Table 1.
Significant SNPs Identified through GWAS and Located at Chromosome 6p21.3
| SNPa | Chr. | Risk Allele | Risk Allele Freq.b |
OR (95% CI)b | Stage I p Value | Stage II p Value | Stage III p Value | Combined p Value | Nearest Gene | |
|---|---|---|---|---|---|---|---|---|---|---|
| Case | Control | |||||||||
| rs2517713 | 6 | A | 0.763 | 0.622 | 1.88 (1.65–2.15) | 3.56E−08∗∗∗ | 2.61E−05∗∗∗ | 4.07E−10∗∗∗ | 3.90E−20∗∗∗ | HLA-A |
| rs2975042 | 6 | A | 0.759 | 0.621 | 1.86 (1.63–2.13) | 2.54E−08∗∗∗ | 9.21E−05∗∗∗ | 7.78E−10∗∗∗ | 1.60E−19∗∗∗ | HLA-A |
| rs9260734 | 6 | G | 0.782 | 0.658 | 1.85 (1.61–2.12) | 2.49E−07∗∗∗ | 6.29E−04∗∗ | 6.14E−10∗∗∗ | 6.77E−18∗∗∗ | HCG9 |
| rs29232 | 6 | A | 0.586 | 0.456 | 1.67 (1.48–1.88) | 1.39E−08∗∗∗ | 4.52E−05∗∗∗ | 1.34E−07∗∗∗ | 8.97E−17∗∗∗ | GABBR1 |
| rs3869062 | 6 | A | 0.792 | 0.683 | 1.78 (1.55–2.05) | 1.58E−06∗∗∗ | 8.13E−04∗∗ | 6.47E−09∗∗∗ | 8.68E−16∗∗∗ | HCG9 |
| rs5009448 | 6 | G | 0.750 | 0.637 | 1.72 (1.51–1.96) | 9.41E−06∗∗∗ | 6.44E−04∗∗ | 1.38E−09∗∗∗ | 1.30E−15∗∗∗ | HCG9 |
| rs3129055 | 6 | G | 0.406 | 0.312 | 1.51 (1.34–1.71) | 2.24E−04∗∗ | 6.28E−03∗ | 1.59E−06 ∗∗∗ | 7.36E−11∗∗∗ | HLA-F |
| rs9258122 | 6 | A | 0.406 | 0.315 | 1.49 (1.32–1.69) | 2.24E−04∗∗ | 2.02E−02∗ | 7.32E−07 ∗∗∗ | 3.33E−10∗∗∗ | HLA-F |
| rs16896923 | 6 | A | 0.850 | 0.768 | 1.66 (1.42–1.94) | 5.63E−06∗∗∗ | 2.29E−03∗ | 2.66E−05 ∗∗∗ | 2.49E−10∗∗∗ | HCG9 |
| rs2267633 | 6 | A | 0.821 | 0.741 | 1.57 (1.36–1.82) | 2.86E−05∗∗∗ | 4.17E−02 | 2.82E−05 ∗∗∗ | 1.28E−09∗∗∗ | GABBR1 |
| rs2076483 | 6 | A | 0.821 | 0.741 | 1.57 (1.36–1.82) | 2.86E−05∗∗∗ | 3.85E−02 | 3.13E−05 ∗∗∗ | 1.49E−09∗∗∗ | GABBR1 |
| rs29230 | 6 | A | 0.819 | 0.743 | 1.56 (1.34–1.80) | 3.99E−05∗∗ | 5.76E−02 | 4.03E−05 ∗∗∗ | 4.77E−09∗∗∗ | GABBR1 |
Significant SNPs identified from GWAS (stage I) and validated by two independent sets of case-control samples (stage II and III). Analysis was adjusted for age and gender with the use of a logistic regression model.
Risk allele frequencies and odds ratios (OR) were calculated on the basis of combined samples.
Permuted p value < 0.01. All permuted p values were computed with 10,000 permutations. For detailed information on assays, see Tables S2 and S7.
Permuted p value < 0.001. All permuted p values were computed with 10,000 permutations. For detailed information on assays, see Tables S2 and S7.
Permuted p value < 0.0001. All permuted p values were computed with 10,000 permutations. For detailed information on assays, see Tables S2 and S7.