Table 2.
The effect of validated polymorphisms included in the simple risk allele count on levels of high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and triglyceride in the InChianti sample, including proxy markers
| Validated SNP | Nearest gene(s) | Allele included in risk count | Hapmap allele frequency | Genotyped proxy | r2a | Per allele effect β (95% CI) | P-valueb | Lipid level variance explained (%) |
|---|---|---|---|---|---|---|---|---|
| LDL-raising variants | ||||||||
| rs693 | APOB | A | 0.492 | 3.25 (0.23, 6.27) | 0.035 | 0.40 | ||
| APOE | ϵ4 | NA | 5.66 (−1.06, 12.4) | 0.098 | 0.51 | |||
| rs646776 | CELSR2-PSRC1-SORT1 | T | 0.712 | 6.70 (2.89, 10.5) | 0.001 | 1.35 | ||
| rs12654264 | HMGCR | T | 0.417 | rs6896136 | 0.87 | 4.57 (1.61, 7.54) | 0.003 | 0.87 |
| rs6511720 | LDLR | G | 0.095 | 8.86 (4.37, 13.3) | 1.1 × 10−4 | 1.29 | ||
| rs11206510 | PCSK9 | T | 0.850 | 4.18 (0.34, 8.02) | 0.033 | 0.54 | ||
| rs16996148 | NCAN/CILP2 | G | 0.939 | 8.25 (1.82, 14.7) | 0.012 | |||
| HDL-lowering variants | ||||||||
| rs4149268 | ABCA1 | C | 0.267 | 0.015 (−0.01, 0.04) | 0.252 | 0.12 | ||
| rs3135506 | APOA1-C3-A4-A5 | G | 0.06 | −0.065 (−0.12, −0.01) | 0.017 | 0.52 | ||
| rs1800775 | CETP | C | 0.425 | −0.078 (−0.10, −0.05) | 1.4 × 10−10 | 4.76 | ||
| rs2144300 | GALNT2 | C | 0.417 | rs10779835 | 0.97 | −0.029 (−0.05, −0.005) | 0.018 | 0.75 |
| rs1800588 | LIPC | C | 0.742 | −0.049 (−0.08, −0.02) | 0.001 | 1.13 | ||
| rs2156552 | LIPG | A | 0.80 | rs4939883 | 0.95 | −0.014 (−0.05, 0.02) | 0.421 | 0.07 |
| rs328 | LPL | C | 0.875 | −0.059 (−0.09, −0.03) | 0.001 | 1.38 | ||
| rs2238104 | MVK-MMAB | C | 0.558 | −0.013 (−0.04, 0.01) | 0.282 | 0.11 | ||
| rs4775041 | LIPC | G | 0.737 | −0.036 (−0.06, −0.01) | 0.012 | |||
| Triglyceride-raising variants | ||||||||
| rs1748195 | ANGPTL3 | C | 0.675 | rs1167998 | 1.00 | 0.022 (−0.02, 0.07) | 0.302 | 0.09 |
| rs662799 | APOA1-C3-A4-A5 | G | 0.017 | 0.118 (0.05, 0.019) | 0.015 | 1.06 | ||
| rs3135506 | APOA1-C3-A4-A5 | G | 0.06 | 0.205 (0.11, 0.30) | 2.2 × 10−5 | 2.02 | ||
| rs693 | APOB | A | 0.492 | 0.041 (−0.0001, 0.08) | 0.009 | 0.40 | ||
| rs2144300 | GALNT2 | C | 0.417 | rs10779835 | 0.97 | 0.018 (−0.02, 0.06) | 0.166 | 0.08 |
| rs780094 | GCKR | T | 0.383 | 0.057 (0.02, 0.10) | 0.016 | 0.75 | ||
| rs328 | LPL | C | 0.875 | 0.104 (0.05, 0.16) | 0.013 | 1.24 | ||
| rs17145738 | MLXIPL | C | 0.881 | rs2240466 | 1.00 | 0.111 (0.03, 0.19) | 0.036 | 0.79 |
| rs17321515 | TRIB1 | A | 0.602 | rs6982636 | 1.00 | 0.052 (0.01, 0.09) | 0.041 | 0.65 |
| rs4775041 | LIPC | C | 0.263 | 0.006 (−0.04, 0.06) | 0.806 | |||
| rs16996148 | NCAN/CILP2 | G | 0.939 | 0.145 (0.06, 0.23) | 0.001 | |||
ar2 Values between validated SNP and genotyped proxy obtained from Hapmap CEU population.
bSignificance level for association between lipid level-altering SNP and associated serum lipid level.