Table 2.
SNPs with P values < 1 × 10–4 in joint analysis.
| Chr | SNP | Position | Gene | Allele format | Risk allele | Stage | Control/case | RAF controls | RAF cases | Trend P | OR | 95% CI | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 9 | rs10739199 | 9,707,144 | PTPRD | GA | A | GWAS | 96/126 | 0.6094 | 0.8016 | 1.70E−05 | 2.59 | 1.695 | 3.958 |
| GA | Replication | 75/133 | 0.6486 | 0.7154 | 1.73E−01 | 1.361 | 0.8841 | 2.097 | |||||
| GA | Combined | 171/259 | 0.6265 | 0.7578 | 6.75E−05 | 1.866 | 1.384 | 2.515 | |||||
| 9 | rs2025392 | 9,733,309 | PTPRD | TC | C | GWAS | 96/126 | 0.8542 | 0.964 | 7.30E−05 | 4.572 | 2.103 | 9.941 |
| TC | Replication | 75/133 | 0.9189 | 0.947 | 2.45E−01 | 1.576 | 0.7088 | 3.503 | |||||
| TC | Combined | 171/259 | 0.8824 | 0.9553 | 8.01E−05 | 2.846 | 1.671 | 4.848 | |||||
| 14 | rs1998998 | 97,680,819 | – | AG | A | GWAS | 96/126 | 0.1146 | 0.268 | 5.31E−05 | 2.829 | 1.674 | 4.782 |
| AG | Replication | 75/133 | 0.1486 | 0.2386 | 2.38E−02 | 1.795 | 1.052 | 3.062 | |||||
| AG | Combined | 171/259 | 0.1294 | 0.2529 | 6.50E−06 | 2.277 | 1.567 | 3.31 | |||||
| 15 | rs6576560 | 26,577,347 | – | TC | C | GWAS | 96/126 | 0.4896 | 0.6905 | 3.09E−05 | 2.326 | 1.576 | 3.432 |
| TC | Replication | 75/133 | 0.527 | 0.6364 | 3.78E−02 | 1.571 | 1.044 | 2.363 | |||||
| TC | Combined | 171/259 | 0.5059 | 0.6628 | 9.70E−06 | 1.92 | 1.451 | 2.541 | |||||
RAF risk allele frequency, Trend P P vale of Trend test, OR odds ratio, CI confidence interval.