Table 2. Loci with multiple independent single-variant association signals to SNPs with MAF>0.1%.
| Trait/Locus1 | Gene | Variant | MAF | Allele | Type | Beta2 | P-value3 | PV array SNP only4 | PV array SNP+sequence variants5 |
| LDL-C in ABCG8 | rs6756629 | .090 | A | array SNP | −0.15 | 1.3E-05 | |||
| ABCG8 | rs145756111 | .011 | A | synonymous | 0.31 | 6.1E-04 | 1.2% | 1.4% | |
| FG in G6PC2 | rs560887 | .310 | A | array SNP | −0.15 | 9.0E-12 | |||
| G6PC2 | rs138726309 | .014 | T | missense probably damaging | −0.41 | 2.6E-06 | 1.2% | 1.7% | |
| HDL-C in LPL | rs10096633 | .100 | A | array SNP | 0.15 | 6.8E-06 | |||
| LPL | rs268 | .018 | G | missense benign | −0.38 | 2.2E-07 | 0.72% | 1.2% | |
| TG in LPL | rs10096633 | .100 | A | array SNP | −0.19 | 1.9E-08 | |||
| LPL | rs268 | .018 | G | missense benign | 0.31 | 9.2E-05 | 0.59% | 0.85% | |
| HDL-C in ABCA1 | rs2575875 | .300 | A | array SNP | −0.08 | 8.4E-05 | |||
| ABCA1 | rs2066718 | .015 | T | missense benign | 0.32 | 9.3E-05 | |||
| ABCA1 | rs2066715 | .055 | T | missense benign | 0.15 | 5.1E-04 | 0.62% | 1.1% | |
| TG in APOA1 | rs12805061 | .270 | G | array SNP | 0.004 | .86 | |||
| APOA5 | rs2266788 | .089 | G | 3′-UTR | 0.27 | 7.7E-13 | |||
| APOA5 | rs3135506 | .059 | C | coding-synonymous | 0.24 | 6.9E-08 | 0.4% | 1.6% | |
| LDL-C in APOA1 | rs11216267 | .460 | G | array SNP | 0.08 | 2.3E-05 | |||
| APOA5 | rs651821 | .085 | C | 5′-UTR | 0.13 | 2.2E-04 | 1.4% | 1.6% | |
| TC in APOA1 | rs11216267 | .460 | G | array SNP | 0.08 | 1.3E-04 | |||
| APOA5 | rs651821 | .085 | C | 5′-UTR | 0.14 | 9.3E-05 | 1.1% | 1.4% | |
| HDL-C in LIPC | rs1532085 | .440 | A | array SNP | 0.13 | 9.4E-12 | |||
| LIPC | rs28933094 | .016 | T | missense probably damaging | 0.42 | 7.0E-08 | 1.2% | 1.8% | |
| TG in LIPC | rs261336 | .230 | G | array SNP | 0.09 | 1.4E-04 | |||
| LIPC | rs28933094 | .016 | T | missense probably damaging | 0.33 | 2.7E-05 | 0.2% | 0.5% | |
| HDL-C in CETP | rs3764261 | .270 | A | array SNP | 0.27 | 1.6E-40 | |||
| CETP | rs5880 | .024 | C | missense probably damaging | −0.26 | 1.8E-05 | 3.3% | 3.6% |
1
FG and TG were LN transformed prior to analysis; the regression coefficient is on the LN scale.
2
Beta is the estimate of the regression coefficient, and provides the amount and direction the phenotype changes for each copy of the indicated allele.
3
The p-values come from separate multivariate models for each locus that include all variants listed below, and the first five PCs. P-values shown here represent the independent evidence for the specified variant, after conditioning on the array SNP.
4
The percent variance in the phenotype accounted for by just the array SNP.
5
The percent variance in the phenotype accounted for by the array SNP and the independent sequence variants.