Table 1.
SNPs with primary model p-value < 0.0001. Listed genes are within 10kb of the SNP position
| SNP | Gene | Chr | Pos(bp) | Risk Allele h | Primary p-value | Male odds ratio (95%CI) | Female odds ratio (95% CI) |
|---|---|---|---|---|---|---|---|
| rs2836823 | 21 | 39,302,119 | T (0.48/0.4) | 1.53E-06 | 1.35 (1.08-1.68) | 1.46 (1.23-1.73) | |
| rs4142041 | CTNNA3 | 10a | 68,310,957 | G (0.41/0.34) | 5.64E-06 | 1.73 (1.37-2.2)* | 1.14 (0.97-1.35)* |
| rs999i | GPSM3, AGPAT1, NOTCH4, RNF5, AGER, PBX2, AGER | 6 | 32,261,864 | C (0.96/0.94) | 1.42E-05 | 1.92 (1.06-3.45) | 2.53 (1.62-3.95) |
| rs12623467 | NRXN1 | 2g | 51,136,740 | C (0.96/0.92) | 1.48E-05 | 2.42 (1.51-3.88) | 1.57 (1.14-2.16) |
| rs1782159 | 14b | 40,826,319 | C (0.25/0.2) | 1.87E-05 | 1.97 (1.46-2.65)* | 1.09 (0.87-1.36)* | |
| rs12380218 | VPS13A | 9c | 77,165,214 | G (0.24/0.19) | 2.09E-05 | 1.18 (0.9-1.55) | 1.56 (1.28-1.91) |
| rs2022443 | VPS13A | 9c | 77,099,406 | G (0.24/0.19) | 2.49E-05 | 1.12 (0.86-1.45)* | 1.57 (1.29-1.91)* |
| rs2673931 | TRPC7 | 5d | 135,717,335 | T (0.66/0.61) | 3.89E-05 | 1.68 (1.34-2.12)* | 1.04 (0.87-1.24)* |
| rs4142603 | 9c | 76,998,948 | C (0.25/0.19) | 4.05E-05 | 1.15 (0.9-1.47) | 1.52 (1.26-1.84) | |
| rs1031006 | 5 | 14,040,103 | A (0.67/0.62) | 4.30E-05 | 0.98 (0.78-1.24)* | 1.49 (1.25-1.78)* | |
| rs2791480 | CLCA1 | 1 | 86,680,605 | G (0.78/0.72) | 4.38E-05 | 1.53 (1.19-1.97) | 1.33 (1.1-1.61) |
| rs10049135 | 3 | 72,731,670 | A (0.89/0.86) | 4.65E-05 | 2.09 (1.51-2.91)* | 0.96 (0.75-1.24)* | |
| rs11145381 | VPS13A | 9c | 77,144,695 | C (0.23/0.18) | 4.72E-05 | 1.19 (0.91-1.57) | 1.54 (1.26-1.88) |
| rs2798983 | 14b | 40,841,983 | C (0.28/0.22) | 4.77E-05 | 1.63 (1.25-2.13) | 1.28 (1.05-1.55) | |
| rs2546657 | TRPC7 | 5d | 135,711,634 | A (0.66/0.62) | 4.96E-05 | 1.67 (1.33-2.09)* | 1.01 (0.85-1.2)* |
| rs1782182 | 14b | 40,766,891 | G (0.31/0.25) | 5.28E-05 | 1.72 (1.33-2.22)* | 1.14 (0.95-1.38)* | |
| rs10490162 | NRXN1 | 2 | 51,159,308 | T (0.91/0.86) | 5.66E-05 | 1.92 (1.34-2.75) | 1.39 (1.08-1.79) |
| rs11694463 | 2 | 12,732,219 | C (0.12/0.09) | 6.10E-05 | 2.1 (1.4-3.15) | 1.37 (1.05-1.78) | |
| rs17706334 | 11e | 108,486,074 | A (0.97/0.94) | 6.38E-05 | 1.71 (1.05-2.8) | 2.19 (1.44-3.33) | |
| rs17706299 | 11e | 108,486,027 | C (0.97/0.94) | 6.51E-05 | 1.71 (1.05-2.79) | 2.19 (1.44-3.33) | |
| rs13277254 | CHRNB3 | 8f | 42,669,139 | A (0.81/0.76) | 6.54E-05 | 1.19 (0.92-1.55) | 1.55 (1.26-1.91) |
| rs12467557 | NRXN1 | 2g | 51,153,921 | A (0.96/0.93) | 6.88E-05 | 2.53 (1.48-4.31) | 1.62 (1.14-2.3) |
| rs17633258 | 11e | 108,491,084 | C (0.97/0.94) | 7.31E-05 | 1.9 (1.14-3.15) | 2.11 (1.38-3.23) | |
| rs4859365 | 4 | 35,345,098 | G (0.52/0.45) | 7.72E-05 | 1.49 (1.2-1.86) | 1.24 (1.04-1.47) | |
| rs10793832 | FBXL17 | 5 | 107,348,129 | C (0.32/0.26) | 8.13E-05 | 1.11 (0.87-1.41) | 1.47 (1.23-1.76) |
| rs1782134 | 14b | 40,785,318 | T (0.3/0.25) | 8.18E-05 | 1.68 (1.3-2.18)* | 1.15 (0.96-1.39)* | |
| rs11157219 | 14b | 40,852,451 | G (0.3/0.24) | 8.78E-05 | 1.7 (1.31-2.2)* | 1.16 (0.96-1.4)* | |
| rs2302673 | FTO | 16 | 52,625,622 | T (0.87/0.84) | 8.85E-05 | 1.04 (0.76-1.44)* | 1.69 (1.33-2.16)* |
| rs1612945 | 14b | 40,805,691 | C (0.3/0.24) | 8.91E-05 | 1.66 (1.29-2.15)* | 1.18 (0.98-1.42)* | |
| rs1782145 | 14b | 40,800,126 | C (0.3/0.24) | 9.06E-05 | 1.65 (1.28-2.14)* | 1.18 (0.98-1.42)* | |
| rs1782141 | 14b | 40,795,921 | A (0.3/0.25) | 9.20E-05 | 1.68 (1.3-2.16)* | 1.15 (0.96-1.39)* | |
| rs17633211 | 11e | 108,490,715 | T (0.97/0.94) | 9.33E-05 | 1.9 (1.14-3.15) | 2.09 (1.37-3.19) | |
| rs6474413 | CHRNB3 | 8f | 42,670,221 | T (0.81/0.76) | 9.36E-05 | 1.18 (0.91-1.53) | 1.54 (1.25-1.9) |
| rs9332406 | CTNNA3 | 10a | 68,340,205 | A (0.4/0.34) | 9.71E-05 | 1.63 (1.28-2.06)* | 1.11 (0.94-1.32)* |
| rs1782144 | 14b | 40,799,523 | G (0.3/0.24) | 9.88E-05 | 1.65 (1.28-2.14)* | 1.18 (0.98-1.43)* |
Significantly different Odds Ratio for men and women.
Two Chr 10 SNPs with r2 correlation of 0.89
Nine Chr 14 SNPs with minimum pair-wise r2 correlation of >0.85
Four Chr 9 SNPs with minimum pair-wise r2 correlation of >0.85
Two Chr 5 SNPs with r2 correlation of 0.99 (the other two Chr 5 SNPs are uncorrelated)
Four Chr 11 SNPs with minimum pair-wise r2 correlation of >0.95
Two Chr 8 SNPs with r2 correlation of 1
Two Chr 2 SNPs with r2 correlation of 0.91 (the other two Chr 2 SNPs have pair-wise correlations of <50%).
The risk allele is chosen arbitrarily to be the allele more prevalent in cases to facilitate comparison of effect sizes across SNPs. This does not imply that the effect of the variant is known in any case; the other allele could be protective. In addition, the alleles could be complementary to those reported in dbSNP (see online SNP information).
The allele frequency for rs999 is quite different in these data than reported in dbSNP; this may represent a failure to accurately genotype this SNP in this study.