Table 2.
SNPs with P values < 1 × 10−5 in the Joint Analysis.
| Chr. | SNP | Position | Gene | Allele format | Risk allele | Stage | control/case | RAF controls | RAF cases | Trend P | OR | 95%CI | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 3 | rs2594966 | 11325276 | ATG7 | GA | GWAS | 1731/342 | 0.6155 | 0.6959 | 7.00E-05 | 1.43 | 1.198 | 1.706 | |
| GA | A | Replication | 1265/188 | 0.6105 | 0.6765 | 1.31E-02 | 1.334 | 1.059 | 1.681 | ||||
| GA | Combined | 2996/530 | 0.6133 | 0.689 | 2.52E-06 | 1.397 | 1.214 | 1.607 | |||||
| 3 | rs2594973 | 11395821 | ATG7 | CG | GWAS | 1731/342 | 0.5948 | 0.6795 | 3.24E-05 | 1.445 | 1.212 | 1.722 | |
| CG | G | Replication | 1265/188 | 0.5918 | 0.6489 | 3.38E-02 | 1.275 | 1.017 | 1.598 | ||||
| CG | Combined | 2996/530 | 0.5935 | 0.6686 | 3.81E-06 | 1.381 | 1.203 | 1.587 | |||||
| 3 | rs4684776 | 11443223 | ATG7 | CT | GWAS | 1731/342 | 0.6096 | 0.6877 | 1.08E-04 | 1.41 | 1.183 | 1.681 | |
| CT | T | Replication | 1265/188 | 0.6067 | 0.6729 | 1.19E-02 | 1.334 | 1.06 | 1.678 | ||||
| CT | Combined | 2996/530 | 0.6084 | 0.6824 | 3.59E-06 | 1.383 | 1.203 | 1.59 | |||||
| 3 | rs4686799 | 186451236 | KNG1 | TC | GWAS | 1731/342 | 0.6598 | 0.7108 | 9.95E-03 | 1.268 | 1.057 | 1.521 | |
| TC | C | Replication | 1265/188 | 0.6454 | 0.7486 | 1.06E-04 | 1.637 | 1.276 | 2.099 | ||||
| TC | Combined | 2996/530 | 0.6537 | 0.7244 | 8.91E-06 | 1.392 | 1.202 | 1.612 | |||||
| 4 | rs78868369 | 126077143 | ANKRD50, FAT4 | TC | GWAS | 1731/342 | 0.08449 | 0.1268 | 4.81E-04 | 1.574 | 1.219 | 2.033 | |
| TC | T | Replication | 1265/188 | 0.08796 | 0.133 | 4.55E-03 | 1.59 | 1.146 | 2.208 | ||||
| TC | Combined | 2996/530 | 0.08595 | 0.129 | 7.61E-06 | 1.575 | 1.288 | 1.927 | |||||
| 6 | rs536348 | 168098215 | LOC441178, C6orf123 | TC | GWAS | 1731/342 | 0.6407 | 0.7132 | 2.52E-04 | 1.395 | 1.165 | 1.67 | |
| TC | C | Replication | 1265/188 | 0.6395 | 0.7234 | 1.26E-03 | 1.474 | 1.16 | 1.874 | ||||
| TC | Combined | 2996/530 | 0.6402 | 0.7169 | 1.12E-06 | 1.423 | 1.232 | 1.643 | |||||
| 8 | rs17201317 | 104096256 | ATP6V1C1, BAALCOS | CT | GWAS | 1731/342 | 0.1096 | 0.1485 | 3.45E-03 | 1.417 | 1.118 | 1.796 | |
| CT | C | Replication | 1265/188 | 0.1093 | 0.1738 | 2.99E-04 | 1.715 | 1.276 | 2.304 | ||||
| CT | Combined | 2996/530 | 0.1095 | 0.1575 | 6.67E-06 | 1.521 | 1.265 | 1.829 | |||||
| 14 | rs11846182 | 80872021 | DIO2-AS1 | CT | GWAS | 1731/342 | 0.602 | 0.6754 | 2.58E-04 | 1.376 | 1.156 | 1.638 | |
| CT | T | Replication | 1265/188 | 0.6135 | 0.6818 | 9.98E-03 | 1.35 | 1.07 | 1.702 | ||||
| CT | Combined | 2996/530 | 0.6069 | 0.6777 | 9.48E-06 | 1.362 | 1.185 | 1.565 | |||||
Chr., chromosome; gene, genes containing the SNP or the closest gene up to 50 kb upstream or downstream of the SNP; RAF controls, risk allele frequency in controls; RAF cases, risk allele frequency in SVO stroke; OR, odds ratio; 95% CI, 95% confidence interval.