, family 27, subfamily B, polypeptide 1" 4557 rs8176786 NELL1 4745 11 20915970 NM_006157 NP_006148 C/T R354W plus 24148029 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.05 0.03 134 3 123 "by cluster,freq" Probably damaging 2.011 16 Borderline 0.18 2.83 38 moderately radical 602319 11p15.2-p15.1 NEL-like 1 (chicken) 4558 rs8176919 DNASE1 1773 16 3646698 NM_005223 NP_005214 A/G G127R plus 8819934 506 NCBI NIHPDR NIHPDR 154 0.01 0.01 0 154 1 0.02 0.04 206 2 123 "by cluster,freq" Probably damaging 2.065 24 Intolerant 0.01 2.8 40 moderately radical 125505 16p13.3 deoxyribonuclease I 4559 rs8176927 DNASE1 1773 16 3645381 NM_005223 NP_005214 G/T R2S plus 8819942 506 NCBI NIHPDR NIHPDR 178 0.04 0.04 0 178 1 0.03 0 174 1 120 "HapMap,freq,cluster" moderately radical 125505 16p13.3 deoxyribonuclease I 4560 rs8178318 LPO 4025 17 53679987 NM_006151 NP_006142 C/T T105I plus 9806368 693 EGP_SNPS PDR90 NIHPDR 176 0.03 0.03 0 176 1 0.07 0 46 1 123 "by cluster,freq" Potentially damaging 1.471 20 Potentially intolerant 0.09 2.77 33 moderately conservative 150205 17q23.1 lactoperoxidase 4561 rs8178338 LPO 4025 17 53682931 NM_006151 NP_006142 A/G A244T plus 9806390 693 EGP_SNPS PDR90 NIHPDR 176 0.01 0.01 0 176 1 0.04 0 48 1 123 by freq Benign 0.037 20 Tolerant 0.34 2.77 33 moderately conservative 150205 17q23.1 lactoperoxidase 4562 rs8178847 APOH 350 17 61647277 NM_000042 NP_000033 A/G R154H minus 9807015 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 44 0.07 0.07 0 44 1 0.05 0 44 1 117 by freq Potentially damaging 1.397 12 conservative 138700 17q23-qter apolipoprotein H (beta-2-glycoprotein I) 4563 rs8178967 GPX4 2879 19 1055047 NM_002085 NP_002076 A/G S2N plus 9807170 693 EGP_SNPS PDR90 NIHPDR 156 0.04 0.04 0 156 1 117 by freq Benign 0.675 9 conservative 138322 19p13.3 glutathione peroxidase 4 (phospholipid hydroperoxidase) 4564 rs8179183 LEPR 3953 1 65787973 NM_002303 NP_002294 C/G K656N plus 12568604 887 CUORCGL AMERICAN CAUCASIANS American Caucasians 1775 0.18 0.18 0.01 1959 2 123 "by cluster,freq" Possibly damaging 1.497 29 Borderline 0.14 2.94 48 moderately conservative 601007 1p31 leptin receptor 4565 rs8179183 LEPR 3953 1 65787973 NM_002303 NP_002294 C/G K656N plus 24796666 1303 SEQUENOM CEPH CEPH (92) 184 0.2 0.18 0.01 1959 2 123 "by cluster,freq" Possibly damaging 1.497 29 Borderline 0.14 2.94 48 moderately conservative 601007 1p31 leptin receptor 4566 rs8187710 ABCC2 1244 10 101601284 NM_000392 NP_000383 A/G C1515Y plus 23597239 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.13 0.04 530 2 123 "by cluster,freq" Probably damaging 2.298 12 Tolerant 0.85 2.79 51 radical 601107 10q24 "ATP-binding cassette, sub-family C (CFTR/MRP), member 2" 4567 rs8190955 GSR 2936 8 30685166 NM_000637 NP_000628 C/T R110C minus 12584758 693 EGP_SNPS PDR90 NIHPDR 172 0.03 0.03 0 172 1 117 by freq Probably damaging 2.572 32 radical 138300 8p21.1 glutathione reductase 4568 rs8190976 GSR 2936 8 30677141 NM_000637 NP_000628 A/G G189S minus 12584781 693 EGP_SNPS PDR90 NIHPDR 170 0.01 0.01 0 170 1 117 by freq Benign 0.338 32 moderately conservative 138300 8p21.1 glutathione reductase 4569 rs8191136 HSD17B2 3294 16 80659371 NM_002153 NP_002144 A/G A121T plus 12584980 693 EGP_SNPS PDR90 NIHPDR 176 0.01 0.01 0 176 1 0.02 0 46 1 123 "by cluster,freq" Intolerant 0.02 2.8 30 moderately conservative 109685 16q24.1-q24.2 hydroxysteroid (17-beta) dehydrogenase 2 4570 rs8191246 HSD17B2 3294 16 80689541 NM_002153 NP_002144 A/G STOP388W plus 12585112 693 EGP_SNPS PDR90 NIHPDR 178 0.03 0.03 0 178 1 0.02 0 94 2 123 "by cluster,freq" Probably damaging Intolerant radical 109685 16q24.1-q24.2 hydroxysteroid (17-beta) dehydrogenase 2 4571 rs8191371 GPI 2821 19 39560616 NM_000175 NP_000166 C/T I208T plus 12585263 693 EGP_SNPS PDR90 NIHPDR 174 0.02 0.02 0.01 220 2 123 by freq Probably damaging 2.228 122 Intolerant 0 2.76 229 moderately conservative 172400 19q13.1 glucose phosphate isomerase 4572 rs8191371 GPI 2821 19 39560616 NM_000175 NP_000166 C/T I208T plus 24527843 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.04 0.02 0.01 220 2 123 by freq Probably damaging 2.228 122 Intolerant 0 2.76 229 moderately conservative 172400 19q13.1 glucose phosphate isomerase 4573 rs8191746 IGF2R 3482 6 160416109 NM_000876 NP_000867 C/T P203L plus 12585723 693 EGP_SNPS PDR90 NIHPDR 176 0.02 0.02 0 176 1 117 by freq Probably damaging 2.199 17 moderately conservative 147280 6q26 insulin-like growth factor 2 receptor 4574 rs8191754 IGF2R 3482 6 160418735 NM_000876 NP_000867 C/G L252V plus 12585734 693 EGP_SNPS PDR90 NIHPDR 174 0.14 0.16 0.04 222 2 0.18 0.07 94 2 123 "by cluster,freq" Potentially damaging 1.343 17 Borderline 0.14 3.09 25 conservative 147280 6q26 insulin-like growth factor 2 receptor 4575 rs8191754 IGF2R 3482 6 160418735 NM_000876 NP_000867 C/G L252V plus 24053159 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.16 0.04 222 2 0.18 0.07 94 2 123 "by cluster,freq" Potentially damaging 1.343 17 Borderline 0.14 3.09 25 conservative 147280 6q26 insulin-like growth factor 2 receptor 4576 rs8191797 IGF2R 3482 6 160437232 NM_000876 NP_000867 A/G G604S plus 12585792 693 EGP_SNPS PDR90 NIHPDR 180 0.01 0.01 0 180 1 117 by freq Benign 0.523 15 Tolerant 0.65 2.99 28 moderately conservative 147280 6q26 insulin-like growth factor 2 receptor 4577 rs8191819 IGF2R 3482 6 160441967 NM_000876 NP_000867 A/G G856S plus 12585826 693 EGP_SNPS PDR90 NIHPDR 178 0.02 0.02 0 178 1 117 by freq Potentially damaging 1.37 17 Borderline 0.2 2.96 26 moderately conservative 147280 6q26 insulin-like growth factor 2 receptor 4578 rs8191842 IGF2R 3482 6 160453003 NM_000876 NP_000867 C/T T1107M plus 12585853 693 EGP_SNPS PDR90 NIHPDR 180 0.02 0.02 0 180 1 117 by freq Potentially damaging 1.348 17 Borderline 0.18 2.99 28 moderately conservative 147280 6q26 insulin-like growth factor 2 receptor 4579 rs8191844 IGF2R 3482 6 160453340 NM_000876 NP_000867 C/G T1184S plus 12585855 693 EGP_SNPS PDR90 NIHPDR 178 0.01 0.01 0 178 1 117 by freq Possibly damaging 1.6 17 Tolerant 0.32 3.02 28 moderately conservative 147280 6q26 insulin-like growth factor 2 receptor 4580 rs8192111 MGST2 4258 4 140982286 NM_002413 NP_002404 C/T A101V plus 12586204 693 EGP_SNPS PDR90 NIHPDR 176 0.01 0.01 0 176 1 117 by freq Borderline 0.19 2.81 18 moderately conservative 601733 4q28.3 microsomal glutathione S-transferase 2 4581 rs8192284 IL6R 3570 1 151240043 NM_000565 NP_000556 A/C D358A plus 16338697 1120 WIPGA POP-WIPGA-12-05-2003 CORIELL Mixed 60 0.25 0.25 0 60 1 0.42 0 600 1 120 "by doubleHit,freq,cluster" Potentially damaging 1.432 5 Tolerant 0.66 2.9 11 moderately radical 147880 1q21 interleukin 6 receptor 4582 rs8192297 ANPEP 290 15 88145356 NM_001150 NP_001141 A/G I603M minus 23530830 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.17 0 48 1 0.18 0.05 94 2 123 "by doubleHit,freq,cluster" Benign 0.01 14 Tolerant 0.22 2.77 26 conservative 151530 15q25-q26 "alanyl (membrane) aminopeptidase (aminopeptidase N, aminopeptidase M, microsomal aminopeptidase, CD13, p150)" 4583 rs8192506 DBI 1622 2 119846071 NM_020548 NP_065438 A/G M88V plus 24318039 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 123 by freq Potentially damaging 1.483 27 Potentially intolerant 0.07 2.82 93 conservative 125950 2q12-q21 "diazepam binding inhibitor (GABA receptor modulator, acyl-Coenzyme A binding protein)" 4584 rs8192548 MFNG 4242 22 36190563 NM_002405 NP_002396 C/T R302C minus 12586875 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.14 0.11 0.06 168 2 123 "HapMap,freq" Probably damaging 2.332 24 radical 602577 22q12 manic fringe homolog (Drosophila) 4585 rs8192548 MFNG 4242 22 36190563 NM_002405 NP_002396 C/T R302C minus 24601914 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.11 0.06 168 2 123 "HapMap,freq" Probably damaging 2.332 24 radical 602577 22q12 manic fringe homolog (Drosophila) 4586 rs8192678 PPARGC1A 10891 4 23491931 NM_013261 NP_037393 A/G G482S minus 12587287 928 IBARROSO ELY UK (Ely region of East Anglia) 921 0.36 0.36 0.01 969 2 0.27 0.16 94 2 123 "by doubleHit,freq,cluster" Benign 0.146 6 moderately conservative 604517 4p15.1 "peroxisome proliferative activated receptor, gamma, coactivator 1, alpha" 4587 rs8192678 PPARGC1A 10891 4 23491931 NM_013261 NP_037393 A/G G482S minus 23944454 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.36 0.01 969 2 0.27 0.16 94 2 123 "by doubleHit,freq,cluster" Benign 0.146 6 moderately conservative 604517 4p15.1 "peroxisome proliferative activated receptor, gamma, coactivator 1, alpha" 4588 rs8192683 ENPP1 5167 6 132253223 NM_006208 NP_006199 C/G R834T plus 12587307 928 IBARROSO ELY UK (Ely region of East Anglia) 921 0.01 0.01 0 921 1 117 by freq Borderline 1.225 10 Tolerant 0.29 3.06 23 moderately conservative 173335 6q22-q23 ectonucleotide pyrophosphatase/phosphodiesterase 1 4589 rs8192690 ABCC8 6833 11 17371146 NM_000352 NP_000343 A/G V1572I minus 12587333 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.08 0.07 0 1041 2 117 "HapMap,freq" Benign 0.822 18 Tolerant 0.65 2.8 45 conservative 600509 11p15.1 "ATP-binding cassette, sub-family C (CFTR/MRP), member 8" 4590 rs8192690 ABCC8 6833 11 17371146 NM_000352 NP_000343 A/G V1572I minus 12587333 928 IBARROSO ELY UK (Ely region of East Anglia) 921 0.07 0.07 0 1041 2 117 "HapMap,freq" Benign 0.822 18 Tolerant 0.65 2.8 45 conservative 600509 11p15.1 "ATP-binding cassette, sub-family C (CFTR/MRP), member 8" 4591 rs8192708 PCK1 5105 20 55572027 NM_002591 NP_002582 A/G I267V plus 12587404 928 IBARROSO ELY UK (Ely region of East Anglia) 921 0.12 0.12 0.01 969 2 0.07 0 46 1 123 "by cluster,freq" Possibly damaging 1.546 53 conservative 261680 20q13.31 phosphoenolpyruvate carboxykinase 1 (soluble) 4592 rs8192708 PCK1 5105 20 55572027 NM_002591 NP_002582 A/G I267V plus 24451444 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.12 0.01 969 2 0.07 0 46 1 123 "by cluster,freq" Possibly damaging 1.546 53 conservative 261680 20q13.31 phosphoenolpyruvate carboxykinase 1 (soluble) 4593 rs8192917 GZMB 3002 14 24172000 NM_004131 NP_004122 A/G R55Q minus 23799430 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.19 0 48 1 0.34 0.16 94 2 123 "by doubleHit,freq,cluster" Benign 0.382 51 conservative 123910 14q11.2 "granzyme B (granzyme 2, cytotoxic T-lymphocyte-associated serine esterase 1)" 4594 rs9262138 DHX16 8449 6 30735846 NM_003587 NP_003578 C/T D566G plus 23415058 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.04 0 46 1 123 "by cluster,freq" Possibly damaging 1.766 13 Borderline 0.12 2.8 49 moderately conservative 603405 6p21.3 DEAH (Asp-Glu-Ala-His) box polypeptide 16 4595 rs9272430 HLA-DQA1 3117 6 32713235 NM_002122 NP_002113 A/C L8M plus 24796310 1303 SEQUENOM CEPH CEPH (92) 184 0.13 0.13 0 184 1 123 by freq Benign 0.792 54 Tolerant 0.29 3.21 145 conservative 146880 6p21.3 "major histocompatibility complex, class II, DQ alpha 1" 4596 rs9272745 HLA-DQA1 3117 6 32717784 NM_002122 NP_002113 C/T T130I plus 24816074 1303 SEQUENOM CEPH CEPH (92) 184 0.39 0.39 0 184 1 123 by freq Benign 0.062 191 Tolerant 0.64 2.84 305 moderately conservative 146880 6p21.3 "major histocompatibility complex, class II, DQ alpha 1" 4597 rs9272793 HLA-DQA1 3117 6 32718473 NM_002122 NP_002113 A/G Q241R plus 24796311 1303 SEQUENOM CEPH CEPH (92) 184 0.06 0.1 0.06 368 2 123 "by cluster,freq" Benign 0.218 162 Tolerant 0.81 2.84 257 conservative 146880 6p21.3 "major histocompatibility complex, class II, DQ alpha 1" 4598 rs9272793 HLA-DQA1 3117 6 32718473 NM_002122 NP_002113 A/G Q241R plus 24816235 1303 SEQUENOM CEPH CEPH (92) 184 0.14 0.1 0.06 368 2 123 "by cluster,freq" Benign 0.218 162 Tolerant 0.81 2.84 257 conservative 146880 6p21.3 "major histocompatibility complex, class II, DQ alpha 1" 4599 rs9282553 ABCA6 23460 17 64619957 NM_080284 NP_525023 C/G M698I minus 12674809 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.08 0.06 0.02 182 2 0.22 0.13 338 4 123 "HapMap,freq" Benign 0.15 14 Tolerant 0.34 2.84 32 conservative 17q24.3 "ATP-binding cassette, sub-family A (ABC1), member 6" 4600 rs9282553 ABCA6 23460 17 64619957 NM_080284 NP_525023 C/G M698I minus 13747705 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.05 0.06 0.02 182 2 0.22 0.13 338 4 123 "HapMap,freq" Benign 0.15 14 Tolerant 0.34 2.84 32 conservative 17q24.3 "ATP-binding cassette, sub-family A (ABC1), member 6" 4601 rs9282564 ABCB1 5243 7 86874091 NM_000927 NP_000918 A/G N21D minus 12674822 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.06 0.06 0 62 1 0.04 0.02 346 4 123 by freq Potentially damaging 1.248 13 Tolerant 0.67 3.02 26 conservative 171050 7q21.1 "ATP-binding cassette, sub-family B (MDR/TAP), member 1" 4602 rs9282628 CBR3 874 21 36429610 NM_001236 NP_001227 C/G L84V plus 12674900 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.02 0.02 0 60 1 0.02 0.01 298 3 118 by freq Benign 0.58 32 Borderline 0.14 2.83 36 conservative 603608 21q22.2 carbonyl reductase 3 4603 rs9282671 CYP1B1 1545 2 38213942 NM_000104 NP_000095 A/T Y81N minus 12674945 775 SNP500CANCER CAUC1 Caucasian (31) 60 0.02 0.02 0 60 1 0.01 0 202 1 118 by freq Probably damaging 2.616 9 Intolerant 0 2.79 90 moderately radical 601771 2p21 "cytochrome P450, family 1, subfamily B, polypeptide 1" 4604 rs9282681 FANCA 2175 16 88333415 NM_000135 NP_000126 A/G T1328A minus 12674957 775 SNP500CANCER CAUC1 Caucasian (31) 58 0.07 0.07 0 58 1 0.07 0.03 294 3 123 by freq moderately conservative 607139 16q24.3 "Fanconi anemia, complementation group A" 4605 rs9282731 IGFALS 3483 16 1780778 NM_004970 NP_004961 C/T R548W minus 12675011 775 SNP500CANCER CAUC1 Caucasian (31) 54 0.04 0.04 0 54 1 0.09 0.05 290 3 118 by freq Probably damaging 2.495 7 Intolerant 0.05 2.87 12 moderately radical 601489 16p13.3 "insulin-like growth factor binding protein, acid labile subunit" 4606 rs9282734 IGFBP3 3486 7 45730209 NM_000598 NP_000589 A/C H158P minus 12675014 775 SNP500CANCER CAUC1 Caucasian (31) 62 0.07 0.07 0 62 1 0.05 0.01 346 4 118 by freq Borderline 1.146 19 Tolerant 0.34 2.82 33 moderately conservative 146732 7p13-p12 insulin-like growth factor binding protein 3 4607 rs9283633 SI 6476 3 166265867 NM_001041 NP_001032 C/T T231A plus 13480520 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.33 0.33 0 120 1 121 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.625 13 moderately conservative 222900 3q25.2-q26.2 sucrase-isomaltase (alpha-glucosidase) 4608 rs9288513 PECR 55825 2 216729525 NM_018441 NP_060911 A/T F297L plus 14889099 902 AFFY Caucasian 24 0.08 0.09 0.01 84 3 0.27 0.06 166 5 123 "by cluster,freq" conservative 605843 2q35 peroxisomal trans-2-enoyl-CoA reductase 4609 rs9288513 PECR 55825 2 216729525 NM_018441 NP_060911 A/T F297L plus 14889099 904 AFFY CEPH 12 0.08 0.09 0.01 84 3 0.27 0.06 166 5 123 "by cluster,freq" conservative 605843 2q35 peroxisomal trans-2-enoyl-CoA reductase 4610 rs9288513 PECR 55825 2 216729525 NM_018441 NP_060911 A/T F297L plus 23291931 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.09 0.01 84 3 0.27 0.06 166 5 123 "by cluster,freq" conservative 605843 2q35 peroxisomal trans-2-enoyl-CoA reductase 4611 rs9296419 POLH 5429 6 43689563 NM_006502 NP_006493 C/T T478M plus 12709524 693 EGP_SNPS PDR90 NIHPDR 178 0.01 0.01 0 178 1 0.04 0 48 1 119 "by cluster,freq" Possibly damaging 1.725 5 Intolerant 0.03 2.83 15 moderately conservative 603968 6p21.1 "polymerase (DNA directed), eta" 4612 rs9297605 TAF2 6873 8 120872818 NM_003184 NP_003175 C/G S447T plus 24411593 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.35 0 48 1 0.26 0.05 94 2 123 "by cluster,freq" Borderline 1.013 8 moderately conservative 604912 8q24.12 "TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa" 4613 rs9298814 IFNA17 3451 9 21217622 NM_021268 NP_067091 G/T I184R minus 12709272 683 O_LEUT HUTTERITE USA Caucasians (German ancestry) 1386 0.18 0.17 0.03 1570 2 123 "by doubleHit,freq,cluster" Probably damaging 2.749 163 Tolerant 1 2.95 160 moderately conservative 147583 9p22 "interferon, alpha 17" 4614 rs9298814 IFNA17 3451 9 21217622 NM_021268 NP_067091 G/T I184R minus 24812379 1303 SEQUENOM CEPH CEPH (92) 184 0.12 0.17 0.03 1570 2 123 "by doubleHit,freq,cluster" Probably damaging 2.749 163 Tolerant 1 2.95 160 moderately conservative 147583 9p22 "interferon, alpha 17" 4615 rs9306198 BCL2L13 23786 22 16584474 NM_015367 NP_056182 C/T P360S plus 14867081 902 AFFY Caucasian 24 0.25 0.22 0.11 78 3 0.05 0.02 94 2 123 by freq Possibly damaging 1.849 6 moderately conservative 22q11 BCL2-like 13 (apoptosis facilitator) 4616 rs9306198 BCL2L13 23786 22 16584474 NM_015367 NP_056182 C/T P360S plus 14867081 904 AFFY CEPH 6 0.5 0.22 0.11 78 3 0.05 0.02 94 2 123 by freq Possibly damaging 1.849 6 moderately conservative 22q11 BCL2-like 13 (apoptosis facilitator) 4617 rs9306198 BCL2L13 23786 22 16584474 NM_015367 NP_056182 C/T P360S plus 24700974 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.22 0.11 78 3 0.05 0.02 94 2 123 by freq Possibly damaging 1.849 6 moderately conservative 22q11 BCL2-like 13 (apoptosis facilitator) 4618 rs9318600 ADPRTL1 143 13 23966808 NM_006437 NP_006428 A/T F215Y plus 24445498 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.15 0.15 0 46 1 0.07 0.02 154 4 123 "by doubleHit,freq" conservative 607519 13q11 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1 4619 rs9323183 CDKL1 8814 14 49866631 NM_004196 NP_004187 C/G L330V plus 16342989 693 EGP_SNPS PDR90 NIHPDR 178 0.02 0.02 0 178 1 120 "by cluster,freq" Borderline 1.18 9 conservative 603441 14q22.1 cyclin-dependent kinase-like 1 (CDC2-related kinase) 4620 rs9324700 FAT2 2196 5 150926629 NM_001447 NP_001438 A/G F686S plus 24686768 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.48 0.48 0 44 1 0.35 0.06 74 2 123 "by doubleHit,freq,cluster" radical 604269 5q32-q33 FAT tumor suppressor homolog 2 (Drosophila) 4621 rs9325593 SNCG 6623 10 88712378 NM_003087 NP_003078 A/T E110V plus 24647118 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.25 0 48 1 0.11 0.13 94 2 123 "by doubleHit,freq" moderately radical 602998 10q23.2-q23.3 "synuclein, gamma (breast cancer-specific protein 1)" 4622 rs9332739 C2 717 6 32011783 NM_000063 NP_000054 C/G E318D plus 12674494 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.09 0.09 0 46 1 119 by freq Borderline 1.042 7 Tolerant 0.6 2.79 25 conservative 217000 6p21.3 complement component 2 4623 rs9332745 MLL 4297 11 117812526 NM_005933 NP_005924 C/G A30G plus 12674503 693 EGP_SNPS PDR90 NIHPDR 154 0.03 0.03 0 154 1 119 by freq moderately conservative 159555 11q23 "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)" 4624 rs9332747 MLL 4297 11 117812595 NM_005933 NP_005924 C/T A53V plus 12674505 693 EGP_SNPS PDR90 NIHPDR 172 0.03 0.03 0 172 1 119 by freq moderately conservative 159555 11q23 "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)" 4625 rs9332838 MLL 4297 11 117878887 NM_005933 NP_005924 C/G P2354R plus 12674611 693 EGP_SNPS PDR90 NIHPDR 178 0.01 0.01 0 178 1 119 by freq Possibly damaging 1.785 5 moderately radical 159555 11q23 "myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)" 4626 rs9333269 ITGA8 8516 10 15689704 XM_167711 XP_167711 A/C Q711P minus 12676090 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.07 0.07 0 92 2 120 "by cluster,freq" moderately conservative 604063 10p13 "integrin, alpha 8" 4627 rs9333269 ITGA8 8516 10 15689704 XM_167711 XP_167711 A/C Q711P minus 16361675 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.07 0.07 0 92 2 120 "by cluster,freq" moderately conservative 604063 10p13 "integrin, alpha 8" 4628 rs9333554 POLH 5429 6 43689881 NM_006502 NP_006493 C/T L584P plus 12709526 693 EGP_SNPS PDR90 NIHPDR 160 0.01 0.01 0 160 1 119 by freq Potentially intolerant 0.09 2.96 12 moderately conservative 603968 6p21.1 "polymerase (DNA directed), eta" 4629 rs9333555 POLH 5429 6 43689913 NM_006502 NP_006493 A/G M595V plus 12709527 693 EGP_SNPS PDR90 NIHPDR 160 0.03 0.03 0 160 1 119 by freq conservative 603968 6p21.1 "polymerase (DNA directed), eta" 4630 rs9353689 MDN1 23195 6 90447164 NM_014611 NP_055426 A/C A4044S plus 12805748 885 TSC-CSHL HapMap-CEPH-30-trios 110 0.42 0.42 0 110 1 121 "HapMap,doubleHit,freq,cluster" moderately conservative 6q15 "MDN1, midasin homolog (yeast)" 4631 rs9369738 GPR115 221393 6 47790563 NM_153838 NP_722580 A/C K598N plus 23335395 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 0.28 0.11 88 2 123 "by doubleHit,freq,cluster" Tolerant 0.55 2.84 29 moderately conservative 6p12.3 G protein-coupled receptor 115 4632 rs9373985 FHL5 9457 6 97170243 NM_020482 NP_065228 C/G S243R plus 23369363 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.35 0 48 1 0.36 0.13 94 2 123 "by doubleHit,freq,cluster" Probably damaging 2.101 17 Tolerant 1 2.86 51 moderately radical 605126 6q16.1-q16.3 four and a half LIM domains 5 4633 rs9381594 GPR111 222611 6 47757653 NM_153839 NP_722581 A/G I467V plus 23334554 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.31 0 48 1 0.35 0.08 94 2 123 "by doubleHit,freq,cluster" Tolerant 0.41 2.75 31 conservative 6p12.3 G protein-coupled receptor 111 4634 rs9382658 DST 667 6 56579361 NM_020388 NP_065121 A/G P2138L plus 23348342 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.38 0 48 1 0.35 0.15 94 2 123 "by doubleHit,freq,cluster" moderately conservative 113810 6p12-p11 "bullous pemphigoid antigen 1, 230/240kDa" 4635 rs9390698 HELIC1 10973 6 101403110 NM_006828 NP_006819 A/G L146F plus 24378963 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.44 0 48 1 0.22 0.08 92 2 123 by freq conservative 6q16 "helicase, ATP binding 1" 4636 rs9449444 IBTK 25998 6 82957530 XM_371835 XP_371835 A/G A1185V plus 24485758 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.27 0 48 1 0.24 0.02 94 2 123 "by doubleHit,freq" Tolerant 1 2.83 11 moderately conservative 606457 6q14.3 inhibitor of Bruton agammaglobulinemia tyrosine kinase 4637 rs9462088 FANCE 2178 6 35538664 NM_021922 NP_068741 A/G A502T plus 23720125 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.2 0.1 92 2 123 "by cluster,freq" moderately conservative 600901 6p21-p22 "Fanconi anemia, complementation group E" 4638 rs9469203 HLA-DQA1 3117 6 32713244 NM_002122 NP_002113 A/G A11T plus 24816025 1303 SEQUENOM CEPH CEPH (92) 184 0.06 0.06 0 184 1 123 "by doubleHit,freq,cluster" Benign 0.114 54 Tolerant 0.33 3.2 146 moderately conservative 146880 6p21.3 "major histocompatibility complex, class II, DQ alpha 1" 4639 rs9473558 MUT 4594 6 49520392 NM_000255 NP_000246 C/T R532H plus 24315860 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.44 0 48 1 0.23 0.11 94 2 123 "by doubleHit,freq" Borderline 1.136 57 conservative 251000 6p21 methylmalonyl Coenzyme A mutase 4640 rs9507425 TDRD4 54513 13 24338318 NM_019038 NP_061911 A/G E527K plus 24448373 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.3 0.3 0 46 1 0.16 0.12 92 2 123 by freq moderately conservative 13q12.13 tudor domain containing 4 4641 rs9516771 HS6ST3 266722 13 96282831 NM_153456 NP_703157 A/G K265R plus 13180074 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.04 0.04 0 120 1 119 "HapMap,freq" Potentially damaging 1.252 27 conservative 13q32.2 heparan sulfate 6-O-sulfotransferase 3 4642 rs9532758 MTRF1 9617 13 40733039 NM_004294 NP_004285 C/T N2S plus 23723247 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 0.15 0 46 1 123 "by doubleHit,freq,cluster" conservative 604601 13q14.1-q14.3 mitochondrial translational release factor 1 4643 rs9568497 GUCY1B2 2974 13 50501769 NM_004129 NP_004120 C/T Y55C plus 23343600 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.46 0 48 1 0.41 0.09 94 2 123 "by doubleHit,freq,cluster" Probably damaging 2.407 10 Intolerant 0 2.83 38 radical 603695 13q14.2-q14.3 "guanylate cyclase 1, soluble, beta 2" 4644 rs9576175 CSNK1A1L 122011 13 36577268 NM_145203 NP_660204 G/T D42E plus 23391652 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.48 0 48 1 0.3 0.2 69 2 123 "by doubleHit,freq,cluster" Benign 0.613 199 conservative 13q13.2 "casein kinase 1, alpha 1-like" 4645 rs9578751 ADPRTL1 143 13 23972490 NM_006437 NP_006428 C/T S122N plus 24445590 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.08 0.01 94 2 123 by freq conservative 607519 13q11 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1 4646 rs9606739 SEC14L4 284904 22 29215848 NM_174977 NP_777637 C/G R124G plus 24587801 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.21 0 48 1 0.13 0 46 1 123 by freq Possibly damaging 1.54 21 Borderline 0.11 2.85 29 moderately radical 22q12.2 SEC14-like 4 (S. cerevisiae) 4647 rs9608956 SEC14L4 284904 22 29226146 NM_174977 NP_777637 C/T S3G plus 23630492 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.25 0 48 1 0.2 0.25 92 2 123 "by doubleHit,freq,cluster" Possibly damaging 1.722 18 Tolerant 1 3.14 24 moderately conservative 22q12.2 SEC14-like 4 (S. cerevisiae) 4648 rs9614653 SMC1L2 27127 22 44087928 NM_148674 NP_683515 C/T R758Q plus 19497612 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.08 0.08 0 168 2 0.28 0 46 1 123 "HapMap,doubleHit,freq,cluster" Benign 0.405 15 Tolerant 0.22 2.79 24 conservative 608685 22q13.31 SMC1 structural maintenance of chromosomes 1-like 2 (yeast) 4649 rs9614653 SMC1L2 27127 22 44087928 NM_148674 NP_683515 C/T R758Q plus 24106075 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 168 2 0.28 0 46 1 123 "HapMap,doubleHit,freq,cluster" Benign 0.405 15 Tolerant 0.22 2.79 24 conservative 608685 22q13.31 SMC1 structural maintenance of chromosomes 1-like 2 (yeast) 4650 rs9624909 MYO18B 84700 22 24547008 NM_032608 NP_115997 C/T S925L plus 23622904 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.21 0 48 1 0.22 0 46 1 123 "by cluster,freq" Tolerant 0.21 2.8 124 moderately radical 607295 22q11.2-q12.1 myosin XVIIIB 4651 rs9640663 PTPN12 5782 7 76892472 NM_002835 NP_002826 A/G V322I plus 24444534 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.4 0 48 1 0.15 0 94 2 123 "by doubleHit,freq,cluster" Benign 0.119 7 conservative 600079 7q11.23 "protein tyrosine phosphatase, non-receptor type 12" 4652 rs9657979 TNFRSF9 3604 1 7929356 NM_001561 NP_001552 A/C A176D minus 13452250 693 EGP_SNPS PDR90 NIHPDR 176 0.01 0.01 0 176 1 119 by freq Tolerant 0.62 2.89 17 moderately radical 602250 1p36 "tumor necrosis factor receptor superfamily, member 9" 4653 rs9658625 SOAT2 8435 12 51783669 NM_003578 NP_003569 A/G E14G plus 13453036 693 EGP_SNPS PDR90 NIHPDR 162 0.12 0.12 0 162 1 119 by freq moderately conservative 601311 12q13.13 sterol O-acyltransferase 2 4654 rs9666607 CD44 960 11 35182731 NM_000610 NP_000601 A/G K417R plus 24544229 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.23 0 48 1 0.06 0.05 90 2 123 "by cluster,freq" Benign 0.092 5 conservative 107269 11p13 CD44 antigen (homing function and Indian blood group system) 4655 rs9675365 ANKRD30B 374860 18 14769969 XM_371111 XP_371111 C/G F477L plus 13473099 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.49 0.49 0 120 1 121 "HapMap,doubleHit,freq,cluster" conservative 18p11.21 ankyrin repeat domain 30B 4656 rs9678851 SLC4A1AP 22950 2 27798685 NM_018158 NP_060628 A/C P139T plus 13477310 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.38 0.44 0.06 324 3 0.13 0.12 294 3 123 "HapMap,doubleHit,freq,cluster" conservative 602655 2p23.3 "solute carrier family 4 (anion exchanger), member 1, adaptor protein" 4657 rs9678851 SLC4A1AP 22950 2 27798685 NM_018158 NP_060628 A/C P139T plus 24292954 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.44 0.06 324 3 0.13 0.12 294 3 123 "HapMap,doubleHit,freq,cluster" conservative 602655 2p23.3 "solute carrier family 4 (anion exchanger), member 1, adaptor protein" 4658 rs9678851 SLC4A1AP 22950 2 27798685 NM_018158 NP_060628 A/C P139T plus 28459346 549 KYUGEN CP CEPH (78) 156 0.49 0.44 0.06 324 3 0.13 0.12 294 3 123 "HapMap,doubleHit,freq,cluster" conservative 602655 2p23.3 "solute carrier family 4 (anion exchanger), member 1, adaptor protein" 4659 rs9808232 ROCK2 9475 2 11309718 NM_004850 NP_004841 G/T T431N plus 13639652 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.42 0.43 0.03 166 2 0.37 0.08 90 2 123 "HapMap,doubleHit,freq" Benign 0.073 11 Tolerant 0.49 2.82 37 moderately conservative 604002 2p24 "Rho-associated, coiled-coil containing protein kinase 2" 4660 rs9808232 ROCK2 9475 2 11309718 NM_004850 NP_004841 G/T T431N plus 24645383 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.46 0.43 0.03 166 2 0.37 0.08 90 2 123 "HapMap,doubleHit,freq" Benign 0.073 11 Tolerant 0.49 2.82 37 moderately conservative 604002 2p24 "Rho-associated, coiled-coil containing protein kinase 2" 4661 rs9808753 IFNGR2 3460 21 33709182 NM_005534 NP_005525 A/G Q64R plus 24116479 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.32 0.17 94 2 123 "by doubleHit,freq,cluster" conservative 147569 21q22.11 interferon gamma receptor 2 (interferon gamma transducer 1) 4662 rs9841174 SERPINI2 5276 3 168667580 NM_006217 NP_006208 C/T E148G plus 13674733 885 TSC-CSHL HapMap-CEPH-30-trios 112 0.3 0.34 0.09 160 2 0.48 0 94 2 123 "HapMap,doubleHit,freq,cluster" Tolerant 0.34 2.76 16 moderately conservative 605587 3q26.1-q26.2 "serine (or cysteine) proteinase inhibitor, clade I (neuroserpin), member 2" 4663 rs9841174 SERPINI2 5276 3 168667580 NM_006217 NP_006208 C/T E148G plus 23900541 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.34 0.09 160 2 0.48 0 94 2 123 "HapMap,doubleHit,freq,cluster" Tolerant 0.34 2.76 16 moderately conservative 605587 3q26.1-q26.2 "serine (or cysteine) proteinase inhibitor, clade I (neuroserpin), member 2" 4664 rs9862221 CIDE-3 63924 3 9883881 NM_022094 NP_071377 G/T E218D plus 23246730 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.07 0.07 0 46 1 0.24 0.23 92 2 123 by freq Borderline 1.072 6 Intolerant 0.04 3.09 17 conservative 3p25.3 cell death activator CIDE-3 4665 rs9868848 ZFYVE20 64145 3 15090876 NM_022340 NP_071735 A/G L591P plus 13703998 885 TSC-CSHL HapMap-CEPH-30-trios 114 0.03 0.03 0 114 1 119 "HapMap,doubleHit,freq" moderately conservative 3p25.1 "zinc finger, FYVE domain containing 20" 4666 rs9876921 TGM4 7047 3 44923594 NM_003241 NP_003232 A/G V409I plus 24370808 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.46 0 48 1 0.26 0.23 94 2 123 by freq Tolerant 0.81 2.78 17 conservative 600585 3p22-p21.33 transglutaminase 4 (prostate) 4667 rs9901675 CD68 968 17 7425536 NM_001251 NP_001242 A/G A350T plus 24584026 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.11 0.11 0 46 1 0.06 0.01 94 2 123 by freq Potentially damaging 1.486 7 Tolerant 0.46 2.76 24 moderately conservative 153634 17p13 CD68 antigen 4668 rs9908414 ZNF594 84622 17 5027764 XM_290737 XP_290737 A/G I103T plus 24705184 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.46 0 48 1 0.11 0.13 90 2 123 "by doubleHit,freq,cluster" Tolerant 1 2.77 51 moderately conservative 17p13 zinc finger protein 594 4669 rs9909216 ABCA10 10349 17 64724018 NM_080282 NP_525021 A/G P203S plus 24124412 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.35 0 48 1 0.37 0.16 94 2 123 "by doubleHit,freq,cluster" Benign 0.225 16 Tolerant 0.63 2.8 28 moderately conservative 17q24 "ATP-binding cassette, sub-family A (ABC1), member 10" 4670 rs9967382 SERPINB10 5273 18 59738047 NM_005024 NP_005015 C/T P140S plus 24058697 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.19 0 48 1 0.38 0.06 94 2 123 "by doubleHit,freq,cluster" Tolerant 0.63 2.76 58 moderately conservative 602058 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10" 4671 rs9973235 M6PRBP1 10226 19 4798713 NM_005817 NP_005808 A/G V275A plus 13815244 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.11 0.13 0.05 164 2 0.08 0.04 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.091 7 moderately conservative 602702 19p13.3 mannose-6-phosphate receptor binding protein 1 4672 rs9973235 M6PRBP1 10226 19 4798713 NM_005817 NP_005808 A/G V275A plus 24542743 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.13 0.05 164 2 0.08 0.04 94 2 123 "HapMap,doubleHit,freq,cluster" Benign 0.091 7 moderately conservative 602702 19p13.3 mannose-6-phosphate receptor binding protein 1 4673 rs9975588 MCM3AP 8888 21 46529324 NM_003906 NP_003897 A/G S102L plus 13817821 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.41 0.41 0 116 1 120 "HapMap,doubleHit,freq,cluster" moderately radical 603294 21q22.3 MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein 4674 rs10034345 GRID2 2895 4 94701220 NM_001510 NP_001501 A/G V490I plus 23282315 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.15 0 46 1 123 "by cluster,freq" Benign 0.736 6 Borderline 0.11 2.8 42 conservative 602368 4q22 "glutamate receptor, ionotropic, delta 2" 4675 rs10036727 SLIT3 6586 5 168112659 NM_003062 NP_003053 C/T G618S plus 24671734 1371 PERLEGEN AFD_EUR_PANEL European American (24) 24 0.5 0.5 0 24 1 0.44 0.06 92 2 123 "by cluster,freq" moderately conservative 603745 5q35 slit homolog 3 (Drosophila) 4676 rs10066063 PDZK3 23037 5 32126051 NM_178140 NP_835260 A/G R2247Q plus 24009451 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.13 0.12 94 2 123 "by cluster,freq" conservative 5p13.3 PDZ domain containing 3 4677 rs10067096 ADAM19 8728 5 156849918 NM_033274 NP_150377 A/C S740A plus 15357338 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.23 0.23 0 40 1 0.19 0 48 1 120 "by doubleHit,freq,cluster" Tolerant 0.84 3.05 15 moderately conservative 603640 5q32-q33 a disintegrin and metalloproteinase domain 19 (meltrin beta) 4678 rs10081139 NT5E 4907 6 86255962 NM_002526 NP_002517 C/T M379T plus 23447732 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.18 0.12 92 2 123 "by doubleHit,freq,cluster" Possibly damaging 1.849 9 Tolerant 0.6 2.86 19 moderately conservative 129190 6q14-q21 "5'-nucleotidase, ecto (CD73)" 4679 rs10093885 PKHD1L1 93035 8 110517811 NM_177531 NP_803875 A/G T1192A plus 23573502 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.35 0 48 1 0.43 0 46 1 123 "by cluster,freq" moderately conservative 607843 8q23.2 polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1 4680 rs10115703 CER1 9350 9 14712616 NM_005454 NP_005445 A/G R19W plus 23542825 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.13 0 46 1 123 "by cluster,freq" moderately radical 603777 9p23-p22 "cerberus 1 homolog, cysteine knot superfamily (Xenopus laevis)" 4681 rs10134365 MIA2 117153 14 38791774 NM_054024 NP_473365 C/G D547H plus 24112861 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.47 0.03 66 2 123 "by cluster,freq" moderately conservative 608001 14q13.2 melanoma inhibitory activity 2 4682 rs10146482 NEK9 91754 14 74643840 NM_033116 NP_149107 C/T R429H plus 24606789 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.45 0.02 232 2 0.27 0.14 94 2 123 "by doubleHit,freq,cluster" conservative 14q24.2 NIMA (never in mitosis gene a)- related kinase 9 4683 rs10146482 NEK9 91754 14 74643840 NM_033116 NP_149107 C/T R429H plus 24791796 1303 SEQUENOM CEPH CEPH (92) 184 0.44 0.45 0.02 232 2 0.27 0.14 94 2 123 "by doubleHit,freq,cluster" conservative 14q24.2 NIMA (never in mitosis gene a)- related kinase 9 4684 rs10157992 NFASC 23114 1 201647596 XM_046808 XP_046808 C/T F150S plus 24640392 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.29 0 48 1 0.18 0.05 94 2 123 "by doubleHit,freq,cluster" radical 1q32.1 neurofascin 4685 rs10266424 MTERF 7978 7 91147879 NM_006980 NP_008911 C/T A294T plus 24488414 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.48 0 48 1 0.3 0.05 94 2 123 "by doubleHit,freq,cluster" Tolerant 0.99 2.98 13 moderately conservative 602318 7q21-q22 "transcription termination factor, mitochondrial" 4686 rs10283100 ENPP2 5168 8 120665204 NM_006209 NP_006200 A/G S545P plus 24409953 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 123 "by cluster,freq" Probably damaging 2.274 8 moderately conservative 601060 8q24.1 ectonucleotide pyrophosphatase/phosphodiesterase 2 (autotaxin) 4687 rs10407022 AMH 268 19 2200477 NM_000479 NP_000470 G/T S49I plus 14699093 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.19 0.19 0 118 1 121 "HapMap,doubleHit,freq,cluster" moderately radical 600957 19p13.3 anti-Mullerian hormone 4688 rs10409531 ZFP28 140612 19 61757825 NM_020828 NP_065879 C/T A620V plus 24225772 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.35 0 48 1 0.33 0.12 92 2 123 "by doubleHit,freq,cluster" Borderline 1.219 5 Tolerant 0.27 2.82 27 moderately conservative 19q13.43 zinc finger protein 28 homolog (mouse) 4689 rs10409962 SIGLEC8 27181 19 56652752 NM_014442 NP_055257 A/G S170P plus 14703561 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.04 0.04 0 118 1 119 "HapMap,doubleHit,freq" Probably damaging 2.174 14 Tolerant 1 2.77 33 moderately conservative 605639 19q13.33-q13.41 sialic acid binding Ig-like lectin 8 4690 rs10419832 ILT7 23547 19 59541211 NM_012276 NP_036408 C/T I155V plus 23778067 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.08 0.09 94 2 123 "by cluster,freq" Benign 0.692 65 Tolerant 0.37 2.83 143 conservative 607517 19q13.4 "leukocyte immunoglobulin-like receptor, subfamily A (without TM domain), member 4" 4691 rs10421121 ZNF556 80032 19 2828365 NM_024967 NP_079243 C/T R137C plus 14720864 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.03 0.03 0 120 1 119 "HapMap,freq" Intolerant 0.02 2.74 31 radical 19p13.3 zinc finger protein 556 4692 rs10421769 GPATC1 55094 19 38297152 NM_018025 NP_060495 C/T L728S plus 24525144 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.38 0 48 1 0.09 0.05 94 2 123 "by cluster,freq" moderately radical 19q13.12 G patch domain containing 1 4693 rs10429965 NEK2 4751 1 208228893 NM_002497 NP_002488 C/T N354S plus 23874326 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.16 0.01 94 2 123 "by cluster,freq" Benign 0.496 16 Tolerant 0.47 3.01 17 conservative 604043 1q32.2-q41 NIMA (never in mitosis gene a)-related kinase 2 4694 rs10467770 CHD8 57680 14 20969471 XM_370738 XP_370738 C/T V58M plus 14826604 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.26 0.26 0 118 1 119 "HapMap,doubleHit,freq" conservative 14q11.2 helicase with SNF2 domain 1 4695 rs10482810 TGFB2 7042 1 214995927 NM_003238 NP_003229 C/G V207L plus 14865977 693 EGP_SNPS PDR90 NIHPDR 172 0.01 0.01 0.01 212 2 120 "by cluster,freq" Potentially damaging 1.43 26 Tolerant 0.35 2.9 47 conservative 190220 1q41 "transforming growth factor, beta 2" 4696 rs10482810 TGFB2 7042 1 214995927 NM_003238 NP_003229 C/G V207L plus 15356657 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.03 0.01 0.01 212 2 120 "by cluster,freq" Potentially damaging 1.43 26 Tolerant 0.35 2.9 47 conservative 190220 1q41 "transforming growth factor, beta 2" 4697 rs10484847 DNAH8 1769 6 39088059 NM_001371 NP_001362 C/T I4271V minus 14870164 902 AFFY Caucasian 24 0.33 0.22 0.11 72 2 0.09 0.07 154 4 123 by freq Benign 0.13 8 conservative 603337 6p21.31-p21.1 "dynein, axonemal, heavy polypeptide 8" 4698 rs10484847 DNAH8 1769 6 39088059 NM_001371 NP_001362 C/T I4271V minus 24439091 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.22 0.11 72 2 0.09 0.07 154 4 123 by freq Benign 0.13 8 conservative 603337 6p21.31-p21.1 "dynein, axonemal, heavy polypeptide 8" 4699 rs10491178 ABCA10 10349 17 64661568 NM_080282 NP_525021 C/T R1322X minus 14878795 902 AFFY Caucasian 24 0.04 0.03 0.01 70 2 0.11 0.06 148 4 123 "by cluster,freq" Probably damaging Intolerant radical 17q24 "ATP-binding cassette, sub-family A (ABC1), member 10" 4700 rs10491178 ABCA10 10349 17 64661568 NM_080282 NP_525021 C/T R1322X minus 24124211 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.02 0.03 0.01 70 2 0.11 0.06 148 4 123 "by cluster,freq" Probably damaging Intolerant radical 17q24 "ATP-binding cassette, sub-family A (ABC1), member 10" 4701 rs10494217 TBX15 6913 1 119181230 XM_371284 XP_371284 G/T H50N plus 14883431 902 AFFY Caucasian 24 0.13 0.14 0.01 72 2 0.06 0.02 150 4 123 by freq Probably damaging 2.059 13 moderately conservative 604127 1p11.1 T-box 15 4702 rs10494217 TBX15 6913 1 119181230 XM_371284 XP_371284 G/T H50N plus 24617250 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.14 0.01 72 2 0.06 0.02 150 4 123 by freq Probably damaging 2.059 13 moderately conservative 604127 1p11.1 T-box 15 4703 rs10494745 FHR-4 10877 1 193619114 NM_006684 NP_006675 A/G G306E plus 14884176 902 AFFY Caucasian 24 0.04 0.06 0.02 82 3 0.05 0.04 88 2 123 by freq Borderline 0.2 2.83 20 moderately conservative 605337 1q32 complement factor H-related 4 4704 rs10494745 FHR-4 10877 1 193619114 NM_006684 NP_006675 A/G G306E plus 14884176 904 AFFY CEPH 10 0.1 0.06 0.02 82 3 0.05 0.04 88 2 123 by freq Borderline 0.2 2.83 20 moderately conservative 605337 1q32 complement factor H-related 4 4705 rs10494745 FHR-4 10877 1 193619114 NM_006684 NP_006675 A/G G306E plus 24285476 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0.02 82 3 0.05 0.04 88 2 123 by freq Borderline 0.2 2.83 20 moderately conservative 605337 1q32 complement factor H-related 4 4706 rs10495960 ALF 11036 2 48871683 NM_172196 NP_751946 A/G A444T plus 14885973 902 AFFY Caucasian 24 0.21 0.17 0.14 84 3 0.29 0.07 98 3 123 "by doubleHit,freq,cluster" moderately conservative 605358 2p21 TFIIA-alpha/beta-like factor 4707 rs10495960 ALF 11036 2 48871683 NM_172196 NP_751946 A/G A444T plus 14885973 904 AFFY CEPH 12 0.42 0.17 0.14 84 3 0.29 0.07 98 3 123 "by doubleHit,freq,cluster" moderately conservative 605358 2p21 TFIIA-alpha/beta-like factor 4708 rs10495960 ALF 11036 2 48871683 NM_172196 NP_751946 A/G A444T plus 24157139 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.17 0.14 84 3 0.29 0.07 98 3 123 "by doubleHit,freq,cluster" moderately conservative 605358 2p21 TFIIA-alpha/beta-like factor 4709 rs10498796 TINAG 27283 6 54327285 NM_014464 NP_055279 A/G R381H plus 14890384 902 AFFY Caucasian 22 0.14 0.16 0.02 68 2 0.14 0.04 106 3 123 by freq Probably damaging 2.409 5 conservative 606749 6p11.2-p12 tubulointerstitial nephritis antigen 4710 rs10498796 TINAG 27283 6 54327285 NM_014464 NP_055279 A/G R381H plus 24689856 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.17 0.16 0.02 68 2 0.14 0.04 106 3 123 by freq Probably damaging 2.409 5 conservative 606749 6p11.2-p12 tubulointerstitial nephritis antigen 4711 rs10500557 ZNF19 7567 16 70067280 NM_006961 NP_008892 C/T R224Q plus 14892929 902 AFFY Caucasian 24 0.08 0.05 0.03 72 2 0.04 0 48 1 123 by freq Intolerant 0.03 2.77 57 conservative 194525 16q22 zinc finger protein 19 (KOX 12) 4712 rs10500557 ZNF19 7567 16 70067280 NM_006961 NP_008892 C/T R224Q plus 24429756 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.05 0.03 72 2 0.04 0 48 1 123 by freq Intolerant 0.03 2.77 57 conservative 194525 16q22 zinc finger protein 19 (KOX 12) 4713 rs10502001 MMP7 4316 11 101903803 NM_002423 NP_002414 C/T R77H plus 14894860 902 AFFY Caucasian 22 0.23 0.19 0.04 70 2 0.14 0.06 158 5 123 "by cluster,freq" Benign 0.338 6 Borderline 0.15 2.7 73 conservative 178990 11q21-q22 "matrix metalloproteinase 7 (matrilysin, uterine)" 4714 rs10502001 MMP7 4316 11 101903803 NM_002423 NP_002414 C/T R77H plus 24071430 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.19 0.04 70 2 0.14 0.06 158 5 123 "by cluster,freq" Benign 0.338 6 Borderline 0.15 2.7 73 conservative 178990 11q21-q22 "matrix metalloproteinase 7 (matrilysin, uterine)" 4715 rs10509332 UNC5B 219699 10 72721446 NM_170744 NP_734465 A/G A516T plus 14906289 902 AFFY Caucasian 24 0.04 0.06 0.06 82 3 0.1 0.1 106 3 123 "by cluster,freq" Benign 0.67 16 moderately conservative 607870 10q22.2 unc-5 homolog B (C. elegans) 4716 rs10509332 UNC5B 219699 10 72721446 NM_170744 NP_734465 A/G A516T plus 14906289 904 AFFY CEPH 12 0.17 0.06 0.06 82 3 0.1 0.1 106 3 123 "by cluster,freq" Benign 0.67 16 moderately conservative 607870 10q22.2 unc-5 homolog B (C. elegans) 4717 rs10509332 UNC5B 219699 10 72721446 NM_170744 NP_734465 A/G A516T plus 23606676 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.04 0.06 0.06 82 3 0.1 0.1 106 3 123 "by cluster,freq" Benign 0.67 16 moderately conservative 607870 10q22.2 unc-5 homolog B (C. elegans) 4718 rs10509681 CYP2C8 1558 10 96788739 NM_000770 NP_000761 C/T K399R plus 14906800 902 AFFY Caucasian 24 0.13 0.07 0.04 252 3 0.02 0 94 2 123 "by cluster,freq" Possibly damaging 1.642 143 Borderline 0.17 2.78 165 conservative 601129 10q24.1 "cytochrome P450, family 2, subfamily C, polypeptide 8" 4719 rs10509681 CYP2C8 1558 10 96788739 NM_000770 NP_000761 C/T K399R plus 16356494 693 EGP_SNPS PDR90 NIHPDR 180 0.05 0.07 0.04 252 3 0.02 0 94 2 123 "by cluster,freq" Possibly damaging 1.642 143 Borderline 0.17 2.78 165 conservative 601129 10q24.1 "cytochrome P450, family 2, subfamily C, polypeptide 8" 4720 rs10509681 CYP2C8 1558 10 96788739 NM_000770 NP_000761 C/T K399R plus 24554781 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.07 0.04 252 3 0.02 0 94 2 123 "by cluster,freq" Possibly damaging 1.642 143 Borderline 0.17 2.78 165 conservative 601129 10q24.1 "cytochrome P450, family 2, subfamily C, polypeptide 8" 4721 rs10512747 CARD6 84674 5 40877498 NM_032587 NP_115976 C/T S86L plus 14911603 902 AFFY Caucasian 24 0.08 0.08 0 72 2 123 by freq moderately radical 5p13.1 "caspase recruitment domain family, member 6" 4722 rs10512747 CARD6 84674 5 40877498 NM_032587 NP_115976 C/T S86L plus 24415924 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 72 2 123 by freq moderately radical 5p13.1 "caspase recruitment domain family, member 6" 4723 rs10733133 NID 4811 1 232534814 NM_002508 NP_002499 C/T V246I plus 23195534 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.44 0 48 1 0.46 0.03 92 2 123 "by doubleHit,freq,cluster" Benign 0.225 7 conservative 131390 1q43 nidogen (enactin) 4724 rs10735810 VDR 7421 12 46559162 NM_000376 NP_000367 A/G M1T plus 16359158 693 EGP_SNPS PDR90 NIHPDR 180 0.31 0.31 0 180 1 0.32 0 598 1 121 "by doubleHit,freq,cluster" Probably damaging 2.505 8 moderately conservative 601769 12q12-q14 "vitamin D (1,25- dihydroxyvitamin D3) receptor" 4725 rs10759326 IKBKAP 8518 9 108739038 NM_003640 NP_003631 G/T I816L plus 23784454 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.39 0.12 92 2 123 "by doubleHit,freq,cluster" Benign 0.242 9 Tolerant 0.36 2.84 14 conservative 603722 9q31 "inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein" 4726 rs10787428 GPAM 57678 10 113925369 NM_020918 NP_065969 C/T E131G plus 23630682 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.42 0 48 1 0.46 0.03 94 2 123 "by doubleHit,freq,cluster" Possibly damaging 1.586 6 Intolerant 0.05 2.82 16 moderately conservative 602395 10q25.3 "glycerol-3-phosphate acyltransferase, mitochondrial" 4727 rs10795446 CUBN 8029 10 17187527 NM_001081 NP_001072 G/T P389T plus 18655303 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.34 0.3 0.05 304 2 123 "HapMap,doubleHit,freq,cluster" Potentially intolerant 0.1 2.84 6 conservative 602997 10p12.31 cubilin (intrinsic factor-cobalamin receptor) 4728 rs10795446 CUBN 8029 10 17187527 NM_001081 NP_001072 G/T P389T plus 24796398 1303 SEQUENOM CEPH CEPH (92) 184 0.27 0.3 0.05 304 2 123 "HapMap,doubleHit,freq,cluster" Potentially intolerant 0.1 2.84 6 conservative 602997 10p12.31 cubilin (intrinsic factor-cobalamin receptor) 4729 rs10801922 PTGFRN 5738 1 117241500 NM_020440 NP_065173 A/G V837I plus 24264587 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.46 0 48 1 0.39 0.02 94 2 123 "by doubleHit,freq" Benign 0.089 5 conservative 601204 1p13.1 prostaglandin F2 receptor negative regulator 4730 rs10821668 ANK3 288 10 61501277 NM_020987 NP_066267 C/T K3123R plus 24510382 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.21 0.21 0 42 1 0.05 0.03 80 2 123 by freq conservative 600465 10q21 "ankyrin 3, node of Ranvier (ankyrin G)" 4731 rs10825269 PCDH15 65217 10 55625616 NM_033056 NP_149045 C/T G380S plus 23479727 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.25 0.3 94 2 123 "by doubleHit,freq,cluster" Benign 0.146 5 Tolerant 0.83 2.82 34 moderately conservative 605514 10p11.2-q21 protocadherin 15 4732 rs10828317 PIP5K2A 5305 10 22879634 NM_005028 NP_005019 C/T N251S plus 24008949 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.42 0 48 1 0.26 0.31 94 2 123 "by doubleHit,freq,cluster" Benign 0.441 24 Tolerant 0.67 2.75 36 conservative 603140 10p12.32 "phosphatidylinositol-4-phosphate 5-kinase, type II, alpha" 4733 rs10828833 GPR158 57512 10 25928186 NM_020752 NP_065803 A/G I1206V plus 24471570 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.29 0 48 1 0.13 0.08 86 2 123 "by doubleHit,freq,cluster" conservative 10p12.31 G protein-coupled receptor 158 4734 rs10853751 EXOSC5 56915 19 46595060 NM_020158 NP_064543 C/T T5M minus 24570354 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.48 0.03 204 2 0.42 0.1 294 3 123 "by cluster,freq" moderately conservative 606492 19q13.1 exosome component 5 4735 rs10853751 EXOSC5 56915 19 46595060 NM_020158 NP_064543 C/T T5M minus 28459296 549 KYUGEN CP CEPH (78) 156 0.49 0.48 0.03 204 2 0.42 0.1 294 3 123 "by cluster,freq" moderately conservative 606492 19q13.1 exosome component 5 4736 rs10883841 NT5C2 22978 10 104924699 NM_012229 NP_036361 C/T T3A plus 18907816 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.12 0.12 0.01 164 2 0.13 0 48 1 123 "HapMap,doubleHit,freq,cluster" moderately conservative 600417 10q24.33 "5'-nucleotidase, cytosolic II" 4737 rs10883841 NT5C2 22978 10 104924699 NM_012229 NP_036361 C/T T3A plus 24498667 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.12 0.01 164 2 0.13 0 48 1 123 "HapMap,doubleHit,freq,cluster" moderately conservative 600417 10q24.33 "5'-nucleotidase, cytosolic II" 4738 rs10887063 TACC2 10579 10 123834493 NM_206862 NP_996744 C/T L830F plus 23608548 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.21 0 48 1 0.15 0.13 92 2 123 "by doubleHit,freq,cluster" conservative 605302 10q26 "transforming, acidic coiled-coil containing protein 2" 4739 rs10888390 CTSS 1520 1 147540612 NM_004079 NP_004070 A/G R113W plus 24276633 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.41 0.41 0 46 1 0.34 0.05 88 2 123 "by doubleHit,freq,cluster" Borderline 1.231 45 Borderline 0.19 2.75 120 moderately radical 116845 1q21 cathepsin S 4740 rs10889205 RLF 6018 1 40374819 NM_012421 NP_036553 A/T E1784D plus 16394890 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.23 0.23 0 120 1 120 "HapMap,doubleHit,freq,cluster" conservative 180610 1p32 rearranged L-myc fusion sequence 4741 rs10896380 IGHMBP2 3508 11 68438978 NM_002180 NP_002171 A/G I275V plus 15913512 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.27 0.28 0.03 166 2 0.15 0 46 1 123 "HapMap,doubleHit,freq,cluster" Benign 0.086 5 conservative 600502 11q13.2-q13.4 immunoglobulin mu binding protein 2 4742 rs10896380 IGHMBP2 3508 11 68438978 NM_002180 NP_002171 A/G I275V plus 24567514 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.28 0.03 166 2 0.15 0 46 1 123 "HapMap,doubleHit,freq,cluster" Benign 0.086 5 conservative 600502 11q13.2-q13.4 immunoglobulin mu binding protein 2 4743 rs10920551 PPFIA4 8497 1 199736024 XM_046751 XP_046751 C/T A62V plus 23850942 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.21 0 48 1 0.2 0.13 90 2 123 "by doubleHit,freq,cluster" moderately conservative 603145 1q32.1 "protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4" 4744 rs10927851 FBLP-1 54751 1 15842240 NM_017556 NP_060026 C/T S191F plus 23160459 1371 PERLEGEN AFD_EUR_PANEL European American (24) 38 0.24 0.24 0 38 1 0.21 0.26 62 2 123 "by doubleHit,freq,cluster" Benign 0.079 7 radical 607747 1p36.13 filamin-binding LIM protein-1 4745 rs10930046 IFIH1 64135 2 162963490 NM_022168 NP_071451 C/T H460R plus 23232900 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.02 0.02 0 46 1 0.24 0.2 82 2 123 "by doubleHit,freq,cluster" Benign 0.32 5 Tolerant 0.84 2.82 22 conservative 606951 2p24.3-q24.3 melanoma differentiation associated protein-5 4746 rs10931715 DNAH7 56171 2 196677417 NM_018897 NP_061720 A/G R545C plus 23914092 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.17 0 48 1 0.34 0.11 94 2 123 "by doubleHit,freq,cluster" Possibly damaging 1.86 5 Borderline 0.19 2.81 23 radical 2q33.1 "dynein, axonemal, heavy polypeptide 7" 4747 rs10935070 TOPBP1 11073 3 134824686 NM_007027 NP_008958 A/G N955S minus 24334172 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.42 0 48 1 0.04 0 46 1 123 "by cluster,freq" Potentially damaging 1.269 7 conservative 607760 3q22.1 topoisomerase (DNA) II binding protein 4748 rs10941412 OSMR 9180 5 38954915 NM_003999 NP_003990 A/G E527K plus 23431084 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.33 0 46 1 123 "by doubleHit,freq,cluster" Tolerant 0.36 2.8 12 moderately conservative 601743 5p13.2 oncostatin M receptor 4749 rs10943299 IMPG1 3617 6 76697523 NM_001563 NP_001554 A/G R704W plus 23388243 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.13 0 46 1 123 "by doubleHit,freq,cluster" Probably damaging 3.312 5 moderately radical 602870 6q14.2-q15 interphotoreceptor matrix proteoglycan 1 4750 rs10948072 ZNF318 24149 6 43415839 NM_014345 NP_055160 A/G T1112I plus 23675564 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.15 0 46 1 123 "by doubleHit,freq,cluster" moderately conservative 6pter-p12.1 zinc finger protein 318 4751 rs10957393 CPA6 57094 8 68699024 NM_020361 NP_065094 A/G F45L plus 23569677 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.23 0 48 1 0.17 0.13 94 2 123 "by doubleHit,freq,cluster" Tolerant 0.29 2.81 50 conservative 8q13.1 carboxypeptidase A6 4752 rs10979601 IKBKAP 8518 9 108740406 NM_003640 NP_003631 C/T G765E plus 23784459 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 0.38 0.11 94 2 123 "by doubleHit,freq" Benign 0.138 9 Tolerant 1 2.84 14 moderately conservative 603722 9q31 "inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein" 4753 rs11004439 PCDH15 65217 10 56093974 NM_033056 NP_149045 A/C S19A plus 24563608 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.33 0 48 1 0.14 0.04 94 2 123 by freq Benign 0.675 5 moderately conservative 605514 10p11.2-q21 protocadherin 15 4754 rs11006128 TFAM 7019 10 59815348 NM_003201 NP_003192 C/G S12T plus 24116170 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.21 0 48 1 123 "by cluster,freq" moderately conservative 600438 10q21 "transcription factor A, mitochondrial" 4755 rs11022079 USP47 55031 11 11870161 NM_017944 NP_060414 G/T G75V plus 16514526 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.34 0.34 0 120 1 120 "HapMap,doubleHit,freq,cluster" moderately radical 11p15.3 ubiquitin specific protease 47 4756 rs11041108 ZNF215 7762 11 6910434 NM_013250 NP_037382 A/G M119V plus 24062249 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.29 0 48 1 0.19 0.17 94 2 123 "by doubleHit,freq,cluster" Tolerant 1 2.77 15 conservative 605016 11p15.4 zinc finger protein 215 4757 rs11071990 CALML4 91860 15 66284651 NM_033429 NP_219501 A/G R40X plus 15405365 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.01 0.01 0 116 1 120 HapMap Probably damaging Intolerant radical 15q22.31 serologically defined breast cancer antigen NY-BR-20 4758 rs11073964 VPS33B 26276 15 89344765 NM_018668 NP_061138 C/T G514S plus 24664476 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.38 0 48 1 0.02 0 92 2 123 "by doubleHit,freq,cluster" moderately conservative 608552 15q26.1 vacuolar protein sorting 33B (yeast) 4759 rs11074359 COQ7 10229 16 18992799 NM_016138 NP_057222 C/T T103M plus 16705525 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.38 0.38 0 120 1 121 "HapMap,doubleHit,freq,cluster" Possibly damaging 1.563 13 Borderline 0.11 2.86 29 moderately conservative 601683 16p13.11-p12.3 "coenzyme Q7 homolog, ubiquinone (yeast)" 4760 rs11076256 GOT2 2806 16 57309967 NM_002080 NP_002071 A/G G188S minus 24788039 1303 SEQUENOM CEPH CEPH (92) 184 0.05 0.05 0 184 1 123 "by doubleHit,cluster" Benign 0.961 67 Borderline 0.18 2.74 83 moderately conservative 138150 16q21 "glutamic-oxaloacetic transaminase 2, mitochondrial (aspartate aminotransferase 2)" 4761 rs11079339 EPX 8288 17 53625441 NM_000502 NP_000493 A/G I40M plus 23791672 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 0.15 0 94 2 123 "by doubleHit,freq,cluster" Benign 0.252 20 Tolerant 0.31 2.8 32 conservative 131399 17q23.1 eosinophil peroxidase 4762 rs11080149 OMG 4974 17 26647414 NM_002544 NP_002535 A/G G21D minus 16745079 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.15 0.14 0.03 168 2 0.04 0 46 1 123 "HapMap,freq,cluster" Potentially intolerant 0.1 2.92 16 moderately conservative 164345 17q11.2 oligodendrocyte myelin glycoprotein 4763 rs11080149 OMG 4974 17 26647414 NM_002544 NP_002535 A/G G21D minus 24706008 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.14 0.03 168 2 0.04 0 46 1 123 "HapMap,freq,cluster" Potentially intolerant 0.1 2.92 16 moderately conservative 164345 17q11.2 oligodendrocyte myelin glycoprotein 4764 rs11084162 ZNF534 147658 19 57630229 XM_496320 XP_496320 A/G I89V plus 24204256 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.2 0.1 94 2 123 "by doubleHit,freq,cluster" Tolerant 0.55 2.75 31 conservative 19q13.41 zinc finger protein 534 4765 rs11086998 TNFRSF5 958 20 44190931 NM_001250 NP_001241 C/G P227A plus 16340762 693 EGP_SNPS PDR90 NIHPDR 158 0.03 0.03 0 158 1 120 "by cluster,freq" Benign 0.347 6 Potentially intolerant 0.09 3.24 8 conservative 109535 20q12-q13.2 "tumor necrosis factor receptor superfamily, member 5" 4766 rs11090143 BIK 638 22 41844603 NM_001197 NP_001188 C/T T26I plus 16359900 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.01 0.02 0.01 160 2 120 HapMap moderately conservative 603392 22q13.31 BCL2-interacting killer (apoptosis-inducing) 4767 rs11090143 BIK 638 22 41844603 NM_001197 NP_001188 C/T T26I plus 16359901 649 FHCRC POPU1 USA (20) 40 0.03 0.02 0.01 160 2 120 HapMap moderately conservative 603392 22q13.31 BCL2-interacting killer (apoptosis-inducing) 4768 rs11090865 TRMT1 55687 22 45052208 NM_018006 NP_060476 G/T A10S plus 23613711 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.21 0 48 1 0.26 0 46 1 123 "by doubleHit,freq,cluster" Intolerant 0.01 2.75 102 moderately conservative 22q13 tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase 1 4769 rs11096955 TLR10 81793 4 38598673 NM_030956 NP_112218 A/C I369L minus 15357143 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.28 0.27 0.05 46 2 0.46 0 48 1 120 "by cluster,freq" Tolerant 0.31 2.82 32 conservative 606270 4p14 toll-like receptor 10 4770 rs11096955 TLR10 81793 4 38598673 NM_030956 NP_112218 A/C I369L minus 15357143 848 IIPGA-WEISS-MARTINEZ E-1 CEPH 6 0.17 0.27 0.05 46 2 0.46 0 48 1 120 "by cluster,freq" Tolerant 0.31 2.82 32 conservative 606270 4p14 toll-like receptor 10 4771 rs11096957 TLR10 81793 4 38599057 NM_030956 NP_112218 A/C N241H minus 15357137 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.28 0.27 0.05 46 2 0.46 0 48 1 120 "by cluster,freq" Tolerant 0.59 2.82 32 moderately conservative 606270 4p14 toll-like receptor 10 4772 rs11096957 TLR10 81793 4 38599057 NM_030956 NP_112218 A/C N241H minus 15357137 848 IIPGA-WEISS-MARTINEZ E-1 CEPH 6 0.17 0.27 0.05 46 2 0.46 0 48 1 120 "by cluster,freq" Tolerant 0.59 2.82 32 moderately conservative 606270 4p14 toll-like receptor 10 4773 rs11099592 HPSE 10855 4 84587798 NM_006665 NP_006656 C/T K307R plus 17030608 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.22 0.22 0 120 1 121 "HapMap,doubleHit,freq,cluster" Benign 0.141 6 conservative 604724 4q21.3 heparanase 4774 rs11130097 TDGF1 6997 3 46595618 NM_003212 NP_003203 C/T V22A plus 16986518 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.42 0.42 0 120 1 121 "HapMap,doubleHit,freq,cluster" moderately conservative 187395 3p21.31 teratocarcinoma-derived growth factor 1 4775 rs11155242 GPR126 57211 6 142733242 NM_020455 NP_065188 A/C K230Q plus 24429937 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.25 0 48 1 0.12 0.14 94 2 123 "by doubleHit,freq,cluster" moderately conservative 6q24.1 G protein-coupled receptor 126 4776 rs11190305 DNMBP 23268 10 101629867 NM_015221 NP_056036 A/C C1413W plus 24562407 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.36 0.06 232 2 0.18 0.13 92 2 123 "by doubleHit,freq,cluster" radical 10q24.31 dynamin binding protein 4777 rs11190305 DNMBP 23268 10 101629867 NM_015221 NP_056036 A/C C1413W plus 24792835 1303 SEQUENOM CEPH CEPH (92) 184 0.34 0.36 0.06 232 2 0.18 0.13 92 2 123 "by doubleHit,freq,cluster" radical 10q24.31 dynamin binding protein 4778 rs11200385 TACC2 10579 10 123832513 NM_206862 NP_996744 A/G V170I plus 23608540 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.21 0 48 1 0.17 0.14 90 2 123 "by doubleHit,freq,cluster" conservative 605302 10q26 "transforming, acidic coiled-coil containing protein 2" 4779 rs11209026 IL23R 149233 1 67417979 NM_144701 NP_653302 A/G R381Q plus 15355790 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.1 0.11 0.03 46 2 120 "by cluster,freq" conservative 607562 1p31.3-p31.2 interleukin-23 receptor 4780 rs11209026 IL23R 149233 1 67417979 NM_144701 NP_653302 A/G R381Q plus 15355790 848 IIPGA-WEISS-MARTINEZ E-1 CEPH 6 0.17 0.11 0.03 46 2 120 "by cluster,freq" conservative 607562 1p31.3-p31.2 interleukin-23 receptor 4781 rs11254408 DNMT2 1787 10 17239784 NM_176086 NP_788274 A/C D112Y plus 23575139 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.11 0.11 0 44 1 0.09 0.1 90 2 123 "by cluster,freq" radical 602478 10p15.1 DNA (cytosine-5-)-methyltransferase 2 4782 rs11465228 ADAM19 8728 5 156935273 NM_033274 NP_150377 A/G G4S minus 15354975 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.05 0.05 0 40 1 0.15 0 48 1 120 by freq moderately conservative 603640 5q32-q33 a disintegrin and metalloproteinase domain 19 (meltrin beta) 4783 rs11466004 LY96 23643 8 75103829 NM_015364 NP_056179 C/T P157S plus 15356093 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.05 0.05 0 40 1 120 by freq Benign 0.671 6 moderately conservative 605243 8q13.3 lymphocyte antigen 96 4784 rs11466111 NGFB 4803 1 115541220 NM_002506 NP_002497 A/G R80Q minus 15356261 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 36 0.03 0.05 0.07 42 2 120 by freq Possibly damaging 1.696 34 Intolerant 0.04 2.72 85 conservative 162030 1p13.1 "nerve growth factor, beta polypeptide" 4785 rs11466111 NGFB 4803 1 115541220 NM_002506 NP_002497 A/G R80Q minus 15356261 848 IIPGA-WEISS-MARTINEZ E-1 CEPH 6 0.17 0.05 0.07 42 2 120 by freq Possibly damaging 1.696 34 Intolerant 0.04 2.72 85 conservative 162030 1p13.1 "nerve growth factor, beta polypeptide" 4786 rs11466649 TLR10 81793 4 38599291 NM_030956 NP_112218 G/T A163S minus 15357135 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.03 0.03 0 40 1 0.08 0 48 1 120 by freq Tolerant 0.21 2.82 32 moderately conservative 606270 4p14 toll-like receptor 10 4787 rs11466651 TLR10 81793 4 38598886 NM_030956 NP_112218 A/G V298I minus 15357138 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.03 0.03 0 40 1 0.08 0 48 1 120 by freq Tolerant 0.49 2.82 32 conservative 606270 4p14 toll-like receptor 10 4788 rs11466653 TLR10 81793 4 38598801 NM_030956 NP_112218 C/T M326T minus 15357140 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.03 0.03 0 40 1 0.06 0 48 1 120 by freq Tolerant 0.26 2.82 32 moderately conservative 606270 4p14 toll-like receptor 10 4789 rs11466656 TLR10 81793 4 38598373 NM_030956 NP_112218 C/G R469G minus 15357145 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.03 0.03 0 40 1 0.02 0 48 1 120 by freq Intolerant 0.01 2.82 31 moderately radical 606270 4p14 toll-like receptor 10 4790 rs11466657 TLR10 81793 4 38598360 NM_030956 NP_112218 C/T I473T minus 15357146 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.05 0.07 0.06 46 2 0.02 0 48 1 120 by freq Intolerant 0.01 2.82 31 moderately conservative 606270 4p14 toll-like receptor 10 4791 rs11466657 TLR10 81793 4 38598360 NM_030956 NP_112218 C/T I473T minus 15357146 848 IIPGA-WEISS-MARTINEZ E-1 CEPH 6 0.17 0.07 0.06 46 2 0.02 0 48 1 120 by freq Intolerant 0.01 2.82 31 moderately conservative 606270 4p14 toll-like receptor 10 4792 rs11466658 TLR10 81793 4 38598205 NM_030956 NP_112218 C/T R525W minus 15357147 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 40 0.05 0.05 0 40 1 120 by freq Intolerant 0.02 2.82 31 moderately radical 606270 4p14 toll-like receptor 10 4793 rs11466803 ADAM19 8728 5 156847901 NM_033274 NP_150377 C/G P834A minus 15357346 847 IIPGA-WEISS-MARTINEZ E-0 CEPH 36 0.06 0.06 0 36 1 120 by freq Tolerant 0.68 3.06 12 conservative 603640 5q32-q33 a disintegrin and metalloproteinase domain 19 (meltrin beta) 4794 rs11488569 INPP5B 3633 1 38007888 XM_375718 XP_375718 A/G M769T plus 24127713 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.38 0 48 1 0.38 0.06 94 2 123 "by cluster,freq" moderately conservative 147264 1p34 "inositol polyphosphate-5-phosphatase, 75kDa" 4795 rs11539696 ZNF277 11179 7 111574958 NM_021994 NP_068834 A/G V352M plus 24461665 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 0.02 0 46 1 123 by freq Benign 0.941 7 Potentially intolerant 0.08 3.21 13 conservative 605465 7q31.1 zinc finger protein (C2H2 type) 277 4796 rs11541244 COL15A1 1306 9 98911550 NM_001855 NP_001846 A/G V1332I plus 24796377 1303 SEQUENOM CEPH CEPH (92) 184 0.12 0.12 0 184 1 123 by freq conservative 120325 9q21-q22 "collagen, type XV, alpha 1" 4797 rs11545941 PON2 5445 7 94685667 NM_000305 NP_000296 C/G A148G minus 23760956 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.23 0.03 232 2 0.18 0.08 90 2 123 "by cluster,freq" Benign 0.089 52 Borderline 0.18 2.79 30 moderately conservative 602447 7q21.3 paraoxonase 2 4798 rs11545941 PON2 5445 7 94685667 NM_000305 NP_000296 C/G A148G minus 24796342 1303 SEQUENOM CEPH CEPH (92) 184 0.24 0.23 0.03 232 2 0.18 0.08 90 2 123 "by cluster,freq" Benign 0.089 52 Borderline 0.18 2.79 30 moderately conservative 602447 7q21.3 paraoxonase 2 4799 rs11547284 NDUFB9 4715 8 125631210 NM_005005 NP_004996 C/T P146S plus 23954281 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.13 0.03 94 2 123 "by cluster,freq" Potentially damaging 1.414 7 moderately conservative 601445 8q13.3 "NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 9, 22kDa" 4800 rs11549147 FDFT1 2222 8 11703746 NM_004462 NP_004453 A/G K45R plus 24796361 1303 SEQUENOM CEPH CEPH (92) 184 0.08 0.08 0 184 1 123 by freq Benign 0.113 8 Tolerant 0.44 2.76 43 conservative 184420 8p23.1-p22 farnesyl-diphosphate farnesyltransferase 1 4801 rs11549918 ICAM5 7087 19 10263938 NM_003259 NP_003250 A/G V301I plus 24787559 1303 SEQUENOM CEPH CEPH (92) 184 0.41 0.42 0.01 368 2 123 by freq conservative 601852 19p13.2 "intercellular adhesion molecule 5, telencephalin" 4802 rs11549918 ICAM5 7087 19 10263938 NM_003259 NP_003250 A/G V301I plus 24796573 1303 SEQUENOM CEPH CEPH (92) 184 0.42 0.42 0.01 368 2 123 by freq conservative 601852 19p13.2 "intercellular adhesion molecule 5, telencephalin" 4803 rs11552377 CCM2 83605 7 44877371 NM_031443 NP_113631 A/G V120I plus 24459073 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.21 0 48 1 0.17 0 48 1 123 by freq Benign 0.089 5 conservative 607929 7p13 cerebral cavernous malformation 2 4804 rs11558492 GNPAT 8443 1 227714826 NM_014236 NP_055051 C/T D519G minus 24634450 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.27 0 48 1 0.08 0.01 94 2 123 by freq Potentially damaging 1.385 5 Tolerant 0.39 2.85 14 moderately conservative 602744 1q42.11-42.3 glyceronephosphate O-acyltransferase 4805 rs11568658 ABCC4 10257 13 94661009 NM_005845 NP_005836 G/T G187W minus 24224453 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.06 0.04 600 2 123 by freq Probably damaging 2.031 6 Intolerant 0.02 2.95 34 radical 605250 13q32 "ATP-binding cassette, sub-family C (CFTR/MRP), member 4" 4806 rs11568849 EGF 1950 4 111192141 NM_001963 NP_001954 A/C S16R plus 16340127 693 EGP_SNPS PDR90 NIHPDR 174 0.01 0.01 0 174 1 120 by freq Possibly damaging 1.556 9 moderately radical 131530 4q25 epidermal growth factor (beta-urogastrone) 4807 rs11568943 EGF 1950 4 111240725 NM_001963 NP_001954 A/G R431K plus 16340249 693 EGP_SNPS PDR90 NIHPDR 166 0.1 0.09 0.04 214 2 0.23 0.19 94 2 123 by freq Benign 0.121 10 Tolerant 0.92 2.77 35 conservative 131530 4q25 epidermal growth factor (beta-urogastrone) 4808 rs11568943 EGF 1950 4 111240725 NM_001963 NP_001954 A/G R431K plus 23276314 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.09 0.04 214 2 0.23 0.19 94 2 123 by freq Benign 0.121 10 Tolerant 0.92 2.77 35 conservative 131530 4q25 epidermal growth factor (beta-urogastrone) 4809 rs11569017 EGF 1950 4 111259715 NM_001963 NP_001954 A/T D784V plus 16340347 693 EGP_SNPS PDR90 NIHPDR 166 0.05 0.05 0 166 1 120 by freq Possibly damaging 1.647 10 Intolerant 0.03 2.9 31 radical 131530 4q25 epidermal growth factor (beta-urogastrone) 4810 rs11569046 EGF 1950 4 111266537 NM_001963 NP_001954 C/T M842T plus 16340383 693 EGP_SNPS PDR90 NIHPDR 164 0.04 0.04 0 164 1 0.11 0 44 1 123 "by cluster,freq" Potentially damaging 1.338 10 Tolerant 0.62 2.92 29 moderately conservative 131530 4q25 epidermal growth factor (beta-urogastrone) 4811 rs11569098 EGF 1950 4 111278560 NM_001963 NP_001954 C/T L1043F plus 16340448 693 EGP_SNPS PDR90 NIHPDR 176 0.01 0.01 0 176 1 120 by freq Borderline 1.242 10 conservative 131530 4q25 epidermal growth factor (beta-urogastrone) 4812 rs11569636 PLTP 5360 20 43971676 NM_006227 NP_006218 A/C S124Y minus 16341183 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.02 0.02 0 46 1 0.02 0 42 1 120 by freq Potentially damaging 1.311 12 Intolerant 0 2.78 20 moderately radical 172425 20q12-q13.1 phospholipid transfer protein 4813 rs11569892 TNFRSF8 943 1 12109924 NM_001243 NP_001234 A/G C273Y plus 16341576 693 EGP_SNPS PDR90 NIHPDR 176 0.02 0.02 0 176 1 120 by freq Intolerant 0 2.78 78 radical 153243 1p36 "tumor necrosis factor receptor superfamily, member 8" 4814 rs11569913 TNFRSF8 943 1 12120324 NM_001243 NP_001234 A/G S402G plus 16341603 693 EGP_SNPS PDR90 NIHPDR 152 0.09 0.09 0 152 1 120 by freq moderately conservative 153243 1p36 "tumor necrosis factor receptor superfamily, member 8" 4815 rs11570222 CTNND1 1500 11 57339484 NM_001331 NP_001322 A/G R888K plus 16342054 693 EGP_SNPS PDR90 NIHPDR 170 0.08 0.08 0 170 1 0.24 0 46 1 123 "by cluster,freq" Benign 0.093 21 Tolerant 0.89 3.07 26 conservative 601045 11q11 "catenin (cadherin-associated protein), delta 1" 4816 rs11570605 PLA2G6 8398 22 36889762 NM_003560 NP_003551 A/G V58I minus 16342600 693 EGP_SNPS PDR90 NIHPDR 176 0.02 0.02 0 176 1 120 by freq Benign 0.945 11 Tolerant 0.72 2.98 13 conservative 603604 22q13.1 "phospholipase A2, group VI (cytosolic, calcium-independent)" 4817 rs11570606 PLA2G6 8398 22 36889747 NM_003560 NP_003551 A/G R63G minus 16342601 693 EGP_SNPS PDR90 NIHPDR 176 0.02 0.02 0 176 1 120 by freq Potentially damaging 1.473 11 Tolerant 0.39 2.89 14 moderately radical 603604 22q13.1 "phospholipase A2, group VI (cytosolic, calcium-independent)" 4818 rs11571147 PGR 5241 11 100503972 NM_000926 NP_000917 C/G C347S minus 16343361 693 EGP_SNPS PDR90 NIHPDR 170 0.02 0.02 0 170 1 120 by freq Benign 0.763 12 Tolerant 1 3.15 21 moderately radical 607311 11q22-q23 progesterone receptor 4819 rs11571150 PGR 5241 11 100503682 NM_000926 NP_000917 G/T A444S minus 16343365 693 EGP_SNPS PDR90 NIHPDR 170 0.02 0.02 0 170 1 120 by freq Benign 0.103 12 Tolerant 0.66 2.89 97 moderately conservative 607311 11q22-q23 progesterone receptor 4820 rs11571707 BRCA2 675 13 31828598 NM_000059 NP_000050 C/T I2490T plus 16355882 693 EGP_SNPS PDR90 NIHPDR 168 0.04 0.04 0 168 1 120 by freq Possibly damaging 1.673 9 moderately conservative 600185 13q12.3 "breast cancer 2, early onset" 4821 rs11571746 BRCA2 675 13 31843108 NM_000059 NP_000050 C/T S2835P plus 16355930 693 EGP_SNPS PDR90 NIHPDR 162 0.01 0.01 0 162 1 120 by freq Benign 0.381 9 moderately conservative 600185 13q12.3 "breast cancer 2, early onset" 4822 rs11571769 BRCA2 675 13 31851550 NM_000059 NP_000050 A/G A2951T plus 16355965 693 EGP_SNPS PDR90 NIHPDR 168 0.01 0.01 0 168 1 120 by freq Potentially damaging 1.413 9 moderately conservative 600185 13q12.3 "breast cancer 2, early onset" 4823 rs11572243 CYP2J2 1573 1 60093633 NM_000775 NP_000766 A/G N124S minus 16356586 693 EGP_SNPS PDR90 NIHPDR 166 0.01 0.01 0 166 1 120 by freq Possibly damaging 1.712 22 Tolerant 0.4 2.8 39 conservative 601258 1p31.3-p31.2 "cytochrome P450, family 2, subfamily J, polypeptide 2" 4824 rs11573021 IGFBP7 3490 4 57817415 NM_001553 NP_001544 C/T L11F minus 16357740 693 EGP_SNPS PDR90 NIHPDR 176 0.07 0.07 0 176 1 120 by freq conservative 602867 4q12 insulin-like growth factor binding protein 7 4825 rs11573162 PLA2G2A 5320 1 20050309 NM_000300 NP_000291 C/T H19Y minus 16357935 693 EGP_SNPS PDR90 NIHPDR 174 0.01 0.01 0 174 1 0.04 0 48 1 123 "by cluster,freq" Possibly damaging 1.846 11 Intolerant 0 2.87 227 moderately conservative 172411 1p35 "phospholipase A2, group IIA (platelets, synovial fluid)" 4826 rs11573578 PTCH2 8643 1 44964426 NM_003738 NP_003729 C/G E346Q minus 16358464 693 EGP_SNPS PDR90 NIHPDR 178 0.01 0.01 0 178 1 120 by freq Borderline 1.199 11 Borderline 0.14 2.81 39 conservative 603673 1p33-p34 patched homolog 2 (Drosophila) 4827 rs11573590 PTCH2 8643 1 44961266 NM_003738 NP_003729 C/T T988M minus 16358481 693 EGP_SNPS PDR90 NIHPDR 166 0.05 0.06 0.02 214 2 0.17 0 48 1 123 "by cluster,freq" Possibly damaging 1.912 10 Intolerant 0.01 2.78 35 moderately conservative 603673 1p33-p34 patched homolog 2 (Drosophila) 4828 rs11573590 PTCH2 8643 1 44961266 NM_003738 NP_003729 C/T T988M minus 23840500 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.06 0.02 214 2 0.17 0 48 1 123 "by cluster,freq" Possibly damaging 1.912 10 Intolerant 0.01 2.78 35 moderately conservative 603673 1p33-p34 patched homolog 2 (Drosophila) 4829 rs11573986 TNFRSF14 8764 1 2524597 NM_003820 NP_003811 A/G G174E minus 16359070 693 EGP_SNPS PDR90 NIHPDR 176 0.01 0.01 0 176 1 120 by freq Potentially intolerant 0.1 2.76 51 moderately conservative 602746 1p36.3-p36.2 "tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)" 4830 rs11574151 PURG 29942 8 31009119 NM_013357 NP_037489 G/T E241A plus 16359291 693 EGP_SNPS PDR90 NIHPDR 180 0.02 0.02 0 180 1 120 by freq Possibly damaging 1.591 11 Borderline 0.18 3.13 31 moderately radical 8p11 purine-rich element binding protein G 4831 rs11574153 PURG 29942 8 31009765 NM_013357 NP_037489 C/T S26G plus 16359293 693 EGP_SNPS PDR90 NIHPDR 176 0.05 0.05 0 176 1 120 by freq moderately conservative 8p11 purine-rich element binding protein G 4832 rs11574395 WRN 7486 8 31144112 NM_000553 NP_000544 A/G V1339I plus 16359636 693 EGP_SNPS PDR90 NIHPDR 180 0.01 0.01 0 180 1 120 by freq Benign 0.62 6 Intolerant 0.02 2.98 23 conservative 604611 8p12-p11.2 Werner syndrome 4833 rs11574527 BIK 638 22 41849769 NM_001197 NP_001188 C/T L148P plus 16359911 649 FHCRC POPU1 USA (20) 40 0.05 0.05 0 40 1 120 by freq moderately conservative 603392 22q13.31 BCL2-interacting killer (apoptosis-inducing) 4834 rs11574542 ITGB7 3695 12 51872856 NM_000889 NP_000880 A/G G611E minus 16359937 649 FHCRC POPU1 USA (20) 3 0.03 0.05 0.01 42 2 120 by freq Possibly damaging 1.8 5 Tolerant 0.9 2.79 51 moderately conservative 147559 12q13.13 "integrin, beta 7" 4835 rs11574542 ITGB7 3695 12 51872856 NM_000889 NP_000880 A/G G611E minus 16359937 649 FHCRC POPU1 USA (20) 39 0.05 0.05 0.01 42 2 120 by freq Possibly damaging 1.8 5 Tolerant 0.9 2.79 51 moderately conservative 147559 12q13.13 "integrin, beta 7" 4836 rs11574570 LILRB4 11006 19 59866821 NM_006847 NP_006838 G/T R18S plus 16359978 649 FHCRC POPU1 USA (20) 40 0.13 0.13 0 40 1 120 by freq Possibly damaging 1.557 18 Tolerant 0.49 2.91 190 moderately radical 604821 19q13.4 "leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4" 4837 rs11574575 LILRB4 11006 19 59869960 NM_006847 NP_006838 A/G C330Y plus 16359995 649 FHCRC POPU1 USA (20) 40 0.05 0.05 0 40 1 120 by freq Probably damaging 2.373 29 Tolerant 0.43 2.94 123 radical 604821 19q13.4 "leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4" 4838 rs11574576 LILRB4 11006 19 59869974 NM_006847 NP_006838 A/G N335D plus 16359996 649 FHCRC POPU1 USA (20) 40 0.25 0.25 0 40 1 120 by freq Benign 0.154 29 Tolerant 1 2.9 134 conservative 604821 19q13.4 "leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4" 4839 rs11574589 LILRB4 11006 19 59870941 NM_006847 NP_006838 A/C K362T plus 16360013 649 FHCRC POPU1 USA (20) 40 0.08 0.08 0 40 1 120 by freq Borderline 1.219 29 Intolerant 0.01 2.88 131 moderately conservative 604821 19q13.4 "leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4" 4840 rs11574606 LILRA3 11026 19 59495979 NM_006865 NP_006856 C/T P3S minus 16360032 649 FHCRC POPU1 USA (20) 40 0.13 0.13 0 40 1 120 by freq Probably damaging 2.131 57 moderately conservative 604818 19q13.4 "leukocyte immunoglobulin-like receptor, subfamily A (without TM domain), member 3" 4841 rs11574633 ITGAX 3687 16 31274819 NM_000887 NP_000878 C/T W48R plus 16360081 649 FHCRC POPU1 USA (20) 40 0.05 0.05 0 40 1 120 by freq Benign 0.514 10 Tolerant 0.88 3.25 10 moderately radical 151510 16p11.2 "integrin, alpha X (antigen CD11C (p150), alpha polypeptide)" 4842 rs11574696 CASP6 839 4 110976511 NM_001226 NP_001217 A/C A34E minus 16360208 649 FHCRC POPU1 USA (20) 40 0.05 0.05 0 40 1 120 by freq Potentially damaging 1.324 10 Tolerant 0.3 2.89 29 moderately radical 601532 4q25 "caspase 6, apoptosis-related cysteine protease" 4843 rs11574697 CASP6 839 4 110976509 NM_001226 NP_001217 A/G E35K minus 16360209 649 FHCRC POPU1 USA (20) 40 0.2 0.2 0 40 1 120 by freq Potentially damaging 1.336 10 Tolerant 0.86 2.9 30 moderately conservative 601532 4q25 "caspase 6, apoptosis-related cysteine protease" 4844 rs11574885 NOTCH1 4851 9 136689080 NM_017617 NP_060087 A/G Q300R minus 16360541 649 FHCRC POPU1 USA (20) 40 0.2 0.2 0 40 1 120 by freq Possibly damaging 1.55 22 Tolerant 0.52 2.86 25 conservative 190198 9q34.3 "Notch homolog 1, translocation-associated (Drosophila)" 4845 rs11575194 IGFBP5 3488 2 217369234 NM_000599 NP_000590 C/T R138W minus 16361166 693 EGP_SNPS PDR90 NIHPDR 174 0.03 0.03 0 174 1 120 by freq Potentially damaging 1.307 5 Borderline 0.17 2.85 26 moderately radical 146734 2q33-q36 insulin-like growth factor binding protein 5 4846 rs11575216 APOF 319 12 55041724 NM_001638 NP_001629 C/G A178G minus 16361194 693 EGP_SNPS PDR90 NIHPDR 178 0.01 0.01 0 178 1 120 by freq moderately conservative 107760 12q13.13 apolipoprotein F 4847 rs11575245 STAT2 6773 12 55023518 NM_005419 NP_005410 G/T Q826H minus 16361239 693 EGP_SNPS PDR90 NIHPDR 178 0.02 0.02 0 178 1 120 by freq conservative 600556 12q13.13 "signal transducer and activator of transcription 2, 113kDa" 4848 rs11575542 DDC 1644 7 50305196 NM_000790 NP_000781 A/G R462Q minus 16361539 693 EGP_SNPS PDR90 NIHPDR 178 0.06 0.06 0 178 1 120 by freq Benign 0.137 69 Tolerant 0.38 2.8 77 conservative 107930 7p11 dopa decarboxylase (aromatic L-amino acid decarboxylase) 4849 rs11575840 NCR3 259197 6 31665619 NM_147130 NP_667341 A/G A103T minus 24359473 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.04 0.04 0 46 1 0.02 0 92 2 123 by freq Borderline 1.227 13 moderately conservative 6p21.3 natural cytotoxicity triggering receptor 3 4850 rs11598233 SCD 6319 10 102106301 NM_005063 NP_005054 A/C M224L plus 23492118 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.4 0 48 1 0.36 0.07 94 2 123 "by doubleHit,freq,cluster" Benign 0.085 55 Tolerant 1 2.78 138 conservative 604031 10q23-q24 stearoyl-CoA desaturase (delta-9-desaturase) 4851 rs11599164 ANK3 288 10 61501990 NM_020987 NP_066267 G/T H2885Q plus 24510408 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.02 0 44 1 123 by freq conservative 600465 10q21 "ankyrin 3, node of Ranvier (ankyrin G)" 4852 rs11604561 PIK3C2A 5286 11 17075263 NM_002645 NP_002636 C/T T1415A plus 16537813 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.13 0.12 0.02 168 2 0.07 0 46 1 123 "HapMap,freq" Intolerant 0.05 3.1 18 moderately conservative 603601 11p15.5-p14 "phosphoinositide-3-kinase, class 2, alpha polypeptide" 4853 rs11604561 PIK3C2A 5286 11 17075263 NM_002645 NP_002636 C/T T1415A plus 24472154 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.12 0.02 168 2 0.07 0 46 1 123 "HapMap,freq" Intolerant 0.05 3.1 18 moderately conservative 603601 11p15.5-p14 "phosphoinositide-3-kinase, class 2, alpha polypeptide" 4854 rs11604671 ANKK1 255239 11 112773269 NM_178510 NP_848605 A/G G318R plus 24566321 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.46 0 48 1 0.07 0 86 2 123 "by doubleHit,freq,cluster" Tolerant 0.46 3.04 8 moderately radical 608774 11q23.2 ankyrin repeat and kinase domain containing 1 4855 rs11638390 USP8 9101 15 48569995 NM_005154 NP_005145 A/G T739A plus 24665708 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 0.07 0 46 1 123 "by doubleHit,freq" Benign 0.497 9 Tolerant 0.58 2.78 114 moderately conservative 603158 15q15.3 ubiquitin specific protease 8 4856 rs11652709 EPX 8288 17 53626093 NM_000502 NP_000493 C/G Q122H plus 24704221 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.33 0 48 1 0.18 0.08 94 2 123 by freq Probably damaging 2.08 21 Tolerant 0.57 2.8 30 conservative 131399 17q23.1 eosinophil peroxidase 4857 rs11653020 HELZ 9931 17 62535205 XM_375485 XP_375485 A/G A1530V plus 24593875 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 123 "by cluster,freq" moderately conservative 606699 17q24.3 helicase with zinc finger domain 4858 rs11653658 DHX33 56919 17 5294928 NM_020162 NP_064547 C/G H483D plus 16743193 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.08 0.09 0.03 168 2 0.13 0 46 1 123 "HapMap,freq,cluster" Probably damaging 2.039 7 Potentially intolerant 0.1 3.12 31 moderately conservative 17p13.3 DEAH (Asp-Glu-Ala-His) box polypeptide 33 4859 rs11653658 DHX33 56919 17 5294928 NM_020162 NP_064547 C/G H483D plus 23625727 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.09 0.03 168 2 0.13 0 46 1 123 "HapMap,freq,cluster" Probably damaging 2.039 7 Potentially intolerant 0.1 3.12 31 moderately conservative 17p13.3 DEAH (Asp-Glu-Ala-His) box polypeptide 33 4860 rs11669576 LDLR 3949 19 11083300 NM_000527 NP_000518 A/G A391T plus 16797693 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.04 0.04 0 120 1 120 "HapMap,freq" Benign 0.004 35 Tolerant 0.64 2.8 53 moderately conservative 606945 19p13.3 low density lipoprotein receptor (familial hypercholesterolemia) 4861 rs11670727 NAPSA 9476 19 55554580 NM_004851 NP_004842 C/T A310T plus 16801016 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.08 0.08 0 120 1 120 "HapMap,freq" Benign 0.242 6 Tolerant 0.57 2.78 70 moderately conservative 605631 19q13.33 napsin A aspartic peptidase 4862 rs11670988 HIPK4 147746 19 45578833 NM_144685 NP_653286 C/T R302Q plus 16801872 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.09 0.09 0 120 1 120 "HapMap,freq" Intolerant 0.01 3.16 137 conservative 19q13.2 homeodomain interacting protein kinase 4 4863 rs11718329 ZNF589 51385 3 48284832 NM_016089 NP_057173 C/G T213R plus 16981706 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.31 0.31 0 120 1 120 "HapMap,doubleHit,freq" Benign 0.117 5 moderately conservative 3p21 zinc finger protein 589 4864 rs11740179 HSD17B4 3295 5 118889612 NM_000414 NP_000405 A/G I559V plus 23306367 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.4 0 48 1 0.44 0.03 94 2 123 "by cluster,freq" Borderline 1.085 18 Borderline 0.15 3 30 conservative 601860 5q21 hydroxysteroid (17-beta) dehydrogenase 4 4865 rs11749126 ADAMTS19 171019 5 129067955 NM_133638 NP_598377 A/T Y1089F plus 24380118 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.15 0.15 0 46 1 0.02 0 46 1 123 by freq Tolerant 0.69 2.8 18 conservative 607513 5q31 "a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19" 4866 rs11765552 LMTK2 22853 7 97466766 NM_014916 NP_055731 A/T L780M plus 24454657 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.44 0 48 1 0.17 0.03 94 2 123 by freq conservative 7q22.1 lemur tyrosine kinase 2 4867 rs11805194 NUP133 55746 1 225938469 NM_018230 NP_060700 C/T I294V plus 24292795 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.25 0 48 1 0.18 0.07 92 2 123 by freq Benign 0.782 7 Tolerant 0.66 2.8 12 conservative 607613 1q42.13 nucleoporin 133kDa 4868 rs11841997 GUCY1B2 2974 13 50500360 NM_004129 NP_004120 C/G M128I plus 23343593 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.26 0.23 94 2 123 "by doubleHit,freq,cluster" Borderline 1.028 10 Tolerant 0.35 2.89 23 conservative 603695 13q14.2-q14.3 "guanylate cyclase 1, soluble, beta 2" 4869 rs11845046 MIA2 117153 14 38785952 NM_054024 NP_473365 A/G I141M plus 24112809 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.3 0.2 70 2 123 "by doubleHit,freq,cluster" conservative 608001 14q13.2 melanoma inhibitory activity 2 4870 rs11847087 SYNE2 23224 14 63589773 NM_015180 NP_055995 A/G N3129S plus 23647974 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.02 0.02 0 46 1 0.26 0 46 1 123 "by cluster,freq" conservative 608442 14q23.2 "spectrin repeat containing, nuclear envelope 2" 4871 rs11852361 BLM 641 15 89127103 NM_000057 NP_000048 C/T P868L plus 17531281 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.02 0.02 0 120 1 120 "HapMap,freq" Probably damaging 2.724 5 Potentially intolerant 0.1 2.8 18 moderately conservative 604610 15q26.1 Bloom syndrome 4872 rs11858624 PYGO1 26108 15 53625877 NM_015617 NP_056432 G/T P299H plus 24613406 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.07 0 46 1 123 "by doubleHit,freq" Tolerant 0.22 2.94 20 moderately conservative 606902 15q21.1 pygopus 1 4873 rs11861251 ITGAM 3684 16 31196897 NM_000632 NP_000623 C/T M441T plus 17558438 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.15 0.15 0 120 1 120 "HapMap,freq" Borderline 1.095 12 Tolerant 0.63 2.83 19 moderately conservative 120980 16p11.2 "integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide)" 4874 rs11880651 ZNF283 284349 19 49023638 XM_371174 XP_371174 C/T C229R plus 24684906 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.38 0 48 1 0.19 0.06 94 2 123 by freq radical 19q13.32 zinc finger protein 283 4875 rs11896614 PRKCN 23683 2 37455195 NM_005813 NP_005804 C/T N42D plus 24648731 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.04 0.04 0 46 1 123 by freq Borderline 1.193 6 conservative 607077 2p21 "protein kinase C, nu" 4876 rs11908296 DDX27 55661 20 47275067 NM_017895 NP_060365 G/T G206V plus 24792661 1303 SEQUENOM CEPH CEPH (92) 184 0.26 0.26 0 184 1 123 "by doubleHit,cluster" possibly damaging 1.994 5 Borderline 0.12 2.9 14 moderately radical 20q13.13 DEAD (Asp-Glu-Ala-Asp) box polypeptide 27 4877 rs11934749 CORIN 10699 4 47507992 NM_006587 NP_006578 C/T H525R plus 24658457 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.09 0 46 1 123 "by doubleHit,freq,cluster" Tolerant 0.59 3.05 15 conservative 605236 4p13-p12 "corin, serine protease" 4878 rs11959820 PPARGC1B 133522 5 149192703 NM_133263 NP_573570 A/C R292S plus 23726964 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 0.2 0.08 94 2 123 "by cluster,freq" moderately radical 608886 5q33.1 "peroxisome proliferative activated receptor, gamma, coactivator 1, beta" 4879 rs11976480 AOAH 313 7 36536912 NM_001637 NP_001628 C/T D28N plus 24005338 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.31 0 48 1 0.22 0.25 94 2 123 "by doubleHit,freq,cluster" conservative 102593 7p14-p12 acyloxyacyl hydrolase (neutrophil) 4880 rs11993776 ZFPM2 23414 8 106882694 NM_012082 NP_036214 C/G A403G plus 23545420 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.21 0.28 94 2 123 "by doubleHit,freq,cluster" moderately conservative 603693 8q23 "zinc finger protein, multitype 2" 4881 rs12021720 DBT 1629 1 100384081 NM_001918 NP_001909 C/T S384G plus 18070104 885 TSC-CSHL HapMap-CEPH-30-trios 118 0.08 0.08 0 118 1 121 "HapMap,doubleHit,freq" Benign 0.494 10 moderately conservative 248610 1p31 dihydrolipoamide branched chain transacylase (E2 component of branched chain keto acid dehydrogenase complex; maple syrup urine disease) 4882 rs12022378 DCLRE1B 64858 1 114160431 NM_022836 NP_073747 C/T H61Y plus 23851621 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.19 0.19 0 42 1 0.21 0.17 94 2 123 "by cluster,freq" Tolerant 1 2.84 30 moderately conservative 1p13.1 "DNA cross-link repair 1B (PSO2 homolog, S. cerevisiae)" 4883 rs12026290 PHC2 1912 1 33489227 NM_198040 NP_932157 C/T V475M plus 24256743 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.29 0 48 1 0.1 0.07 92 2 123 "by doubleHit,freq" Tolerant 0.23 2.92 11 conservative 602979 1p34.3 polyhomeotic-like 2 (Drosophila) 4884 rs12038198 CGN 57530 1 148310275 NM_020770 NP_065821 A/G R485Q plus 23864934 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 0.19 0 48 1 123 "by cluster,freq" Benign 0.9 6 Tolerant 0.6 2.82 38 conservative 1q21 cingulin 4885 rs12075844 LAMB3 3914 1 206185648 NM_000228 NP_000219 C/T N690S plus 24155065 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.24 0.26 92 2 123 "by cluster,freq" Benign 0.27 5 conservative 150310 1q32 "laminin, beta 3" 4886 rs12110451 MDN1 23195 6 90539118 NM_014611 NP_055426 C/T I660V plus 24016916 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.15 0.15 0 46 1 0.18 0.01 94 2 123 "by cluster,freq" conservative 6q15 "MDN1, midasin homolog (yeast)" 4887 rs12192544 CYP39A1 51302 6 46728211 NM_016593 NP_057677 C/G R23P plus 24145756 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.17 0 48 1 0.12 0.1 90 2 123 "by cluster,freq" Potentially intolerant 0.07 2.75 19 moderately radical 605994 6p21.1-p11.2 "cytochrome P450, family 39, subfamily A, polypeptide 1" 4888 rs12210538 SLC22A16 85413 6 110866701 NM_033125 NP_149116 A/G M409T plus 24462140 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.2 0.2 0 44 1 0.04 0.03 70 2 123 by freq Borderline 1.01 6 Intolerant 0.04 2.79 21 moderately conservative 608276 6q22.1 "solute carrier family 22 (organic cation transporter), member 16" 4889 rs12236219 ZNF169 169841 9 94142536 NM_194320 NP_919301 C/T R368C plus 24071042 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.17 0.14 94 2 123 "by cluster,freq" Probably damaging 2.495 9 Intolerant 0 2.79 31 radical 603404 9q22.32 zinc finger protein 169 4890 rs12313736 SSPN 8082 12 26275226 NM_005086 NP_005077 A/G V228I plus 23433487 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.12 0 42 1 123 "by cluster,freq" Benign 0.86 6 conservative 601599 12p11.2 sarcospan (Kras oncogene-associated gene) 4891 rs12350212 ZNF169 169841 9 94143183 NM_194320 NP_919301 C/G Q583H plus 24529192 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 123 "by doubleHit,freq" Probably damaging 2.125 5 Intolerant 0.01 2.85 23 conservative 603404 9q22.32 zinc finger protein 169 4892 rs12440118 SH3BP3 64397 15 40531386 NM_022473 NP_071918 A/G W103R plus 24393543 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.21 0 48 1 0.04 0 46 1 123 by freq moderately radical 15q14 zinc finger protein 106 homolog (mouse) 4893 rs12440300 GLCE 26035 15 67335392 XM_290631 XP_290631 A/G M65V plus 19321276 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.02 0.02 0 120 1 120 "HapMap,freq" conservative 15q22.31 glucuronyl C5-epimerase 4894 rs12449580 AIPL1 23746 17 6277971 NM_014336 NP_055151 C/G D90H plus 24208893 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.22 0.22 0 46 1 0.25 0.25 94 2 123 "by doubleHit,freq,cluster" Probably damaging 1.997 9 Borderline 0.16 2.96 33 moderately conservative 604392 17p13.1 aryl hydrocarbon receptor interacting protein-like 1 4895 rs12456560 KNTC2 10403 18 2585443 NM_006101 NP_006092 G/T E348D plus 24468834 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.06 0.06 94 2 123 by freq Borderline 1.042 6 Borderline 0.2 2.81 12 conservative 607272 18p11.31 kinetochore associated 2 4896 rs12457323 LAMA3 3909 18 19678984 NM_198129 NP_937762 C/T V1206A plus 24218059 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.07 0.06 92 2 123 by freq moderately conservative 600805 18q11.2 "laminin, alpha 3" 4897 rs12461754 DDX39 10212 19 14381829 NM_138998 NP_620551 A/G L311F plus 19404201 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.11 0.12 0.01 166 2 0.12 0.13 92 2 123 "HapMap,freq,cluster" conservative 19p13.13 DEAD (Asp-Glu-Ala-Asp) box polypeptide 39 4898 rs12461754 DDX39 10212 19 14381829 NM_138998 NP_620551 A/G L311F plus 24061713 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.13 0.12 0.01 166 2 0.12 0.13 92 2 123 "HapMap,freq,cluster" conservative 19p13.13 DEAD (Asp-Glu-Ala-Asp) box polypeptide 39 4899 rs12475068 UGT1A5 54579 2 234404110 NM_019078 NP_061951 C/G A158G plus 19452339 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.13 0.13 0 120 1 120 "HapMap,doubleHit,freq" Benign 0.806 78 Tolerant 1 2.8 156 moderately conservative 606430 2q37 "UDP glycosyltransferase 1 family, polypeptide A5" 4900 rs12514417 ALDH7A1 501 5 125915614 NM_001182 NP_001173 G/T K411Q plus 23939488 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.13 0.13 0 46 1 0.15 0 48 1 123 "by doubleHit,freq,cluster" Benign 0.106 23 Tolerant 0.46 2.81 23 moderately conservative 107323 5q31 "aldehyde dehydrogenase 7 family, member A1" 4901 rs12520591 ITGA1 3672 5 52265502 NM_181501 NP_852478 G/T I961M plus 23983003 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.05 0.04 94 2 123 "by cluster,freq" Potentially intolerant 0.1 2.76 17 conservative 192968 5q11.2 "integrin, alpha 1" 4902 rs12530146 MDN1 23195 6 90465463 NM_014611 NP_055426 C/T E3004K plus 23983289 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.14 0.07 94 2 123 "by cluster,freq" moderately conservative 6q15 "MDN1, midasin homolog (yeast)" 4903 rs12541381 ZNF406 57623 8 135719030 NM_020863 NP_065914 A/G P102S plus 24040982 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.23 0 48 1 0.25 0.19 94 2 123 "by doubleHit,freq,cluster" Intolerant 0.03 3.01 12 moderately conservative 8q24.22 zinc finger protein 406 4904 rs12586264 IPO4 79711 14 23723363 NM_024658 NP_078934 C/G P580A plus 24217271 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.36 0.03 232 2 0.3 0.18 94 2 123 "by cluster,freq" conservative 14q11.2 importin 4 4905 rs12586264 IPO4 79711 14 23723363 NM_024658 NP_078934 C/G P580A plus 24792528 1303 SEQUENOM CEPH CEPH (92) 184 0.37 0.36 0.03 232 2 0.3 0.18 94 2 123 "by cluster,freq" conservative 14q11.2 importin 4 4906 rs12590446 h461 390443 14 20094626 XM_372508 XP_372508 A/G F169S plus 24226634 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.17 0 48 1 0.34 0.08 94 2 123 by freq radical 14q11.2 ribonuclease-like protein 9 4907 rs12615112 ST6GalII 84620 2 106909043 NM_032528 NP_115917 C/T I341V plus 23874968 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.04 0.04 0 46 1 0.37 0.13 70 2 123 "by doubleHit,freq,cluster" Benign 0.336 8 Tolerant 0.63 2.75 69 conservative 608472 2q11.2-q12.1 "beta-galactoside alpha-2,6-sialyltransferase II" 4908 rs12632456 FLNB 2317 3 58093595 NM_001457 NP_001448 A/G V1471M plus 23282968 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.33 0 48 1 0.25 0.3 94 2 123 "by cluster,freq" Potentially damaging 1.43 25 conservative 603381 3p14.3 "filamin B, beta (actin binding protein 278)" 4909 rs12645298 SYNPO2 171024 4 120305588 XM_050219 XP_050219 C/G G154A plus 23910760 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.21 0 48 1 0.25 0.25 94 2 123 "by doubleHit,freq,cluster" moderately conservative 4q27 synaptopodin 2 4910 rs12648093 NUDT6 11162 4 124196363 NM_007083 NP_009014 A/G C114R plus 24348735 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.35 0.35 0 46 1 0.12 0.14 82 2 123 "by doubleHit,freq,cluster" Probably damaging 2.284 8 Tolerant 0.69 2.95 31 radical 606261 4q26 nudix (nucleoside diphosphate linked moiety X)-type motif 6 4911 rs12651301 HOZFP 152518 4 47742404 NM_152995 NP_694540 A/G P246L plus 24658697 1371 PERLEGEN AFD_EUR_PANEL European American (24) 40 0.3 0.3 0 40 1 0.26 0.02 78 2 123 by freq Tolerant 0.21 2.78 25 moderately conservative 4p12 ovarian zinc finger protein 4912 rs12670788 PODXL 5420 7 130652967 NM_005397 NP_005388 A/G S194L plus 24502104 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.44 0 48 1 0.26 0.18 94 2 123 "by doubleHit,freq,cluster" Tolerant 0.22 2.76 9 moderately radical 602632 7q32-q33 podocalyxin-like 4913 rs12692566 LY75 4065 2 160501934 NM_002349 NP_002340 A/C K1321N plus 24313282 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.23 0 48 1 0.1 0.01 92 2 123 "by doubleHit,freq,cluster" Possibly damaging 1.719 5 moderately conservative 604524 2q24 lymphocyte antigen 75 4914 rs12720356 TYK2 7297 19 10330975 NM_003331 NP_003322 G/T I684S minus 20399256 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 46 0.09 0.09 0 46 1 121 by freq Possibly damaging 1.836 6 Intolerant 0 2.82 35 moderately radical 176941 19p13.2 tyrosine kinase 2 4915 rs12722058 HLA-DQA1 3117 6 32717191 NM_002122 NP_002113 A/G R70Q plus 24814207 1303 SEQUENOM CEPH CEPH (92) 184 0.4 0.4 0 184 1 123 by freq Benign 0.568 188 Borderline 0.13 2.84 302 conservative 146880 6p21.3 "major histocompatibility complex, class II, DQ alpha 1" 4916 rs12731961 CAPN9 10753 1 227230048 NM_006615 NP_006606 C/T R522W plus 23236844 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.27 0.13 82 2 123 "by cluster,freq" Possibly damaging 1.858 40 Intolerant 0.01 2.99 75 moderately radical 606401 1q42.11-q42.3 calpain 9 (nCL-4) 4917 rs12748250 LAMB3 3914 1 206184724 NM_000228 NP_000219 A/T M852L plus 24634618 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.17 0 48 1 0.05 0 44 1 123 by freq Benign 0.677 5 conservative 150310 1q32 "laminin, beta 3" 4918 rs12765679 TACC2 10579 10 123893123 NM_206862 NP_996744 A/G E1916K plus 24570998 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.28 0.28 0 46 1 0.07 0 44 1 123 by freq moderately conservative 605302 10q26 "transforming, acidic coiled-coil containing protein 2" 4919 rs12770335 SGPL1 8879 10 72274269 NM_003901 NP_003892 G/T V21L plus 20661200 885 TSC-CSHL HapMap-CEPH-30-trios 120 0.14 0.14 0 120 1 121 "HapMap,freq" Benign 0.793 7 Tolerant 0.54 3.1 10 conservative 603729 10q21 sphingosine-1-phosphate lyase 1 4920 rs12828016 PRKWNK1 65125 12 868626 NM_018979 NP_061852 G/T M1808I plus 23775762 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.46 0 48 1 0.35 0.18 94 2 123 "by doubleHit,freq,cluster" conservative 605232 12p13.3 "protein kinase, lysine deficient 1" 4921 rs12931472 ABCC6 368 16 16188508 NM_001171 NP_001162 A/G V614A plus 23543392 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.33 0.33 0 48 1 0.27 0.14 94 2 123 "by doubleHit,freq,cluster" Tolerant 0.55 2.78 35 moderately conservative 603234 16p13.1 "ATP-binding cassette, sub-family C (CFTR/MRP), member 6" 4922 rs12933084 WFDC1 58189 16 82918034 NM_021197 NP_067020 A/G K217R plus 23509498 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.25 0 48 1 0.31 0.06 94 2 123 "by doubleHit,freq,cluster" conservative 605322 16q24.3 WAP four-disulfide core domain 1 4923 rs12968116 ATP8B1 5205 18 53473500 NM_005603 NP_005594 C/T R952Q plus 24691328 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.02 0 46 1 123 by freq Possibly damaging 1.591 9 Tolerant 0.37 2.79 31 conservative 602397 18q21 "ATPase, Class I, type 8B, member 1" 4924 rs12974842 ZNF100 163227 19 21740410 NM_173531 NP_775802 C/T M8V plus 24679917 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 0.06 0 48 1 123 by freq Borderline 1.07 5 conservative 603982 19p13.11 zinc finger protein 100 4925 rs12990449 LRP1B 53353 2 142401642 NM_018557 NP_061027 C/T Q48R plus 23888425 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.26 0.13 94 2 123 "by cluster,freq" Borderline 1.052 7 Tolerant 0.77 2.86 21 conservative 608766 2q21.2 low density lipoprotein-related protein 1B (deleted in tumors) 4926 rs13096789 TA-KRP 84541 3 67137339 NM_032505 NP_115894 C/T C394R plus 24309129 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.05 0.05 94 2 123 by freq Tolerant 0.51 2.78 24 radical 3p14 T-cell activation kelch repeat protein 4927 rs13144371 IBSP 3381 4 89089925 NM_004967 NP_004958 A/G D213G plus 24294794 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.21 0 48 1 0.12 0.07 86 2 123 by freq Borderline 1.211 9 moderately conservative 147563 4q21-q25 "integrin-binding sialoprotein (bone sialoprotein, bone sialoprotein II)" 4928 rs13166360 ADCY2 108 5 7573881 NM_020546 NP_065433 G/T V142L plus 24313214 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.23 0 48 1 123 by freq Potentially damaging 1.345 13 Potentially intolerant 0.07 2.85 26 conservative 103071 5p15.3 adenylate cyclase 2 (brain) 4929 rs13194995 DST 667 6 56578510 NM_020388 NP_065121 A/T T2422S plus 24379443 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.38 0 48 1 0.24 0.08 94 2 123 "by doubleHit,freq" moderately conservative 113810 6p12-p11 "bullous pemphigoid antigen 1, 230/240kDa" 4930 rs13243961 NUPL2 11097 7 23013503 NM_007342 NP_031368 A/G D391N plus 24397833 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.02 0 94 2 123 by freq Tolerant 0.83 2.81 9 conservative 7p15 nucleoporin like 2 4931 rs13306731 SOAT1 6646 1 176052235 NM_003101 NP_003092 A/G Q526R plus 24152487 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 0.27 0 48 1 123 "by cluster,freq" Benign 0.084 8 Tolerant 1 2.87 28 conservative 102642 1q25 sterol O-acyltransferase (acyl-Coenzyme A: cholesterol acyltransferase) 1 4932 rs13328900 CD5 921 11 60649811 NM_014207 NP_055022 C/T A471V plus 24569941 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.4 0 48 1 0.32 0 44 1 123 "by doubleHit,freq" Potentially damaging 1.413 8 moderately conservative 153340 11q13 CD5 antigen (p56-62) 4933 rs13406898 UGT1A3 54659 2 234420203 NM_019093 NP_061966 C/T T144I plus 23081645 885 TSC-CSHL HapMap-CEPH-30-trios 116 0.11 0.11 0 116 1 121 "HapMap,doubleHit,freq" Potentially damaging 1.425 83 Intolerant 0.01 2.79 161 moderately conservative 606428 2q37 "UDP glycosyltransferase 1 family, polypeptide A3" 4934 rs13434465 ACOX3 8310 4 8509019 NM_003501 NP_003492 C/T D497N plus 23253549 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.04 0 46 1 123 "by cluster,freq" Borderline 1.086 7 Tolerant 0.5 2.83 19 conservative 603402 4p15.3 "acyl-Coenzyme A oxidase 3, pristanoyl" 4935 rs13447459 CDC7 8317 1 91679362 NM_003503 NP_003494 A/C Q23P plus 23133284 693 EGP_SNPS PDR90 NIHPDR 176 0.01 0.01 0 176 1 121 HapMap Benign 0.116 7 moderately conservative 603311 1p22 CDC7 cell division cycle 7 (S. cerevisiae) 4936 rs13447539 CDC7 8317 1 91697849 NM_003503 NP_003494 A/G K441R plus 23133383 693 EGP_SNPS PDR90 NIHPDR 176 0.01 0.01 0 176 1 0.08 0 48 1 123 "by cluster,freq" Potentially damaging 1.252 9 Tolerant 0.72 2.84 15 conservative 603311 1p22 CDC7 cell division cycle 7 (S. cerevisiae) 4937 rs16824518 INPP5B 3633 1 38084408 XM_375718 XP_375718 G/T P55Q plus 23175524 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.35 0 48 1 0.38 0.11 94 2 123 by freq moderately conservative 147264 1p34 "inositol polyphosphate-5-phosphatase, 75kDa" 4938 rs16829204 IL22RA1 58985 1 24199994 NM_021258 NP_067081 C/T V205I plus 23668065 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.26 0 46 1 123 by freq conservative 605457 1p36.11 "interleukin 22 receptor, alpha 1" 4939 rs16840892 SORCS2 57537 4 7834132 NM_020777 NP_065828 C/T T545M plus 24164053 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.15 0.15 94 2 123 by freq Possibly damaging 1.665 5 Borderline 0.11 2.85 39 moderately conservative 606284 4p16.1 sortilin-related VPS10 domain containing receptor 2 4940 rs16841018 DNAH7 56171 2 196546211 NM_018897 NP_061720 C/T I2809V plus 23721205 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.3 0 44 1 123 by freq Benign 0.322 5 Borderline 0.16 2.77 25 conservative 2q33.1 "dynein, axonemal, heavy polypeptide 7" 4941 rs16844401 HGFAC 3083 4 3486621 NM_001528 NP_001519 A/G R509H plus 23895689 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.07 0.04 94 2 123 by freq Possibly damaging 1.582 7 Tolerant 0.21 2.79 46 conservative 604552 4p16 HGF activator 4942 rs16846208 ATF6 22926 1 158492970 NM_007348 NP_031374 C/T P157S plus 23843009 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.27 0.19 94 2 123 by freq Benign 0.442 5 moderately conservative 605537 1q22-q23 activating transcription factor 6 4943 rs16849342 NAV1 89796 1 198486101 NM_020443 NP_065176 C/G Q937H plus 23166081 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.04 0 46 1 123 by freq conservative 1q32.3 neuron navigator 1 4944 rs16851681 ATP10D 57205 4 47419899 NM_020453 NP_065186 A/G R1183K plus 23726989 1371 PERLEGEN AFD_EUR_PANEL European American (24) 40 0.18 0.18 0 40 1 0.32 0.19 78 2 123 by freq Tolerant 1 2.86 15 conservative 4p12 "ATPase, Class V, type 10D" 4945 rs16855035 MORC 27136 3 110160512 NM_014429 NP_055244 C/G S982W plus 23343839 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.05 0.05 0 44 1 0.05 0 44 1 123 by freq radical 603205 3q13 microrchidia homolog (mouse) 4946 rs16858780 CHRD 8646 3 185586605 NM_003741 NP_003732 A/C M630L plus 23391148 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.18 0.18 0 44 1 0.32 0.01 74 2 123 by freq Benign 0.629 6 Tolerant 0.76 2.86 13 conservative 603475 3q27 chordin 4947 rs16858811 IL8RA 3577 2 218855349 NM_000634 NP_000625 G/T M31R minus 28446158 596 PGA-UW-FHCRC PGA-EUROPEAN-PANEL 44 0.02 0.02 0 44 1 0.11 0 44 1 123 by freq Potentially damaging 1.397 22 Tolerant 0.62 2.85 36 moderately conservative 146929 2q35 "interleukin 8 receptor, alpha" 4948 rs16859180 STK36 27148 2 219378973 NM_015690 NP_056505 C/T R477W plus 23727576 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.08 0.01 94 2 123 by freq Probably damaging 2.257 5 moderately radical 607652 2q35 "serine/threonine kinase 36 (fused homolog, Drosophila)" 4949 rs16859886 SAC 55811 1 164597529 NM_018417 NP_060887 A/G T234M plus 23180261 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.09 0.09 0 46 1 0.11 0 46 1 123 by freq moderately conservative 605205 1q24 testicular soluble adenylyl cyclase 4950 rs16867245 TAF1B 9014 2 10010442 NM_005680 NP_005671 C/T T487M plus 24162699 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 0.14 0.16 92 2 123 by freq moderately conservative 604904 2p25 "TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa" 4951 rs16870908 TAP2 6891 6 32898067 NM_018833 NP_061313 A/G L647F plus 23718111 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.21 0 38 1 123 by freq conservative 170261 6p21.3 "transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)" 4952 rs16871473 PRLR 5618 5 35120404 NM_000949 NP_000940 C/T I100V plus 23986596 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.04 0.01 88 2 123 by freq Benign 0.288 18 Tolerant 0.78 2.78 31 conservative 176761 5p14-p13 prolactin receptor 4953 rs16871612 CAPN11 11131 6 44253041 NM_007058 NP_008989 C/T V404A plus 24145548 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.02 0.02 0 46 1 0.36 0 44 1 123 by freq Benign 0.149 44 Tolerant 0.99 2.9 76 moderately conservative 604822 6p12 calpain 11 4954 rs16875099 MEP1A 4224 6 46914768 NM_005588 NP_005579 C/T T726M plus 24796316 1303 SEQUENOM CEPH CEPH (92) 184 0.48 0.48 0 184 1 123 by freq Benign 0.263 8 moderately conservative 600388 6p12-p11 "meprin A, alpha (PABA peptide hydrolase)" 4955 rs16876571 DTNBP1 84062 6 15632658 NM_183040 NP_898861 A/G H297Y plus 28447152 914 HG_BONN_CNS_SNPS EURO96 European 178 0.03 0.03 0 178 1 123 by freq moderately conservative 607145 6p22.3 dystrobrevin binding protein 1 4956 rs16878594 ZCCHC9 84240 5 80636375 NM_032280 NP_115656 C/G P15A plus 23404764 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.02 0 46 1 123 by freq Benign 0.504 8 conservative 5q14.1 "zinc finger, CCHC domain containing 9" 4957 rs16881897 NFE2L3 9603 7 25998101 NM_004289 NP_004280 A/G P515S minus 24811506 1303 SEQUENOM CEPH CEPH (92) 184 0.4 0.4 0 184 1 123 by freq Borderline 1.176 6 Borderline 0.14 2.86 16 moderately conservative 604135 7p15-p14 nuclear factor (erythroid-derived 2)-like 3 4958 rs16882046 MDN1 23195 6 90431004 NM_014611 NP_055426 A/G I4720T plus 23983029 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.04 0.03 94 2 123 by freq moderately conservative 6q15 "MDN1, midasin homolog (yeast)" 4959 rs16885197 TINAG 27283 6 54281314 NM_014464 NP_055279 A/G T3A plus 23339781 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.11 0 46 1 123 by freq Borderline 1.183 5 moderately conservative 606749 6p11.2-p12 tubulointerstitial nephritis antigen 4960 rs16893917 PGBD1 84547 6 28377386 NM_032507 NP_115896 A/G M592I plus 23916061 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.2 0.1 94 2 123 by freq conservative 6p21.33 piggyBac transposable element derived 1 4961 rs16896012 HLA-A 3105 6 30019186 NM_002116 NP_002107 A/G R169H plus 24819835 1303 SEQUENOM CEPH CEPH (92) 184 0.12 0.12 0 184 1 123 by freq Benign 0.296 442 conservative 142800 6p21.3 "major histocompatibility complex, class I, A" 4962 rs16896284 HLA-A 3105 6 30018704 NM_002116 NP_002107 C/G R89G plus 24819802 1303 SEQUENOM CEPH CEPH (92) 184 0.07 0.07 0 184 1 123 by freq Borderline 1.037 442 moderately radical 142800 6p21.3 "major histocompatibility complex, class I, A" 4963 rs16896294 HLA-A 3105 6 30019235 NM_002116 NP_002107 G/T D185E plus 24819847 1303 SEQUENOM CEPH CEPH (92) 184 0.1 0.1 0 184 1 123 by freq Benign 0.683 442 conservative 142800 6p21.3 "major histocompatibility complex, class I, A" 4964 rs16897725 PPP1R10 5514 6 30682340 NM_002714 NP_002705 C/G R173P plus 23310979 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.02 0.02 0 44 1 0.02 0 44 1 123 by freq Possibly damaging 1.594 11 moderately radical 603771 6p21.3 "protein phosphatase 1, regulatory subunit 10" 4965 rs16899974 AGXT2 64902 5 35034634 NM_031900 NP_114106 A/C V498L plus 23986087 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.27 0 48 1 0.21 0.18 92 2 123 by freq Benign 0.3 8 Tolerant 0.6 2.77 36 conservative 5p13 alanine-glyoxylate aminotransferase 2 4966 rs16906862 SYK 6850 9 90685869 NM_003177 NP_003168 A/G R45H plus 23454066 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.02 0.02 0 46 1 0.02 0 44 1 123 by freq Possibly damaging 1.909 24 Borderline 0.12 3 22 conservative 600085 9q22 spleen tyrosine kinase 4967 rs16910239 C5 727 9 120805480 NM_001735 NP_001726 G/T E1437D plus 23677048 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.02 0 46 1 123 by freq Tolerant 0.42 2.83 11 conservative 120900 9q33-q34 complement component 5 4968 rs16910245 C5 727 9 120812070 NM_001735 NP_001726 A/G V1365A plus 24146513 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.03 0 38 1 123 by freq Intolerant 0.05 2.83 11 moderately conservative 120900 9q33-q34 complement component 5 4969 rs16917089 GPR109A 338442 12 121712631 NM_177551 NP_808219 C/T V27A minus 24818467 1303 SEQUENOM CEPH CEPH (92) 184 0.42 0.42 0 184 1 123 by freq Tolerant 0.64 2.81 27 moderately conservative 12q24.31 G protein-coupled receptor 109A 4970 rs16918128 COL15A1 1306 9 98846858 NM_001855 NP_001846 A/G A442T plus 24043035 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.13 0 48 1 123 by freq Tolerant 0.68 3.2 60 moderately conservative 120325 9q21-q22 "collagen, type XV, alpha 1" 4971 rs16919923 LYPLA1 10434 8 55127773 NM_006330 NP_006321 A/G P153S plus 23559512 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.11 0 44 1 123 by freq Borderline 1.012 23 Tolerant 0.24 2.81 33 moderately conservative 605599 8q11.23 lysophospholipase I 4972 rs16924906 ARHGAP21 57584 10 24914339 NM_020824 NP_065875 A/G E1628K minus 24813579 1303 SEQUENOM CEPH CEPH (92) 184 0.44 0.44 0 184 1 123 by freq Potentially damaging 1.47 8 moderately conservative 10p12.31 Rho GTPase activating protein 21 4973 rs16927037 DMRT3 58524 9 980653 NM_021240 NP_067063 G/T G356V plus 23923591 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.07 0.02 80 2 123 by freq Benign 0.003 7 Borderline 0.18 2.85 19 moderately radical 9p24.3 doublesex and mab-3 related transcription factor 3 4974 rs16932912 RECK 8434 9 36077876 NM_021111 NP_066934 A/G V275I plus 24086213 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.21 0.11 94 2 123 by freq conservative 605227 9p13-p12 reversion-inducing-cysteine-rich protein with kazal motifs 4975 rs16932941 GNB3 2784 12 6825125 NM_002075 NP_002066 A/G G272S plus 24796019 1303 SEQUENOM CEPH CEPH (92) 184 0.1 0.23 0.15 552 3 123 by freq Possibly damaging 1.843 88 Intolerant 0.04 2.84 109 moderately conservative 139130 12p13 "guanine nucleotide binding protein (G protein), beta polypeptide 3" 4976 rs16932941 GNB3 2784 12 6825125 NM_002075 NP_002066 A/G G272S plus 24796440 1303 SEQUENOM CEPH CEPH (92) 184 0.39 0.23 0.15 552 3 123 by freq Possibly damaging 1.843 88 Intolerant 0.04 2.84 109 moderately conservative 139130 12p13 "guanine nucleotide binding protein (G protein), beta polypeptide 3" 4977 rs16932941 GNB3 2784 12 6825125 NM_002075 NP_002066 A/G G272S plus 24811747 1303 SEQUENOM CEPH CEPH (92) 184 0.19 0.23 0.15 552 3 123 by freq Possibly damaging 1.843 88 Intolerant 0.04 2.84 109 moderately conservative 139130 12p13 "guanine nucleotide binding protein (G protein), beta polypeptide 3" 4978 rs16938324 IFNA4 3441 9 21177067 NM_021068 NP_066546 C/T T155I minus 24812376 1303 SEQUENOM CEPH CEPH (92) 184 0.22 0.22 0 184 1 123 by freq Potentially damaging 1.477 181 Intolerant 0.02 2.83 176 moderately conservative 147564 9p22 "interferon, alpha 4" 4979 rs16939904 USP30 84749 12 107983489 NM_032663 NP_116052 A/G H348R plus 23948823 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.2 0.2 0 46 1 0.24 0 38 1 123 by freq Benign 0.639 6 Tolerant 0.7 2.86 7 conservative 12q24.12 ubiquitin specific protease 30 4980 rs16943596 ANPEP 290 15 88136792 NM_001150 NP_001141 C/T S752N plus 23530751 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.32 0.05 232 2 0.29 0.11 94 2 123 "by cluster,freq" Benign 0.748 14 Tolerant 0.76 2.76 24 conservative 151530 15q25-q26 "alanyl (membrane) aminopeptidase (aminopeptidase N, aminopeptidase M, microsomal aminopeptidase, CD13, p150)" 4981 rs16943596 ANPEP 290 15 88136792 NM_001150 NP_001141 C/T S752N plus 24787449 1303 SEQUENOM CEPH CEPH (92) 184 0.34 0.32 0.05 232 2 0.29 0.11 94 2 123 "by cluster,freq" Benign 0.748 14 Tolerant 0.76 2.76 24 conservative 151530 15q25-q26 "alanyl (membrane) aminopeptidase (aminopeptidase N, aminopeptidase M, microsomal aminopeptidase, CD13, p150)" 4982 rs16943991 ABC1 63897 17 55476235 NM_022070 NP_071353 A/G S1006L plus 23598229 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.16 0.11 94 2 123 by freq Potentially damaging 1.422 6 moderately radical 17q23.2-q23.3 amplified in breast cancer 1 4983 rs16944148 USP32 84669 17 55613609 NM_032582 NP_115971 C/G A1469G minus 24814072 1303 SEQUENOM CEPH CEPH (92) 184 0.15 0.15 0 184 1 123 by freq Potentially damaging 1.249 7 moderately conservative 607740 17q23.3 ubiquitin specific protease 32 4984 rs16947226 GH2 2689 17 59311624 NM_022557 NP_072051 C/G F232L minus 24819321 1303 SEQUENOM CEPH CEPH (92) 184 0.1 0.1 0 184 1 123 by freq conservative 139240 17q24.2 growth hormone 2 4985 rs16947229 GH2 2689 17 59311697 NM_022557 NP_072051 A/G G208E minus 24819318 1303 SEQUENOM CEPH CEPH (92) 184 0.06 0.06 0 184 1 123 by freq moderately conservative 139240 17q24.2 growth hormone 2 4986 rs16951861 DPH2L1 1801 17 1886982 NM_001383 NP_001374 A/G K146R plus 24792269 1303 SEQUENOM CEPH CEPH (92) 184 0.25 0.19 0.08 368 2 123 by freq Benign 0.076 12 conservative 603527 17p13.3 DPH2-like 1 (S. cerevisiae) 4987 rs16951861 DPH2L1 1801 17 1886982 NM_001383 NP_001374 A/G K146R plus 24796517 1303 SEQUENOM CEPH CEPH (92) 184 0.13 0.19 0.08 368 2 123 by freq Benign 0.076 12 conservative 603527 17p13.3 DPH2-like 1 (S. cerevisiae) 4988 rs16952692 ME2 4200 18 46693267 NM_002396 NP_002387 C/T P114L plus 23768924 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.13 0 46 1 123 by freq Probably damaging 2.956 31 Intolerant 0 2.76 86 moderately conservative 154270 18q21 "malic enzyme 2, NAD(+)-dependent, mitochondrial" 4989 rs16955011 ZNF183L1 140432 13 97627218 NM_178861 NP_849192 C/T V92M plus 23811284 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.12 0.14 94 2 123 by freq Potentially damaging 1.285 14 Intolerant 0.03 2.86 27 conservative 13q32.2 zinc finger protein 183-like 1 4990 rs16956504 CDH5 1003 16 64989882 NM_001795 NP_001786 C/T I503T plus 23757634 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.03 0.01 94 2 123 by freq Benign 0.332 7 Tolerant 0.43 2.82 56 moderately conservative 601120 16q22.1 "cadherin 5, type 2, VE-cadherin (vascular epithelium)" 4991 rs16958654 ZC3HDC7 29066 16 11780659 NM_014153 NP_054872 C/T H57R plus 23528405 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.15 0 46 1 123 by freq Benign 0.074 5 Borderline 0.11 2.93 386 conservative 16p13-p12 zinc finger CCCH type domain containing 7 4992 rs16961689 DSG1 1828 18 27173882 NM_001942 NP_001933 A/C Y528S plus 23766617 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.15 0.1 94 2 123 by freq Benign 0.615 7 Tolerant 0.41 2.8 28 moderately radical 125670 18q12.1 desmoglein 1 4993 rs16963151 ATP8B4 79895 15 48066954 XM_370863 XP_370863 C/T N98S plus 23441605 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.25 0 48 1 0.38 0.07 92 2 123 by freq Borderline 1.049 11 conservative 15q15.3 "ATPase, Class I, type 8B, member 4" 4994 rs16966957 NTAN1 123803 16 15039475 NM_173474 NP_775745 G/T H283N plus 24097373 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.35 0 48 1 0.27 0.19 94 2 123 "by cluster,freq" Benign 0.513 6 Tolerant 0.95 3.11 12 moderately conservative 16p13.13 N-terminal asparagine amidase 4995 rs16971436 ATBF1 463 16 71550264 NM_006885 NP_008816 G/T T428P plus 23619531 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.02 0.02 0 46 1 0.06 0.05 88 2 123 by freq conservative 104155 16q22.3-q23.1 AT-binding transcription factor 1 4996 rs16971625 BCL2A1 597 15 78050461 NM_004049 NP_004040 C/T C19Y plus 24064952 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.3 0.2 70 2 123 by freq Benign 0.54 7 Tolerant 1 3.08 12 radical 601056 15q24.3 BCL2-related protein A1 4997 rs16973716 PMFBP1 83449 16 70714343 NM_031293 NP_112583 G/T K913N plus 23615527 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.4 0 48 1 0.35 0.08 94 2 123 by freq moderately conservative 16q22.2 polyamine modulated factor 1 binding protein 1 4998 rs16975750 LIPE 3991 19 47622844 NM_005357 NP_005348 A/G Y100H plus 23764446 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.16 0 44 1 123 by freq moderately conservative 151750 19q13.2 "lipase, hormone-sensitive" 4999 rs16976816 ZNF283 284349 19 49031217 XM_371174 XP_371174 A/G G305S plus 23765016 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.07 0 46 1 123 by freq moderately conservative 19q13.32 zinc finger protein 283 5000 rs16978899 ZNF233 353355 19 49469392 NM_181756 NP_861421 C/T S247P plus 23765489 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.09 0 46 1 123 by freq Possibly damaging 1.706 6 Intolerant 0.01 2.81 27 moderately conservative 19q13.32 zinc finger protein 233 5001 rs16979670 ZNF559 84527 19 9313879 NM_032497 NP_115886 A/C T251N plus 23400674 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.08 0.09 94 2 123 by freq Tolerant 0.57 2.81 50 moderately conservative 19p13.2 zinc finger protein 559 5002 rs16982743 SIGLECL1 89858 19 56696715 NM_053003 NP_443729 A/G Q29X plus 23813010 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.22 0.22 0 46 1 0.29 0.2 94 2 123 by freq Probably damaging Intolerant radical 606094 19q13.4 SIGLEC-like 1 5003 rs16985486 LILRB3 11025 19 59413028 NM_006864 NP_006855 C/T V574A minus 24817511 1303 SEQUENOM CEPH CEPH (92) 184 0.48 0.48 0 184 1 123 by freq Potentially damaging 1.413 18 Tolerant 1 3.23 32 moderately conservative 604820 19q13.4 "leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3" 5004 rs16987625 RFPL3 10738 22 31078860 NM_006604 NP_006595 C/T M54T plus 24121662 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 0.29 0.25 94 2 123 by freq Possibly damaging 1.752 11 Tolerant 0.36 3.02 13 moderately conservative 605970 22q12.3 ret finger protein-like 3 5005 rs16987632 RFPL2 10739 22 30911581 NM_006605 NP_006596 C/G T200S plus 24810808 1303 SEQUENOM CEPH CEPH (92) 184 0.28 0.28 0 184 1 123 by freq Potentially damaging 1.348 11 moderately conservative 605969 22q12.3 ret finger protein-like 2 5006 rs16995309 PTPN1 5770 20 48631280 NM_002827 NP_002818 C/T P387L plus 28448136 1099 FCOLLINS SUBSET_19_20_21_27 "Finnish (805 type 2 diabetics, 421 normoglycemic controls)" 1226 0.01 0.01 0 1226 1 123 by freq Possibly damaging 1.967 13 moderately conservative 176885 20q13.1-q13.2 "protein tyrosine phosphatase, non-receptor type 1" 5007 rs16995376 CYP4F12 66002 19 15645377 NM_023944 NP_076433 C/T P13L plus 23763398 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.27 0 48 1 0.37 0 46 1 123 by freq moderately conservative 19p13.1 "cytochrome P450, family 4, subfamily F, polypeptide 12" 5008 rs16995378 CYP4F12 66002 19 15645386 NM_023944 NP_076433 C/T T16M plus 23763402 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 0.13 0 46 1 123 by freq moderately conservative 19p13.1 "cytochrome P450, family 4, subfamily F, polypeptide 12" 5009 rs17010021 LOXL3 84695 2 74673194 NM_032603 NP_115992 A/T I615F plus 23876922 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.13 0.15 94 2 123 by freq Potentially damaging 1.409 16 Intolerant 0 3.07 22 conservative 607163 2p13 lysyl oxidase-like 3 5010 rs17011368 XDH 7498 2 31502568 NM_000379 NP_000370 C/T I703V plus 23695148 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.09 0 46 1 123 by freq Potentially damaging 1.413 40 Intolerant 0.04 2.79 126 conservative 607633 2p23-p22 xanthine dehydrogenase 5011 rs17012739 PLK4 10733 4 129172569 NM_014264 NP_055079 G/T E830D plus 23985400 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.29 0.29 0 48 1 0.33 0.22 94 2 123 by freq Borderline 1.042 7 conservative 605031 4q27-q28 polo-like kinase 4 (Drosophila) 5012 rs17013181 IBSP 3381 4 89089942 NM_004967 NP_004958 A/G R219G plus 23231583 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.19 0 48 1 0.31 0.14 92 2 123 by freq Possibly damaging 1.812 9 moderately radical 147563 4q21-q25 "integrin-binding sialoprotein (bone sialoprotein, bone sialoprotein II)" 5013 rs17013285 MEPE 56955 4 89124187 NM_020203 NP_064588 A/G V330I plus 23883524 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.13 0.13 0 46 1 0.2 0.23 90 2 123 by freq conservative 605912 4q21.1 "matrix, extracellular phosphoglycoprotein with ASARM motif (bone)" 5014 rs17015215 IRF6 3664 1 206352475 NM_006147 NP_006138 C/T V274I plus 24155311 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.23 0.3 94 2 123 by freq Benign 0.974 13 Borderline 0.15 2.8 34 conservative 607199 1q32.3-q41 interferon regulatory factor 6 5015 rs17021877 IKBKE 9641 1 203040799 XM_375834 XP_375834 A/G A371T plus 23703050 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.04 0 46 1 123 by freq moderately conservative 605048 1q32.1 "inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase epsilon" 5016 rs17027633 OVGP1 5016 1 111674298 NM_002557 NP_002548 G/T D332E plus 23860906 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 0.15 0 48 1 123 by freq Potentially damaging 1.389 13 conservative 603578 1p13 "oviductal glycoprotein 1, 120kDa (mucin 9, oviductin)" 5017 rs17029215 MTP 4547 4 100878983 NM_000253 NP_000244 A/C D384A plus 23331505 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.15 0 46 1 123 by freq Benign 0.294 9 Tolerant 0.65 2.78 15 moderately radical 157147 4q24 "microsomal triglyceride transfer protein (large polypeptide, 88kDa)" 5018 rs17037102 DKK2 27123 4 108203398 NM_014421 NP_055236 A/G R146Q minus 24169646 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.09 0.01 204 2 0.23 0.11 294 3 123 by freq conservative 605415 4q25 dickkopf homolog 2 (Xenopus laevis) 5019 rs17037102 DKK2 27123 4 108203398 NM_014421 NP_055236 A/G R146Q minus 28459771 549 KYUGEN CP CEPH (78) 156 0.09 0.09 0.01 204 2 0.23 0.11 294 3 123 by freq conservative 605415 4q25 dickkopf homolog 2 (Xenopus laevis) 5020 rs17038460 POLR3B 55703 12 105350881 NM_018082 NP_060552 A/G T740A plus 23270903 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.07 0 46 1 123 by freq Possibly damaging 1.762 30 Intolerant 0.01 2.8 144 moderately conservative 12q24.11 polymerase (RNA) III (DNA directed) polypeptide B 5021 rs17039250 SBLF 11037 2 48719447 NM_006873 NP_006864 A/C K8N plus 24156947 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.42 0.42 0 48 1 0.36 0.11 94 2 123 by freq moderately conservative 605357 2p16.3 stoned B-like factor 5022 rs17040344 GLTDC1 360203 9 135742064 NM_182974 NP_892019 A/G P219S plus 23600318 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.09 0 46 1 123 by freq Probably damaging 2.396 20 Intolerant 0 3.01 162 moderately conservative 9q34.3 galactosyltransferase family 6 domain containing 1 5023 rs17040745 ANAPC1 64682 2 112282895 NM_022662 NP_073153 C/T H1231R plus 24801266 1303 SEQUENOM CEPH CEPH (92) 184 0.37 0.37 0 184 1 123 by freq Benign 0.639 5 Intolerant 0 2.81 11 conservative 608473 2q12.1 anaphase promoting complex subunit 1 5024 rs17041850 ACOXL 55289 2 111566746 NM_018308 NP_060778 C/T P358L plus 23934630 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.15 0.18 94 2 123 by freq Tolerant 0.32 2.81 14 moderately conservative 2q13 acyl-Coenzyme A oxidase-like 5025 rs17046663 GPATC2 55105 1 214181658 NM_018040 NP_060510 A/G R212K minus 24815084 1303 SEQUENOM CEPH CEPH (92) 184 0.37 0.37 0 184 1 123 by freq Borderline 1.132 10 conservative 1q41 G patch domain containing 2 5026 rs17052920 TKT 7086 3 53244127 NM_001064 NP_001055 C/T I181V plus 23273867 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.02 0 46 1 123 by freq Benign 0.888 32 Tolerant 0.24 2.81 40 conservative 606781 3p14.3 transketolase (Wernicke-Korsakoff syndrome) 5027 rs17072097 SERPINB10 5273 18 59733731 NM_005024 NP_005015 G/T S3A plus 23531754 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.19 0 48 1 0.37 0.15 94 2 123 by freq Tolerant 0.67 2.78 55 moderately conservative 602058 18q21.3 "serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10" 5028 rs17072218 ADPRTL1 143 13 23918863 NM_006437 NP_006428 A/G R1108C plus 23434190 1371 PERLEGEN AFD_EUR_PANEL European American (24) 38 0.05 0.05 0 38 1 0.15 0.16 88 2 123 by freq radical 607519 13q11 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1 5029 rs17075173 GUCY1B2 2974 13 50488434 NM_004129 NP_004120 C/T V445I plus 23343471 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.11 0.11 0 46 1 0.43 0 44 1 123 by freq Benign 0.62 10 Intolerant 0 2.83 40 conservative 603695 13q14.2-q14.3 "guanylate cyclase 1, soluble, beta 2" 5030 rs17077022 TGM4 7047 3 44923495 NM_003241 NP_003232 A/G I376V plus 23337753 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.07 0 46 1 123 by freq Tolerant 1 2.78 17 conservative 600585 3p22-p21.33 transglutaminase 4 (prostate) 5031 rs17088980 TNFRSF10A 8797 8 23112849 NM_003844 NP_003835 G/T N297H plus 23497367 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.07 0 46 1 123 by freq Potentially intolerant 0.09 2.85 13 moderately conservative 603611 8p21 "tumor necrosis factor receptor superfamily, member 10a" 5032 rs17088993 TNFRSF10A 8797 8 23114165 NM_003844 NP_003835 A/C E228A minus 24491967 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.38 0.27 0.08 232 2 123 by freq Tolerant 0.68 2.76 18 moderately radical 603611 8p21 "tumor necrosis factor receptor superfamily, member 10a" 5033 rs17088993 TNFRSF10A 8797 8 23114165 NM_003844 NP_003835 A/C E228A minus 24811028 1303 SEQUENOM CEPH CEPH (92) 184 0.24 0.27 0.08 232 2 123 by freq Tolerant 0.68 2.76 18 moderately radical 603611 8p21 "tumor necrosis factor receptor superfamily, member 10a" 5034 rs17090763 ZNF341 84905 20 31842856 NM_032819 NP_116208 A/C T806P plus 23564608 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.15 0 46 1 123 by freq conservative 20q11.22 zinc finger protein 341 5035 rs17093294 TCL1A 8115 14 95248441 NM_021966 NP_068801 C/T V56I plus 24134414 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.02 0.02 0 44 1 0.17 0 46 1 123 by freq Borderline 0.2 2.86 11 conservative 186960 14q32.1 T-cell leukemia/lymphoma 1A 5036 rs17096845 PCDHB2 56133 5 140456579 NM_018936 NP_061759 C/T L674P plus 24811373 1303 SEQUENOM CEPH CEPH (92) 184 0.08 0.08 0 184 1 123 by freq Benign 0.863 102 Tolerant 0.63 2.77 129 moderately conservative 606328 5q31 protocadherin beta 2 5037 rs17096901 PCDHB5 26167 5 140495667 NM_015669 NP_056484 C/T I156T plus 23951172 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.04 0 46 1 123 by freq Benign 0.212 102 Tolerant 0.54 2.77 131 moderately conservative 606331 5q31 protocadherin beta 5 5038 rs17096946 PCDHB7 56129 5 140533159 NM_018940 NP_061763 A/G E187K plus 23675265 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.02 0.02 0 46 1 0.16 0 44 1 123 by freq Benign 0.433 102 Potentially intolerant 0.06 2.78 128 moderately conservative 606333 5q31 protocadherin beta 7 5039 rs17096961 PCDHB8 56128 5 140540033 NM_019120 NP_061993 A/G S745N plus 23351136 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.15 0.2 92 2 123 by freq Benign 0.911 96 Intolerant 0 2.77 128 conservative 606334 5q31 protocadherin beta 8 5040 rs17098707 GRK5 2869 10 121076087 NM_005308 NP_005299 A/T Q41L plus 23617347 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.33 0 46 1 123 by freq Borderline 1.038 36 Borderline 0.12 2.89 57 moderately radical 600870 10q24-qter G protein-coupled receptor kinase 5 5041 rs17099450 MMP8 4317 11 102100789 NM_002424 NP_002415 C/G S3C plus 23555864 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 0.04 0.04 94 2 123 by freq moderately radical 120355 11q22.3 matrix metalloproteinase 8 (neutrophil collagenase) 5042 rs17099455 DHRS4 10901 14 23492847 NM_021004 NP_066284 A/G A4T plus 23799140 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.3 0 46 1 123 by freq Benign 0.9 5 moderately conservative 14q11.2 dehydrogenase/reductase (SDR family) member 4 5043 rs17109924 GPR49 8549 12 70264054 NM_003667 NP_003658 C/T V666A plus 23661065 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.09 0.11 94 2 123 by freq Potentially damaging 1.452 8 Tolerant 0.31 2.8 25 moderately conservative 606667 12q22-q23 G protein-coupled receptor 49 5044 rs17110107 BCAR3 8412 1 93753615 NM_003567 NP_003558 C/G Q593H plus 24157247 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.02 0.02 0 42 1 0.13 0.06 72 2 123 by freq Possibly damaging 1.657 6 Tolerant 0.26 2.89 19 conservative 604704 1p22.1 breast cancer anti-estrogen resistance 3 5045 rs17110563 TPH2 121278 12 70652573 NM_173353 NP_775489 C/T P206S plus 28447407 914 HG_BONN_CNS_SNPS EURO96 European 94 0.02 0.02 0 94 1 123 by freq Probably damaging 2.426 38 Intolerant 0.01 2.82 69 moderately conservative 607478 12q15 tryptophan hydroxylase 2 5046 rs17112809 MMS19L 64210 10 99215836 NM_022362 NP_071757 C/T V526I plus 23584239 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.09 0.08 94 2 123 by freq Benign 0.696 9 Tolerant 0.5 2.79 17 conservative 10q24-q25 "MMS19-like (MET18 homolog, S. cerevisiae)" 5047 rs17114930 UBASH3A 53347 21 42730671 NM_018961 NP_061834 C/G D466E plus 23652455 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.2 0 46 1 123 by freq Benign 0.145 5 Tolerant 1 3.08 146 conservative 605736 21q22.3 "ubiquitin associated and SH3 domain containing, A" 5048 rs17116056 ATP10A 57194 15 23520183 NM_024490 NP_077816 G/T S353Y plus 23748384 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.2 0 46 1 123 by freq Possibly damaging 1.773 7 Intolerant 0.03 2.76 17 moderately radical 605855 15q11-q13 "ATPase, Class V, type 10A" 5049 rs17121493 IL10RA 3587 11 117370056 NM_001558 NP_001549 A/G I224V plus 24101170 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.33 0 48 1 123 by freq conservative 146933 11q23 "interleukin 10 receptor, alpha" 5050 rs17122945 NIN 51199 14 50359676 NM_016350 NP_057434 A/G R33W plus 23641890 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.02 0 46 1 123 by freq moderately radical 608684 14q22.1 ninein (GSK3B interacting protein) 5051 rs17127898 TRIP11 9321 14 91575668 NM_004239 NP_004230 A/T M39L plus 23645191 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.04 0 46 1 123 by freq conservative 604505 14q31-q32 thyroid hormone receptor interactor 11 5052 rs17128572 GOLGA5 9950 14 92333735 NM_005113 NP_005104 C/G A67G plus 24128753 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.19 0 48 1 123 by freq Potentially damaging 1.413 8 moderately conservative 606918 14q32.12-q32.13 "golgi autoantigen, golgin subfamily a, 5" 5053 rs17129219 MFI2 4241 3 198223997 NM_005929 NP_005920 C/T A559T plus 23868025 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.04 0 48 1 123 by freq Borderline 1.227 5 Intolerant 0 2.8 94 moderately conservative 155750 3q28-q29 antigen p97 (melanoma associated) identified by monoclonal antibodies 133.2 and 96.5 5054 rs17135737 TBL3 10607 16 1966892 NM_006453 NP_006444 C/T S457P plus 24810924 1303 SEQUENOM CEPH CEPH (92) 184 0.11 0.11 0 184 1 123 by freq Possibly damaging 1.553 7 Borderline 0.13 2.95 12 moderately conservative 605915 16p13.3 transducin (beta)-like 3 5055 rs17136239 HUS1B 135458 6 601343 NM_148959 NP_683762 C/T Q201R plus 23395005 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.13 0.05 94 2 123 by freq Borderline 0.19 2.9 13 conservative 6p25.3 HUS1 checkpoint homolog b (S. pombe) 5056 rs17145454 HSD17B4 3295 5 118888837 NM_000414 NP_000405 C/T W511R plus 23306348 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.39 0 46 1 123 by freq Probably damaging 3.307 18 Tolerant 0.34 3 30 moderately radical 601860 5q21 hydroxysteroid (17-beta) dehydrogenase 4 5057 rs17160348 LASS4 79603 19 8232866 NM_024552 NP_078828 C/T A353V plus 23582617 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.14 0.01 94 2 123 by freq moderately conservative 19p13.3 LAG1 longevity assurance homolog 4 (S. cerevisiae) 5058 rs17160349 LASS4 79603 19 8232944 NM_024552 NP_078828 A/G R379Q plus 23582644 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.14 0.01 94 2 123 by freq conservative 19p13.3 LAG1 longevity assurance homolog 4 (S. cerevisiae) 5059 rs17162549 MAP3K6 9064 1 27366672 NM_004672 NP_004663 C/G G1233A plus 23683105 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.05 0.05 0 44 1 0.18 0 44 1 123 by freq Tolerant 0.88 3.01 16 moderately conservative 604468 1p35.3 mitogen-activated protein kinase kinase kinase 6 5060 rs17165851 PDLIM4 8572 5 131635487 NM_003687 NP_003678 G/T G259C plus 23950870 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.11 0.11 0 46 1 0.16 0.18 88 2 123 by freq Probably damaging 2.256 7 Intolerant 0 2.81 31 radical 603422 5q31.1 PDZ and LIM domain 4 5061 rs17184326 POP1 10940 8 99222264 NM_015029 NP_055844 A/C K522N plus 24505330 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.13 0.13 0 46 1 0.11 0 46 1 123 by freq moderately conservative 602486 8q22.1 "processing of precursor 1, ribonuclease P/MRP subunit (S. cerevisiae)" 5062 rs17187262 LAMA3 3909 18 19656296 NM_198129 NP_937762 A/C T796N plus 24218055 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.09 0.06 94 2 123 by freq moderately conservative 600805 18q11.2 "laminin, alpha 3" 5063 rs17192170 ZFYVE26 23503 14 67327105 NM_015346 NP_056161 A/T T898S plus 24707373 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.07 0.07 0 46 1 123 by freq moderately conservative 14q24.1 "zinc finger, FYVE domain containing 26" 5064 rs17197552 PPP2R3A 5523 3 137204962 NM_002718 NP_002709 A/G S642G plus 24317227 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.31 0 48 1 0.11 0.08 94 2 123 by freq moderately conservative 604944 3q22.1 "protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha" 5065 rs17202961 LAMA3 3909 18 19678989 NM_198129 NP_937762 A/C P1208T plus 24710451 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.02 0 46 1 123 by freq conservative 600805 18q11.2 "laminin, alpha 3" 5066 rs17203645 MCM2 4171 3 128810007 NM_004526 NP_004517 A/G A396T plus 24620499 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 123 by freq Potentially damaging 1.257 16 Intolerant 0.04 2.83 30 moderately conservative 116945 3q21 "MCM2 minichromosome maintenance deficient 2, mitotin (S. cerevisiae)" 5067 rs17208425 PCDHGC5 56097 5 140851609 NM_032407 NP_115783 A/G E873G plus 24621869 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.24 0.24 0 46 1 0.09 0.06 84 2 123 by freq moderately conservative 606306 5q31 "protocadherin gamma subfamily C, 5" 5068 rs17209274 CDC45L 8318 22 17870618 NM_003504 NP_003495 G/T M356R plus 24210974 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.05 0 40 1 123 by freq Probably damaging 2.157 10 Intolerant 0.01 2.81 11 moderately conservative 603465 22q11.21 CDC45 cell division cycle 45-like (S. cerevisiae) 5069 rs17211369 TEP1 7011 14 19922107 NM_007110 NP_009041 C/T R1155Q plus 24720767 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 123 by freq conservative 601686 14q11.2 telomerase-associated protein 1 5070 rs17211404 TEP1 7011 14 19941813 NM_007110 NP_009041 C/T K368R plus 24720776 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.07 0 46 1 123 by freq conservative 601686 14q11.2 telomerase-associated protein 1 5071 rs17217280 DDX58 23586 9 32470251 NM_014314 NP_055129 A/T D580E plus 24522657 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.03 0.01 94 2 123 by freq Tolerant 0.72 2.8 22 conservative 9p12 DEAD (Asp-Glu-Ala-Asp) box polypeptide 58 5072 rs17218581 HRB2 11103 12 74186649 NM_007043 NP_008974 C/T R134Q plus 24411598 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.27 0 48 1 0.19 0.06 92 2 123 by freq Potentially damaging 1.3 21 Potentially intolerant 0.08 2.78 43 conservative 12q21.1 HIV-1 rev binding protein 2 5073 rs17219559 TAF1L 138474 9 32624467 NM_153809 NP_722516 C/T M371V plus 24523307 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.23 0.23 0 48 1 0.02 0 46 1 123 by freq Benign 0.9 7 conservative 607798 9p13.3 "TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa" 5074 rs17240268 ANPEP 290 15 88148818 NM_001150 NP_001141 A/G A311V plus 24514019 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 0.09 0 46 1 123 by freq Potentially damaging 1.262 14 Borderline 0.12 2.77 27 moderately conservative 151530 15q25-q26 "alanyl (membrane) aminopeptidase (aminopeptidase N, aminopeptidase M, microsomal aminopeptidase, CD13, p150)" 5075 rs17245714 AGXT2 64902 5 35034651 NM_031900 NP_114106 C/G P492R plus 24425464 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.02 0 48 1 123 by freq Benign 0.226 8 Tolerant 0.45 2.77 36 moderately radical 5p13 alanine-glyoxylate aminotransferase 2 5076 rs17246389 SERPINI2 5276 3 168672309 NM_006217 NP_006208 A/C L6V plus 24315969 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.27 0.27 0 48 1 0.09 0.02 94 2 123 by freq Intolerant 0.05 3.01 7 conservative 605587 3q26.1-q26.2 "serine (or cysteine) proteinase inhibitor, clade I (neuroserpin), member 2" 5077 rs17263971 SYNPO2 171024 4 120305649 XM_050219 XP_050219 A/C Q174H plus 24328923 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.31 0 48 1 0.2 0.08 94 2 123 by freq conservative 4q27 synaptopodin 2 5078 rs17265513 ZHX3 23051 20 39266042 NM_015035 NP_055850 C/T N310S plus 24517598 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.21 0 48 1 0.04 0 46 1 123 by freq Potentially damaging 1.494 6 Intolerant 0 2.95 16 conservative 20q12 zinc fingers and homeoboxes 3 5079 rs17286891 PCDHB7 56129 5 140532958 NM_018940 NP_061763 A/G E120K plus 24621855 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.02 0 46 1 123 by freq Possibly damaging 1.822 98 Intolerant 0.04 2.78 126 moderately conservative 606333 5q31 protocadherin beta 7 5080 rs17292725 STARD6 147323 18 50134887 NM_139171 NP_631910 A/G R19X plus 24531481 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 123 by freq Probably damaging Intolerant radical 607051 18q21.2 START domain containing 6 5081 rs17293607 MMP10 4319 11 102155599 NM_002425 NP_002416 C/T G65R plus 24531732 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 0.02 0 46 1 123 by freq Benign 0.59 26 Intolerant 0 2.82 58 moderately radical 185260 11q22.3 matrix metalloproteinase 10 (stromelysin 2) 5082 rs17300141 NQO2 4835 6 2957777 NM_000904 NP_000895 A/G G58D plus 24424040 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.02 0 46 1 123 by freq Possibly damaging 1.947 6 Tolerant 0.39 2.88 25 moderately conservative 160998 6pter-q12 "NAD(P)H dehydrogenase, quinone 2" 5083 rs17300770 GPLD1 2822 6 24570999 NM_001503 NP_001494 C/G D275E plus 24333981 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.15 0.15 0 46 1 0.09 0.09 94 2 123 by freq Borderline 1.078 9 Tolerant 0.21 3.07 31 conservative 602515 6p22.3-p22.2 glycosylphosphatidylinositol specific phospholipase D1 5084 rs17301126 BPIL3 128859 20 31083161 NM_174897 NP_777557 C/T T16M plus 24533879 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.17 0 48 1 0.06 0.06 92 2 123 by freq moderately conservative 20q11.22 bactericidal/permeability-increasing protein-like 3 5085 rs17301750 DNCH2 79659 11 102532444 XM_370652 XP_370652 A/G T1288A plus 24534061 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.04 0 48 1 123 by freq moderately conservative 603297 11q21-q22.1 "dynein, cytoplasmic, heavy polypeptide 2" 5086 rs17301766 TOPBP1 11073 3 134839488 NM_007027 NP_008958 A/G S730L plus 24334264 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.21 0 48 1 0.02 0 46 1 123 by freq Possibly damaging 1.773 7 moderately radical 607760 3q22.1 topoisomerase (DNA) II binding protein 5087 rs17322140 ELF2 1998 4 140350780 NM_006874 NP_006865 A/G P64L plus 24428528 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 123 by freq Probably damaging 2.55 7 Potentially intolerant 0.07 2.82 23 moderately conservative 4q28 E74-like factor 2 (ets domain transcription factor) 5088 rs17323225 XDH 7498 2 31504916 NM_000379 NP_000370 C/T I646V plus 24636534 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.04 0.04 0 46 1 123 by freq Benign 0.287 40 Tolerant 0.48 2.79 126 conservative 607633 2p23-p22 xanthine dehydrogenase 5089 rs17328673 CDH12 1010 5 21852963 NM_004061 NP_004052 C/T I284V plus 24328588 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.02 0 46 1 123 by freq Benign 0.365 51 Tolerant 1 2.85 59 conservative 600562 5p14-p13 "cadherin 12, type 2 (N-cadherin 2)" 5090 rs17333103 PI3 5266 20 43237027 NM_002638 NP_002629 C/T T17M plus 24539392 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.25 0 48 1 0.13 0.1 94 2 123 by freq moderately conservative 182257 20q12-q13 "protease inhibitor 3, skin-derived (SKALP)" 5091 rs17336208 DEK 7913 6 18364604 NM_003472 NP_003463 A/G V140A plus 24438661 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 123 by freq Benign 0.082 6 Tolerant 0.51 2.78 23 moderately conservative 125264 6p23 DEK oncogene (DNA binding) 5092 rs17337252 RB1CC1 9821 8 53749259 NM_014781 NP_055596 A/G M234T plus 24527204 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.48 0.48 0 48 1 0.31 0.11 94 2 123 by freq Possibly damaging 1.773 7 moderately conservative 606837 8p22-q21.13 RB1-inducible coiled-coil 1 5093 rs17343819 CPA6 57094 8 68559469 NM_020361 NP_065094 C/T N249S plus 24540639 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.19 0 48 1 0.11 0 46 1 123 by freq Benign 0.289 6 Tolerant 0.65 2.77 56 conservative 8q13.1 carboxypeptidase A6 5094 rs17348572 CLSTN2 64084 3 141661079 NM_022131 NP_071414 C/T I331T plus 24340383 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 123 by freq Benign 0.03 18 Potentially intolerant 0.06 3.04 24 moderately conservative 3q23-q24 calsyntenin 2 5095 rs17354559 PIAS3 10401 1 143072982 NM_006099 NP_006090 C/G S381C plus 24236227 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 123 by freq Benign 0.637 23 Borderline 0.11 2.79 39 moderately radical 605987 1q21 "protein inhibitor of activated STAT, 3" 5096 rs17356233 CHD1L 9557 1 143965318 NM_004284 NP_004275 C/G H350Q plus 24236709 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.04 0 92 2 123 by freq Possibly damaging 1.972 6 Tolerant 0.51 2.75 55 conservative 1q12 chromodomain helicase DNA binding protein 1-like 5097 rs17366743 ACDC 9370 3 188054791 NM_004797 NP_004788 C/T Y111H plus 24334025 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.02 0 46 1 123 by freq Benign 0.052 19 Tolerant 0.54 2.77 38 moderately conservative 605441 3q27 "adipocyte, C1Q and collagen domain containing" 5098 rs17368402 ATP1A4 480 1 156947129 NM_144699 NP_653300 A/G E297K plus 24239022 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.17 0 48 1 123 by freq Possibly damaging 1.617 143 Tolerant 0.22 2.88 120 moderately conservative 607321 1q21-q23 "ATPase, Na+/K+ transporting, alpha 4 polypeptide" 5099 rs17368528 H6PD 9563 1 9258479 NM_004285 NP_004276 C/T P554L plus 24239061 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 0.06 0.05 90 2 123 by freq Probably damaging 2.479 6 moderately conservative 138090 1p36 hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase) 5100 rs17374285 BCAT1 586 12 24938579 NM_005504 NP_005495 A/G T59M plus 24434401 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.04 0.04 0 46 1 123 by freq Benign 0.472 25 Tolerant 0.35 2.79 41 moderately conservative 113520 12pter-q12 "branched chain aminotransferase 1, cytosolic" 5101 rs17384126 GTF3C3 9330 2 197488032 NM_012086 NP_036218 C/T N70S plus 24345102 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.07 0.08 94 2 123 by freq conservative 604888 2q33.1 "general transcription factor IIIC, polypeptide 3, 102kDa" 5102 rs17388190 CPA5 93979 7 129583803 NM_080385 NP_525124 C/T P79S plus 24436574 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 123 by freq Probably damaging 2.384 41 Tolerant 0.29 2.82 51 moderately conservative 7q32 carboxypeptidase A5 5103 rs17396317 BASE 317716 20 31254038 NM_173859 NP_776258 A/G R138H plus 24535018 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 0.02 0 46 1 123 by freq Tolerant 0.54 2.76 13 conservative 607627 20q11.21 breast cancer and salivary gland expression gene 5104 rs17409304 CLCA2 9635 1 86612393 NM_006536 NP_006527 C/G Q306E plus 24245311 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.4 0.4 0 48 1 0.13 0.08 94 2 123 by freq Intolerant 0.04 2.96 39 conservative 604003 1p31-p22 "chloride channel, calcium activated, family member 2" 5105 rs17414086 SENP6 26054 6 76401151 NM_015571 NP_056386 C/T T121M plus 24451929 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.31 0 48 1 0.02 0 46 1 123 by freq Potentially damaging 1.389 5 moderately conservative 605003 6q13-q14.3 SUMO1/sentrin specific protease 6 5106 rs17416074 CNTN2 6900 1 201774497 NM_005076 NP_005067 A/G V1024I plus 24640725 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 0.02 0 46 1 123 by freq conservative 190197 1q32.1 contactin 2 (axonal) 5107 rs17419546 VWF 7450 12 5998704 NM_000552 NP_000543 C/T T1381A plus 24649631 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.44 0.44 0 48 1 0.23 0.06 92 2 123 by freq Benign 0.222 10 moderately conservative 193400 12p13.3 von Willebrand factor 5108 rs17420378 STK4 6789 20 43062549 NM_006282 NP_006273 A/G V312M plus 24538286 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.25 0 48 1 0.17 0 46 1 123 by freq Benign 0.921 21 Borderline 0.11 2.88 45 conservative 604965 20q11.2-q13.2 serine/threonine kinase 4 5109 rs17424158 MIPEP 4285 13 23334475 NM_005932 NP_005923 C/T R340Q plus 24439618 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.19 0 48 1 0.04 0 46 1 123 by freq Tolerant 0.6 2.82 19 conservative 602241 13q12 mitochondrial intermediate peptidase 5110 rs17432496 SEMA6A 57556 5 115839172 NM_020796 NP_065847 C/T R559H plus 24453575 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 123 by freq Benign 0.289 12 Tolerant 0.57 2.82 115 conservative 605885 5q23.1 "sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A" 5111 rs17462252 ATP10D 57205 4 47411804 NM_020453 NP_065186 A/G S959N plus 24658271 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.02 0 46 1 123 by freq Tolerant 0.83 2.86 15 conservative 4p12 "ATPase, Class V, type 10D" 5112 rs17472401 NPHP4 261734 1 5874509 NM_015102 NP_055917 A/G R848W plus 24250047 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 123 by freq Possibly damaging 1.8 5 moderately radical 607215 1p36.22 nephronophthisis 4 5113 rs17476783 DBC1 1620 9 119050623 NM_014618 NP_055433 C/T R358H plus 24547159 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 123 by freq Benign 0.606 14 conservative 602865 9q32-q33 deleted in bladder cancer 1 5114 rs17502738 ZBTB5 9925 9 37431650 NM_014872 NP_055687 C/T D300G plus 24550956 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.07 0 46 1 123 by freq Possibly damaging 1.7 5 moderately conservative 9p13.1 zinc finger and BTB domain containing 5 5115 rs17511668 N4BP2 55728 4 39926333 NM_018177 NP_060647 G/T S101I plus 24653670 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.21 0 48 1 0.09 0 46 1 123 by freq moderately radical 4p14 Nedd4 binding protein 2 5116 rs17514547 PCM1 5108 8 17874285 NM_006197 NP_006188 A/G R1251H plus 24664236 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 123 by freq Possibly damaging 1.687 5 conservative 600299 8p22-p21.3 pericentriolar material 1 5117 rs17541107 GPR111 222611 6 47757224 NM_153839 NP_722581 A/T L324M plus 24368241 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.31 0 48 1 0.29 0.01 94 2 123 by freq Tolerant 0.27 2.83 27 conservative 6p12.3 G protein-coupled receptor 111 5118 rs17545756 ABCB8 11194 7 150170460 NM_007188 NP_009119 C/T R304C plus 24458174 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.02 0 48 1 123 by freq Probably damaging 2.257 5 Intolerant 0 2.77 31 radical 605464 7q36 "ATP-binding cassette, sub-family B (MDR/TAP), member 8" 5119 rs17555920 ATP10A 57194 15 23504291 NM_024490 NP_077816 C/T E834K plus 24672482 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.08 0.01 94 2 123 by freq Potentially damaging 1.267 7 Tolerant 0.3 2.76 17 moderately conservative 605855 15q11-q13 "ATPase, Class V, type 10A" 5120 rs17572019 PPARGC1B 133522 5 149192664 NM_133263 NP_573570 A/G V279I plus 24658267 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.13 0.13 0 46 1 0.04 0.04 90 2 123 by freq conservative 608886 5q33.1 "peroxisome proliferative activated receptor, gamma, coactivator 1, beta" 5121 rs17574839 NELL2 4753 12 43394747 NM_006159 NP_006150 C/T N347D plus 24474441 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 0.02 0 46 1 123 by freq Borderline 1.014 16 Tolerant 0.64 2.82 27 conservative 602320 12q13.11-q13.12 NEL-like 2 (chicken) 5122 rs17594503 PRSS12 8492 4 119560824 NM_003619 NP_003610 C/T R833Q plus 24664709 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 123 by freq Borderline 0.16 3.22 17 conservative 606709 4q28.1 "protease, serine, 12 (neurotrypsin, motopsin)" 5123 rs17598561 NMB 4828 15 82999610 NM_205858 NP_995580 C/T M120I plus 24365854 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.03 0.01 94 2 123 by freq conservative 162340 15q22-qter neuromedin B 5124 rs17599091 MTP 4547 4 100870097 NM_000253 NP_000244 C/G Q244E plus 24366006 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 0.02 0 46 1 123 by freq Potentially damaging 1.392 9 Tolerant 1 2.78 15 conservative 157147 4q24 "microsomal triglyceride transfer protein (large polypeptide, 88kDa)" 5125 rs17599639 DNAH9 1770 17 11452205 NM_001372 NP_001363 A/G R151H plus 24565947 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.07 0.07 0 46 1 123 by freq Probably damaging 2.409 9 conservative 603330 17p12 "dynein, axonemal, heavy polypeptide 9" 5126 rs17601580 ENPP3 5169 6 132103113 NM_005021 NP_005012 A/G S786N plus 24476640 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.02 0 44 1 123 by freq Potentially damaging 1.348 19 Intolerant 0.03 2.99 22 conservative 602182 6q22 ectonucleotide pyrophosphatase/phosphodiesterase 3 5127 rs17602729 AMPD1 270 1 114948099 NM_000036 NP_000027 A/G Q12X plus 24267495 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 0.02 0 46 1 123 by freq Probably damaging Intolerant radical 102770 1p13 adenosine monophosphate deaminase 1 (isoform M) 5128 rs17610395 CPT1A 1374 11 68318904 NM_001876 NP_001867 C/T A275T plus 24567198 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.19 0 48 1 0.02 0 46 1 123 by freq Benign 0.228 31 Borderline 0.18 2.78 37 moderately conservative 600528 11q13.1-q13.2 carnitine palmitoyltransferase 1A (liver) 5129 rs17611866 ZNF75A 7627 16 3307230 NM_153028 NP_694573 C/T V84A plus 24479598 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.26 0.26 0 46 1 0.1 0.01 94 2 123 by freq Benign 0.9 6 Tolerant 0.51 2.86 16 moderately conservative 601473 16p13.11 zinc finger protein 75a 5130 rs17612126 IGHMBP2 3508 11 68462250 NM_002180 NP_002171 A/C T879K plus 24567692 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.28 0.28 0 46 1 0.14 0.12 90 2 123 by freq moderately conservative 600502 11q13.2-q13.4 immunoglobulin mu binding protein 2 5131 rs17614157 ANP32C 23520 4 165475858 NM_012403 NP_036535 C/T E204G plus 24176274 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 0.1 0.09 88 2 123 by freq moderately conservative 606877 4q32.3 "acidic (leucine-rich) nuclear phosphoprotein 32 family, member C" 5132 rs17618795 UNC93A 54346 6 167680113 NM_018974 NP_061847 A/G W151X plus 24468468 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.15 0.15 0 46 1 0.09 0.09 92 2 123 by freq Probably damaging Intolerant radical 607995 6q27 unc-93 homolog A (C. elegans) 5133 rs17629834 MLF1 4291 3 159803405 NM_022443 NP_071888 A/C P226T plus 24381628 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.46 0.46 0 48 1 0.21 0.09 94 2 123 by freq Possibly damaging 1.645 6 conservative 601402 3q25.1 myeloid leukemia factor 1 5134 rs17632542 KLK3 354 19 56053569 NM_001648 NP_001639 C/T I179T plus 24582338 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.09 0.09 0 46 1 0.02 0 46 1 123 by freq Borderline 1.213 73 Intolerant 0.02 2.75 85 moderately conservative 176820 19q13.41 "kallikrein 3, (prostate specific antigen)" 5135 rs17632786 THBS1 7057 15 37669470 NM_003246 NP_003237 A/G N700S plus 24482845 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 0.07 0 46 1 123 by freq Possibly damaging 1.699 13 Intolerant 0.03 3.02 56 conservative 188060 15q15 thrombospondin 1 5136 rs17635381 PCM1 5108 8 17861833 NM_006197 NP_006188 G/T A691S plus 24179717 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.17 0 48 1 0.25 0.25 94 2 123 by freq Borderline 0.998 5 moderately conservative 600299 8p22-p21.3 pericentriolar material 1 5137 rs17641078 DMRT2 10655 9 1046959 NM_181872 NP_870987 C/G E458Q plus 24683596 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 0.09 0.03 90 2 123 by freq conservative 604935 9p24.3 doublesex and mab-3 related transcription factor 2 5138 rs17646069 DGKH 160851 13 41701263 NM_178009 NP_821077 C/T V1201A plus 24181447 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.02 0.02 0 48 1 0.09 0.09 94 2 123 by freq moderately conservative 604071 13q13.3 "diacylglycerol kinase, eta" 5139 rs17646457 FLRT2 23768 14 85159068 NM_013231 NP_037363 A/G R486Q plus 24585143 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.05 0.02 94 2 123 by freq Tolerant 0.47 2.86 33 conservative 604807 14q24-q32 fibronectin leucine rich transmembrane protein 2 5140 rs17651549 MAPT 4137 17 41417115 NM_016835 NP_058519 C/T R370W plus 24573464 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.25 0.25 0 48 1 0.09 0 44 1 123 by freq Intolerant 0.02 2.83 37 moderately radical 157140 17q21.1 microtubule-associated protein tau 5141 rs17667603 ST14 6768 11 129571471 NM_021978 NP_068813 A/C R381S plus 24576975 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.04 0 46 1 123 by freq Probably damaging 2.045 7 Tolerant 0.24 2.87 20 moderately radical 606797 11q24-q25 "suppression of tumorigenicity 14 (colon carcinoma, matriptase, epithin)" 5142 rs17678945 KRT1 3848 12 51356441 NM_006121 NP_006112 A/C A454S plus 24388958 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 123 by freq Benign 0.617 186 Intolerant 0.03 2.77 148 moderately conservative 139350 12q12-q13 keratin 1 (epidermolytic hyperkeratosis) 5143 rs17679445 PNPO 55163 17 43377064 NM_018129 NP_060599 A/G R116Q plus 24579075 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.04 0.04 0 48 1 123 by freq Potentially damaging 1.357 5 Potentially intolerant 0.06 2.76 59 conservative 603287 17q21.32 pyridoxine-5'-phosphate oxidase 5144 rs17680881 TACC3 10460 4 1700209 NM_006342 NP_006333 A/G G514E plus 24379868 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.31 0.31 0 48 1 0.15 0.06 94 2 123 by freq Tolerant 0.32 2.86 14 moderately conservative 605303 4p16.3 "transforming, acidic coiled-coil containing protein 3" 5145 rs17685621 PCDHB6 56130 5 140512261 NM_018939 NP_061762 C/T Y747H plus 24381416 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.02 0.02 0 46 1 0.02 0 46 1 123 by freq Probably damaging 2.192 100 Intolerant 0 2.77 128 moderately conservative 606332 5q31 protocadherin beta 6 5146 rs17704912 MYO18B 84700 22 24555866 NM_032608 NP_115997 C/G W1037S plus 24582088 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.17 0 48 1 0.04 0 46 1 123 by freq Tolerant 0.58 2.8 124 radical 607295 22q11.2-q12.1 myosin XVIIIB 5147 rs17710008 MYCT1 80177 6 153135149 NM_025107 NP_079383 A/G G119S plus 24495940 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.15 0.15 0 48 1 0.04 0.01 86 2 123 by freq Benign 0.146 7 moderately conservative 6q25.1 myc target 1 5148 rs17711777 PINX1 54984 8 10660650 NM_017884 NP_060354 C/T T220A plus 24394406 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 123 by freq moderately conservative 606505 8p23 PIN2-interacting protein 1 5149 rs17712523 CDH23 64072 10 73207620 NM_022124 NP_071407 A/G V1675I plus 24584606 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.21 0 48 1 0.09 0.09 94 2 123 by freq Tolerant 0.55 2.85 15 conservative 605516 10q21-q22 cadherin-like 23 5150 rs17719808 UBR1 197131 15 41043483 NM_174916 NP_777576 C/T T1548A plus 24395257 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 123 by freq Tolerant 0.22 2.86 18 moderately conservative 605981 15q13 ubiquitin protein ligase E3 component n-recognin 1 5151 rs17736370 KCNG4 93107 16 82814120 NM_172347 NP_758857 C/T C255Y plus 24499318 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 0.02 0 94 2 123 by freq Tolerant 0.59 2.77 46 radical 607603 16q24.1 "potassium voltage-gated channel, subfamily G, member 4" 5152 rs17738527 SEC14L4 284904 22 29213048 NM_174977 NP_777637 C/T E211K plus 24587774 1371 PERLEGEN AFD_EUR_PANEL European American (24) 44 0.23 0.23 0 44 1 0.05 0.05 94 2 123 by freq Possibly damaging 1.609 21 Intolerant 0.01 2.85 29 moderately conservative 22q12.2 SEC14-like 4 (S. cerevisiae) 5153 rs17738540 SEC14L4 284904 22 29213081 NM_174977 NP_777637 C/T V200M plus 24587780 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.21 0 48 1 0.06 0.06 94 2 123 by freq Benign 0.246 21 Intolerant 0.01 2.85 29 conservative 22q12.2 SEC14-like 4 (S. cerevisiae) 5154 rs17740607 HDC 3067 15 48342836 NM_002112 NP_002103 A/G T31M plus 24398534 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.04 0.03 94 2 123 by freq Possibly damaging 1.711 6 Tolerant 0.22 2.78 128 moderately conservative 142704 15q21-q22 histidine decarboxylase 5155 rs17742683 MPP3 4356 17 39234600 NM_001932 NP_001923 C/T R585G plus 24589152 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 123 by freq moderately radical 601114 17q12-q21 "membrane protein, palmitoylated 3 (MAGUK p55 subfamily member 3)" 5156 rs17750870 LAMA5 3911 20 60337441 NM_005560 NP_005551 C/G G1434A plus 24601606 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.05 0.05 0 42 1 0.02 0 86 2 123 by freq Possibly damaging 1.581 6 Tolerant 0.4 2.83 13 moderately conservative 601033 20q13.2-q13.3 "laminin, alpha 5" 5157 rs17751301 SYNE2 23224 14 63539581 NM_015180 NP_055995 C/T R1392W plus 24601749 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 123 by freq moderately radical 608442 14q23.2 "spectrin repeat containing, nuclear envelope 2" 5158 rs17752285 SERPINA11 256394 14 93978748 XM_170754 XP_170754 C/G T588S plus 24602074 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.02 0.02 0 42 1 0.02 0 44 1 123 by freq Tolerant 0.48 2.75 325 moderately conservative 14q32.2 "serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 11" 5159 rs17755373 PRKWNK1 65125 12 869899 NM_018979 NP_061852 C/T P1823L plus 24692066 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.04 0.04 0 46 1 0.02 0 48 1 123 by freq Potentially intolerant 0.06 3.18 9 moderately conservative 605232 12p13.3 "protein kinase, lysine deficient 1" 5160 rs17759929 SLC8A2 6543 19 52652054 XM_375633 XP_375633 C/G V471L plus 24591230 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.02 0.02 0 42 1 0.02 0 46 1 123 by freq Potentially damaging 1.43 45 conservative 601901 19q13.3 "solute carrier family 8 (sodium-calcium exchanger), member 2" 5161 rs17773251 CSNK1A1L 122011 13 36576884 NM_145203 NP_660204 C/G R170S plus 24593846 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.11 0.11 0 46 1 0.05 0 38 1 123 by freq Borderline 1.103 198 Potentially intolerant 0.08 2.8 186 moderately radical 13q13.2 "casein kinase 1, alpha 1-like" 5162 rs17778003 ZNF406 57623 8 135738992 NM_020863 NP_065914 C/T G64R plus 24494351 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.21 0.21 0 48 1 0.17 0 46 1 123 by freq moderately radical 8q24.22 zinc finger protein 406 5163 rs17782839 MLH3 27030 14 74583216 NM_014381 NP_055196 A/G S966P plus 24606778 1371 PERLEGEN AFD_EUR_PANEL European American (24) 46 0.04 0.04 0 46 1 123 by freq moderately conservative 604395 14q24.3 mutL homolog 3 (E. coli) 5164 rs17783344 GCA 25801 2 163034400 NM_012198 NP_036330 G/T S80A plus 24296225 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.13 0.13 0 48 1 0.04 0 46 1 123 by freq Benign 0.582 17 moderately conservative 607030 2q24.3 "grancalcin, EF-hand calcium binding protein" 5165 rs17791931 CYP2A6 1548 19 46046373 NM_000762 NP_000753 A/T L160H plus 24596427 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 123 by freq Probably damaging 2.156 87 Intolerant 0 2.81 162 moderately conservative 122720 19q13.2 "cytochrome P450, family 2, subfamily A, polypeptide 6" 5166 rs17800727 RBL2 5934 16 52038511 NM_005611 NP_005602 A/G Y210C plus 24409521 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.19 0.19 0 48 1 0.11 0 46 1 123 by freq Probably damaging 2.431 13 Tolerant 0.22 2.86 26 radical 180203 16q12.2 retinoblastoma-like 2 (p130) 5167 rs17801309 EPHA3 2042 3 89604354 NM_005233 NP_005224 A/G R914H plus 24300376 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.08 0.08 0 48 1 0.02 0 94 2 123 by freq Possibly damaging 1.616 85 Tolerant 0.22 2.84 81 conservative 179611 3p11.2 EphA3 5168 rs17802155 SFTPD 6441 10 81687848 NM_003019 NP_003010 A/T S290T plus 24409997 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.06 0.06 0 48 1 0.02 0 94 2 123 by freq Potentially damaging 1.323 13 Tolerant 0.85 2.87 42 moderately conservative 178635 10q22.2-q23.1 "surfactant, pulmonary-associated protein D" 5169 rs17811673 PAICS 10606 4 57155833 NM_006452 NP_006443 A/C K201N plus 24401602 1371 PERLEGEN AFD_EUR_PANEL European American (24) 42 0.05 0.05 0 42 1 123 by freq Potentially damaging 1.309 9 Potentially intolerant 0.07 2.78 123 moderately conservative 172439 4pter-q21 "phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase" 5170 rs17818842 TAF2 6873 8 120913963 NM_003184 NP_003175 A/G P8L plus 24411904 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.17 0.17 0 48 1 0.11 0 46 1 123 by freq moderately conservative 604912 8q24.12 "TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa" 5171 rs17827158 LY75 4065 2 160501857 NM_002349 NP_002340 C/T K1347R plus 24313272 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 0.04 0 46 1 123 by freq Borderline 1.047 5 Tolerant 0.37 2.76 22 conservative 604524 2q24 lymphocyte antigen 75 5172 rs17841256 NTAN1 123803 16 15039463 NM_173474 NP_775745 A/G S287P plus 24097366 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.35 0.35 0 48 1 0.27 0.19 94 2 123 by freq Probably damaging 2.274 6 Tolerant 1 3.11 12 moderately conservative 16p13.13 N-terminal asparagine amidase 5173 rs17841292 EEF2K 29904 16 22144774 NM_013302 NP_037434 C/G P75A plus 23961717 1371 PERLEGEN AFD_EUR_PANEL European American (24) 48 0.1 0.1 0 48 1 123 by freq Probably damaging 2.1 8 conservative 606968 16p12.3 elongation factor-2 kinase 5174 rs17841952 HLA-DRB1 3123 6 32657518 NM_002124 NP_002115 A/G N149S minus 24819774 1303 SEQUENOM CEPH CEPH (92) 184 0.39 123 by freq Benign 0.069 453 conservative 142857 6p21.3 "major histocompatibility complex, class II, DR beta 1"