Variants identified by WES that are located within 250kb of an SNP marker identified by GWAS
| Gene symbol . | Chromosome . | Position (bp) . | Variant identifier . | Amino acid change . | WES P value . | Distance to GWAS SNP . | GWAS P value . |
|---|---|---|---|---|---|---|---|
| PON1 | 7 | 94937446 | rs662 | Q192R | 9.0 × 10−4 | 1kb | 4.3 × 10−5 |
| ENPP1 | 6 | 132172368 | rs1044498 | K173Q | 7.7 × 10−5 | 3kb | 7.1 × 10−5 |
| CYP4F2 | 19 | 16008388 | rs3093105 | W12G | 4.1 × 10−4 | 44kb | 6.0 × 10−5 |
| INPPL1 | chr11 | 71948536 | rs11548491 | A1083G | 8.6 × 10−7 | 76kb | 8.8 × 10−5 |
| GOLGB1 | 3 | 121415720 | rs3732410 | Y1212C | 5.6 × 10−4 | 127kb | 9.3 × 10−5 |
| RSAD1 | 17 | 48557326 | rs2290862 | A119T | 6.5 × 10−5 | 129kb | 3.3 × 10−5 |
| PKD1L3 | 16 | 71983772 | rs1035543 | S1176R | 8.7 × 10−7 | 193kb | 6.1 × 10−5 |
| LOC100289165 | 8 | 124658210 | rs16898671 | R128C | 7.3 × 10−4 | 194kb | 7.6 × 10−5 |
| ARGFX | 3 | 121305086 | rs61750878 | T196I | 1.4 × 10−4 | 238kb | 9.3 × 10−5 |
| KRT5 | 12 | 52908917 | rs11549950 | S528G | 2.1 × 10−4 | 243kb | 1.9 × 10−5 |
| HSD3B1 | 1 | 120057246 | rs45609334 | T367N | 1.8 × 10−7 | 248kb | 2.7 × 10−5 |
| Gene symbol . | Chromosome . | Position (bp) . | Variant identifier . | Amino acid change . | WES P value . | Distance to GWAS SNP . | GWAS P value . |
|---|---|---|---|---|---|---|---|
| PON1 | 7 | 94937446 | rs662 | Q192R | 9.0 × 10−4 | 1kb | 4.3 × 10−5 |
| ENPP1 | 6 | 132172368 | rs1044498 | K173Q | 7.7 × 10−5 | 3kb | 7.1 × 10−5 |
| CYP4F2 | 19 | 16008388 | rs3093105 | W12G | 4.1 × 10−4 | 44kb | 6.0 × 10−5 |
| INPPL1 | chr11 | 71948536 | rs11548491 | A1083G | 8.6 × 10−7 | 76kb | 8.8 × 10−5 |
| GOLGB1 | 3 | 121415720 | rs3732410 | Y1212C | 5.6 × 10−4 | 127kb | 9.3 × 10−5 |
| RSAD1 | 17 | 48557326 | rs2290862 | A119T | 6.5 × 10−5 | 129kb | 3.3 × 10−5 |
| PKD1L3 | 16 | 71983772 | rs1035543 | S1176R | 8.7 × 10−7 | 193kb | 6.1 × 10−5 |
| LOC100289165 | 8 | 124658210 | rs16898671 | R128C | 7.3 × 10−4 | 194kb | 7.6 × 10−5 |
| ARGFX | 3 | 121305086 | rs61750878 | T196I | 1.4 × 10−4 | 238kb | 9.3 × 10−5 |
| KRT5 | 12 | 52908917 | rs11549950 | S528G | 2.1 × 10−4 | 243kb | 1.9 × 10−5 |
| HSD3B1 | 1 | 120057246 | rs45609334 | T367N | 1.8 × 10−7 | 248kb | 2.7 × 10−5 |
For all variants with significant association with stroke, the chromosomal position of each variant identified by WES (n = 300; P < .001) was compared with the location of all SNP markers (n = 139; P < .0001). We identified 11 variants by WES where there was at least 1 SNP marker within 250kb. The variants highlighted in dark gray are variants predicted by PolyPhen2 or SIFT to be deleterious.