SNP markers identified by GWAS as being associated with risk for stroke
| SNP ID . | Associated gene . | Chromosome . | Position bp . | Alleles . | MAF in control patients (%) . | MAF in stroke patients (%) . | Odds ratio (95% CI) . | Significance P value . |
|---|---|---|---|---|---|---|---|---|
| rs3803539 | GABARAPL1 | 15 | 88692986 | [A/G] | 5.90 | 23.30 | 4.7 (3.1-7.1) | 2.71 × 10−7 |
| rs10123021 | LPPR1 | 9 | 102491889 | [A/C] | 29.50 | 33.60 | 1.3 (1.1-1.6) | 3.13 × 10−7 |
| rs17329620 | MKRN9P | 12 | 86674908 | [A/C] | 9.80 | 25.80 | 3.2 (2.2-4.5) | 5.52 × 10−7 |
| rs309247 | CCDC102B | 18 | 64534044 | [C/G] | 18.30 | 30.70 | 2.0 (1.5-2.7) | 9.77 × 10−7 |
| rs1481779 | ARHGAP24 | 4 | 86656079 | [C/T] | 19.50 | 33.60 | 2.1 (1.6-2.8) | 1.78 × 10−6 |
| rs16965445 | TSHZ3 | 19 | 36492060 | [A/G] | 9.90 | 19.60 | 2.2 (1.5-3.2) | 3.30 × 10−6 |
| rs4888761 | WWOX | 16 | 76780490 | [C/T] | 16.40 | 27.20 | 1.9 (1.4-2.6) | 4.17 × 10−6 |
| rs7219249 | EIF1 | 17 | 37086202 | [A/G] | 31.80 | 39.70 | 1.4 (1.1-1.8) | 5.80 × 10−6 |
| rs10516451 | DAPP1 | 4 | 100845572 | [C/T] | 13.20 | 21.10 | 1.8 (1.3-2.5) | 6.08 × 10−6 |
| rs572400 | AGPAT9 | 4 | 84669771 | [C/T] | 9.50 | 1.70 | 0.16 (0.1-0.4) | 9.81 × 10−6 |
| SNP ID . | Associated gene . | Chromosome . | Position bp . | Alleles . | MAF in control patients (%) . | MAF in stroke patients (%) . | Odds ratio (95% CI) . | Significance P value . |
|---|---|---|---|---|---|---|---|---|
| rs3803539 | GABARAPL1 | 15 | 88692986 | [A/G] | 5.90 | 23.30 | 4.7 (3.1-7.1) | 2.71 × 10−7 |
| rs10123021 | LPPR1 | 9 | 102491889 | [A/C] | 29.50 | 33.60 | 1.3 (1.1-1.6) | 3.13 × 10−7 |
| rs17329620 | MKRN9P | 12 | 86674908 | [A/C] | 9.80 | 25.80 | 3.2 (2.2-4.5) | 5.52 × 10−7 |
| rs309247 | CCDC102B | 18 | 64534044 | [C/G] | 18.30 | 30.70 | 2.0 (1.5-2.7) | 9.77 × 10−7 |
| rs1481779 | ARHGAP24 | 4 | 86656079 | [C/T] | 19.50 | 33.60 | 2.1 (1.6-2.8) | 1.78 × 10−6 |
| rs16965445 | TSHZ3 | 19 | 36492060 | [A/G] | 9.90 | 19.60 | 2.2 (1.5-3.2) | 3.30 × 10−6 |
| rs4888761 | WWOX | 16 | 76780490 | [C/T] | 16.40 | 27.20 | 1.9 (1.4-2.6) | 4.17 × 10−6 |
| rs7219249 | EIF1 | 17 | 37086202 | [A/G] | 31.80 | 39.70 | 1.4 (1.1-1.8) | 5.80 × 10−6 |
| rs10516451 | DAPP1 | 4 | 100845572 | [C/T] | 13.20 | 21.10 | 1.8 (1.3-2.5) | 6.08 × 10−6 |
| rs572400 | AGPAT9 | 4 | 84669771 | [C/T] | 9.50 | 1.70 | 0.16 (0.1-0.4) | 9.81 × 10−6 |
The top 10 SNP markers associated with stroke were identified by Cochran-Armitage testing on all stroke (n = 177) vs all control (n = 335) samples, assuming an additive model. None of the SNP markers have any predicted effects on gene function, but the associated gene is given for each SNP. The MAF is given for each of the phenotypes. The significance is the Cochran-Armitage P value, and the odds ratios with CIs are given for each associated variant.