Table 2.
Top independent variants associated with ASPD in the meta-analysis of the GWAS data from the UCL and Yale-Penn cohorts
| CHR | SNP IDa | Effect allele | Other allele | Gene | Weight | Z-score | P-value | Effect allele frequency (%) | Direction |
|---|---|---|---|---|---|---|---|---|---|
| 15 | rs9806493 | C | T | SLCO3A1 | 1673 | −5.501 | 3.77 × 10−8 | 47.1 | ––?? |
| 2 | rs10186418 | A | G | KCNS3 | 3197 | 5.137 | 2.79 × 10−7 | 86.8 | ++++ |
| 2 | rs11682196 | C | A | CTNNA2 | 3157 | −5.084 | 3.69 × 10−7 | 86.9 | –––– |
| 7 | rs967758 | C | T | Y_RNA | 2153 | −4.868 | 1.13 × 10−6 | 20.2 | ––?– |
| 20 | rs6076184 | T | C | RP5-1100I6.1 | 2181 | 4.807 | 1.53 × 10−6 | 5.3 | ++?+ |
| 1 | rs6691165 | C | A | MIR552 | 3175 | −4.789 | 1.68 × 10−6 | 45.2 | –––– |
Gene is the gene located closest to the lead SNP; or where there are multiple genes in the region the gene for which the SNP has the most deleterious annotation in ANNOVAR. Direction: - for negative, + for positive and? for missing in the UCL, Yale-Penn Phases 1, 2, and 3 samples respectively. The SNP marked in bold text reached a genome-wide level of significance in the meta-analysis.
CHR, chromosome; SNP, single nucleotide polymorphism.
a
Only SNPs that were present in both UCL and one or more Yale-Penn samples are shown.