Table 1.
Case-control outcome adjusted for admixture (first 2 principal components) and center
| SNP | Chr | Position (Mb) |
Gene | Minor allele |
MAF (case) |
MAF (control) |
Joint p value | Meta p value | OR | 95% CI |
|---|---|---|---|---|---|---|---|---|---|---|
| rs2303565 | 2q35 | 219.254 | STK36 | C | 0.47 | 0.43 | 1.56E-06 (a) | 6.18E-07 (a) | 1.17 | (1.10–1.24) |
| rs1344642 | 2q35 | 219.264 | STK36 | A | 0.47 | 0.43 | 2.30E-06 (a) | 9.92E-07 (a) | 1.17 | (1.10–1.25) |
| rs2814707 | 9p21.2 | 27.526 | C9orf72a, MOBKL2Ba | A | 0.26 | 0.23 | 5.70E-07 (d) | 8.39E-07 (d) | 1.21 | (1.11–1.33) |
| rs3849942 | 9p21.2 | 27.533 | C9orf72a, MOBKL2Ba | A | 0.26 | 0.23 | 4.41E-07 (d) | 6.47E-07 (d) | 1.21 | (1.11–1.33) |
| rs2453556 | 9p21.2 | 27.576 | C9orf72a | G | 0.44 | 0.40 | 8.12E-07 (a) | 6.95E-07 (a) | 1.16 | (1.09–1.24) |
| rs1971791 | 15q23 | 68.363 | None within 150 kb | G | 0.49 | 0.47 | 9.70E-07 (r) | 2.11E-06 (r) | 1.26 | (1.14–1.40) |
| rs8056742 | 16q24.1 | 83.650 | KIAA0513 | C | 0.13 | 0.11 | 4.91E-07 (a) | 2.94E-06 (d) | 1.27 | (1.14–1.41) |
| rs2109262 | 17p11.2 | 16.125 | PIGL | C | 0.47 | 0.51 | 4.67E-07 (a) | 4.12E-07 (d) | 0.78 | (0.71–0.87) |
| rs7477 | 17p11.2 | 16.187 | CENPV | T | 0.52 | 0.48 | 2.89E-07 (r) | 3.05E-07 (r) | 1.30 | (1.16–1.44) |
| rs2006933 | 17q11.2 | 23.625 | FLJ40504a | G | 0.23 | 0.25 | 1.15E-06 (d) | 8.60E-07 (d) | 0.79 | (0.73–0.86) |
| rs11082762 | 18q11.2 | 19.620 | LAMA3 | A | 0.40 | 0.36 | 7.26E-07 (a) | 1.78E-06 (a) | 1.16 | (1.09–1.24) |
| rs12608932 | 19p13.11 | 17.614 | UNC13A | C | 0.38 | 0.34 | 1.29E-07 (a) | 4.96E-08 (r) | 1.37 | (1.21–1.56) |
SNPs are listed that have p < 1 × 10−6 in either the joint analysis or meta-analysis. For joint analysis, the additive model is presented unless the test for lack-of-fit to an additive model was significant (p < 0.05); (a) additive, (d) dominant, (r) recessive. For meta-analysis, the minimum p value of the 3 genetic models is used, noting that quality control standards were applied to ensure only appropriate samples sizes were included in the meta-analysis for each genetic model. There was no evidence for heterogeneity of the odds ratio across centers (p = 0.08, 0.09, and, > 0.20 for rs3849942, rs2814707, and remaining SNPs in the table, respectively). OR shown is from meta-analysis with 95% CI boundaries. Positions are from build 36.3.
Key: Chr, chromosome; CI, confidence interval; kb, kilobases; MAF, minor allele frequency; Mb, megabase; OR, odds ratio; SNP, single nucleotide polymorphism.
Less than 20 kb away.