Table 3.
Summary of most significant stage 1 and stage 2 results
| SNP | Chr | Pos(Mb) | Alleles (+/−) | Freq (+) | Effect (mg/dl) | Association P values
|
Sample sizes
|
Nearby genes | |||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Stage 1 (two-sided) | Stage 2 (one-sided) | Combined (two-sided) | Stage 1 | Stage 2 | |||||||
| SNPs associated with HDL cholesterol | |||||||||||
| rs3764261 | 16 | 55.6 | A/C | 0.69 | 3.47 | 2.8 × 10−19 | 6.4 × 10−43 | 2.3 × 10−57 | 8,656 | 8,072 | CETP |
| rs1864163 | 16 | 55.6 | G/A | 0.80 | 4.12 | 3.0 × 10−17 | 4.3 × 10−28 | 6.9 × 10−39 | 8,656 | 3,684 | CETP |
| rs9989419 | 16 | 55.5 | G/A | 0.65 | 1.72 | 8.0 × 10−16 | 1.8 × 10−17 | 3.2 × 10−31 | 8,656 | 6,981 | CETP |
| rs12596776 | 16 | 55.5 | G/C | 0.13 | 1.26 | 3.7 × 10−5 | 1.0 × 10−4 | 2.8 × 10−8 | 8,656 | 7,030 | CETP |
| rs1566439 | 16 | 55.6 | C/T | 0.45 | 0.96 | 2.0 × 10−5 | 2.1 × 10−4 | 3.3 × 10−8 | 8,656 | 4,881 | CETP |
| rs4775041 | 15 | 56.5 | C/G | 0.67 | 1.38 | 2.8 × 10−9 | 9.6 × 10−13 | 3.2 × 10−20 | 8,656 | 11,426 | LIPC |
| rs261332 | 15 | 56.5 | A/G | 0.19 | 1.41 | 1.7 × 10−9 | 1.3 × 10−7 | 2.3 × 10−15 | 8,656 | 6,956 | LIPC |
| rs10503669 | 8 | 19.9 | A/C | 0.10 | 2.09 | 3.2 × 10−10 | 9.4 × 10−11 | 4.1 × 10−19 | 8,656 | 11,431 | LPL |
| rs2197089 | 8 | 19.9 | A/G | 0.42 | 1.38 | 3.4 × 10−8 | 3.2 × 10−5 | 1.0 × 10−11 | 8,656 | 3,644 | LPL |
| rs6586891 | 8 | 20 | A/C | 0.34 | 1.00 | 3.5 × 10−5 | 9.7 × 10−6 | 2.9 × 10−9 | 8,656 | 7,017 | LPL |
| rs2144300 | 1 | 226.6 | T/C | 0.40 | 1.11 | 6.6 × 10−7 | 4.0 × 10−9 | 2.6 × 10−14 | 8,656 | 11,406 | GALNT2 |
| rs2156552 | 18 | 45.4 | T/A | 0.84 | 1.20 | 8.4 × 10−7 | 7.1 × 10−7 | 6.4 × 10−12 | 8,656 | 11,437 | LIPG |
| rs4149268 | 9 | 104.7 | C/T | 0.355 | 0.82 | 3.3 × 10−7 | 2.2 × 10−5 | 1.2 × 10−10 | 8,656 | 11,327 | ABCA1 |
| rs2338104 | 12 | 108.4 | G/C | 0.45 | 0.48 | 1.9 × 10−6 | 7.6 × 10−4 | 3.4 × 10−8 | 8,656 | 11,399 | MVK/MMAB |
| rs255052 | 16 | 66.6 | A/G | 0.17 | 0.74 | 1.5 × 10−6 | 0.0087 | 1.2 × 10−7 | 8,656 | 4,534 | LCAT |
| rs1323432 | 9 | 101.4 | A/G | 0.88 | −0.03 | 2.5 × 10−8 | 0.82 | 7.7 × 10−4 | 8,656 | 8,176 | GRIN3A |
| SNPs associated with LDL cholesterol | |||||||||||
| rs4420638 | 19 | 50.1 | G/A | 0.82 | 6.61 | 3.2 × 10−21 | 4.9 × 10−24 | 3.0 × 10−43 | 8,589 | 10,806 | APOE/C1/C4 |
| rs10402271 | 19 | 50 | G/T | 0.67 | 2.62 | 9.8 × 10−6 | 1.5 × 10−5 | 1.2 × 10−9 | 8,589 | 6,519 | APOE/C1/C4 |
| rs599839 | 1 | 109.5 | A/G | 0.77 | 5.48 | 1.2 × 10−13 | 2.7 × 10−21 | 6.1 × 10−33 | 8,589 | 10,783 | CELSR2/PSRC1/SORT1 |
| rs6511720 | 19 | 11.1 | G/T | 0.90 | 9.17 | 6.8 × 10−10 | 3.3 × 10−19 | 4.2 × 10−26 | 8,589 | 7,442 | LDLR |
| rs562338 | 2 | 21.2 | G/A | 0.18 | 4.89 | 1.2 × 10−11 | 3.6 × 10−12 | 5.6 × 10−22 | 8,589 | 10,849 | APOB |
| rs754523 | 2 | 21.2 | G/A | 0.28 | 2.78 | 7.0 × 10−7 | 1.3 × 10−6 | 8.3 × 10−12 | 8,589 | 6,542 | APOB |
| rs693 | 2 | 21.1 | A/G | 0.42 | 2.44 | 1.2 × 10−7 | 0.0034 | 3.1 × 10−9 | 8,589 | 3,222 | APOB |
| rs11206510 | 1 | 55.2 | T/C | 0.81 | 3.04 | 7.5 × 10−6 | 5.4 × 10−7 | 3.5 × 10−11 | 8,589 | 10,805 | PCSK9 |
| rs16996148 | 19 | 19.5 | G/T | 0.89 | 3.32 | 2.4 × 10−6 | 8.3 × 10−5 | 2.7 × 10−9 | 8,589 | 10,841 | NCAN/CILP2 |
| rs2254287 | 6 | 33.3 | G/C | 0.38 | 1.91 | 2.9 × 10−6 | 0.0015 | 5.1 × 10−8 | 8,589 | 7,440 | B3GALT4 |
| rs12695382 | 3 | 120.4 | A/G | 0.90 | 2.23 | 4.9 × 10−6 | 0.0067 | 1.0 × 10−6 | 8,589 | 10,802 | B4GALT4 |
| SNPs associated with triglycerides | |||||||||||
| rs780094 | 2 | 27.7 | T/C | 0.39 | 8.59 | 1.7 × 10−14 | 2.0 × 10−19 | 6.1 × 10−32 | 8,684 | 9,723 | GCKR |
| rs11127129 | 2 | 28.0 | C/G | 0.79 | 3.77 | 2.0 × 10−4 | 3.2 × 10−4 | 4.7 × 10−7 | 8,684 | 9,700 | RBKS/GCKR |
| rs12286037 | 11 | 116.2 | T/C | 0.94 | 25.82 | 1.1 × 10−7 | 1.6 × 10−22 | 1.0 × 10−26 | 8,684 | 9,738 | APOA5/A4/C3/A1 |
| rs662799 | 11 | 116.2 | G/A | 0.05 | 16.88 | 4.3 × 10−8 | 2.7 × 10−10 | 2.4 × 10−15 | 8,684 | 3,248 | APOA5/A4/C3/A1 |
| rs2000571 | 11 | 116.1 | A/G | 0.17 | 6.93 | 4.7 × 10−5 | 8.7 × 10−5 | 5.7 × 10−8 | 8,684 | 3,209 | APOA5/A4/C3/A1 |
| rs486394 | 11 | 116.0 | C/A | 0.28 | 1.50 | 1.7 × 10−4 | 0.0073 | 7.4 × 10−6 | 8,684 | 3,597 | APOA5/A4/C3/A1 |
| rs10503669 | 8 | 19.9 | C/A | 0.895 | 11.57 | 1.4 × 10−9 | 1.6 × 10−14 | 3.9 × 10−22 | 8,684 | 9,711 | LPL |
| rs2197089 | 8 | 19.9 | G/A | 0.58 | 3.38 | 3.1 × 10−11 | 0.0029 | 1.1 × 10−12 | 8,684 | 3,202 | LPL |
| rs6586891 | 8 | 20.0 | C/A | 0.66 | 4.60 | 2.4 × 10−4 | 5.0 × 10−4 | 1.1 × 10−6 | 8,684 | 3,622 | LPL |
| rs17321515 | 8 | 126.6 | A/G | 0.56 | 6.42 | 6.8 × 10−8 | 1.0 × 10−6 | 7.0 × 10−13 | 8,684 | 5,312 | TRIB1 |
| rs17145738 | 7 | 72.4 | C/T | 0.84 | 8.21 | 4.1 × 10−6 | 5.0 × 10−8 | 2.0 × 10−12 | 8,684 | 9,741 | MLXIPL |
| rs1748195 | 1 | 62.8 | C/G | 0.70 | 7.12 | 2.3 × 10−4 | 5.4 × 10−8 | 1.7 × 10−10 | 8,684 | 9,559 | ANGPTL3 |
| rs16996148 | 19 | 19.5 | G/T | 0.92 | 6.10 | 6.3 × 10−7 | 2.4 × 10−4 | 2.5 × 10−9 | 8,684 | 9,707 | NCAN/CILP2 |
| rs4775041 | 15 | 56.5 | C/G | 0.67 | 3.62 | 7.3 × 10−5 | 2.9 × 10−5 | 1.6 × 10−8 | 8,684 | 8,462 | LIPC |
| rs2144300 | 1 | 226.6 | C/T | 0.60 | 4.25 | 4.9 × 10−4 | 2.4 × 10−4 | 7.9 × 10−7 | 8,684 | 8,473 | GALNT2 |
The table summarizes association signals after follow-up of the promising SNPs in stage 2 samples. Column 1 headings are as described for Table 2, with the addition of one-sided P values for the stage 2 samples, in which we tested for the same direction of effect as Stage 1—consistent with current best practice for replication of GWAS findings. The effect sizes shown were estimated from stage 2 samples only. SNPs with a combined (stage 1 + 2) P value <10−5 were included, although we also show GRIN3A for completeness because it was significant in the initial scan. Rows corresponding to SNPs with a combined P value < 5 × 10−8 are in boldface. SNPs in this table may not match those in Table 2, which only displays the strongest signal in each locus. The discrepancy also reflects our bias towards genotyped Affymetrix 500K SNPs in the Stage 2 follow-up. Association P values for each of the six stage 2 samples are shown in Supplementary Table 4.