Table 1.
Description of the ten independent genome-wide significant variants identified in our GWAS).
| Cytoband | Best trait | Independent SNP rsID | #SNPs in Credible set 99% (95%) | Candidate gene (kb) | Effect allele/ other allele | Weighted effect allele freq | I2 (%) | (Cond.) Beta | (Cond.) p-val | Exp. Var (%) |
|---|---|---|---|---|---|---|---|---|---|---|
| 2p21 | tSito | rs4299376 | 3 (3) | ABCG8 (0) | T/G | 0.68 | 0 | −0.133 | 9.5 × 10−74 | 3.27 |
| 2p21 | tSito | rs11887534 | 7 (5) | ABCG8 (0) | C/G | 0.065 | 0 | −0.178 | 8.3 × 10−39 | 1.71 |
| 2p21 | tSito | rs7598542 | 16 (7) | ABCG8 (0) | C/G | 0.21 | 52 | −0.052 | 5.1 × 10−10 | 0.39 |
| 2p21 | tSito | rs78451356 | 12 (11) | ABCG5 (5.9) | G/T | 0.17 | 9.4 | 0.069 | 1.1 × 10−14 | 0.61 |
| 5q13.3 | tBras/fLano | rs12916 | 37 (21) | HMGCR (0) | C/T | 0.42 | 0 | −0.059 | 2.3 × 10−11 | 0.51 |
| 7p13 | tCamp | rs217385 | 24 (22) | NPC1L1 (21) | T/G | 0.43 | 0 | −0.041 | 6.3 × 10−15 | 0.62 |
| 9q34.2 | tCamp | rs2519093 | 38 (23) | ABO (0) | T/C | 0.22 | 0 | 0.045 | 1.6 × 10−12 | 0.51 |
| 10q25.3 | tSito | rs2286779 | 4 (4) | PNLIPRP2 (0) | C/G | 0.53 | 15 | 0.054 | 1.9 × 10−15 | 0.64 |
| 12q24.31 | tSito | rs10846744 | 5 (5) | SCARB1 (0) | C/G | 0.17 | 68 | 0.063 | 2.9 × 10−12 | 0.50 |
| 19q13.32 | eStig | rs7412 | 1 (1) | APOE (0) | T/C | 0.088 | 0 | −0.073 | 1.9 × 10−14 | 0.83 |
For the locus 2p21, four independent variants were discovered by Cojo-Select analysis. For the other loci, only a single independent variant was found. For each variant, we present cytoband, best associated trait at this locus, rsID and corresponding statistics (of fixed effect meta-analysis of gene-dose effects). For the 2p21 variants, conditional effect estimates and p-values are shown. The sizes of the 99%, respectively 95% credible sets are also provided. Corresponding variants are annotated in Supplementary Data S8. Annotations are in accordance with genome-build GRCh37. Trait abbreviations are explained in Supplementary Data S18.