Supplementary Figure 3: Regional association plot of the LIPC locus | Nature Genetics

Supplementary Figure 3: Regional association plot of the LIPC locus

From: Systematic evaluation of coding variation identifies a candidate causal variant in TM6SF2 influencing total cholesterol and myocardial infarction risk

Supplementary Figure 3

The regional association plots show the LIPC region on chromosome 15. The –log10 P value for association with HDL cholesterol is shown for several data sets: (a) Global Lipids Genetics Consortium GWAS results 4 in ∼95,000, (b) association in Stage 1 samples (N=5,643), and (c) association in Stage 1 samples conditioning on association with rs113298164 (LIPC p.Thr405Met). Supplementary Figure 3a shows that the LIPC p.Thr405Met and RNF111 p.Pro836Ser were not observed in GWAS. Comparison of Supplementary Figure 3b and the conditional analysis in Supplementary Figure 3c demonstrates that the association signal at RNF111 p.Pro836Ser is due to linkage disequilibrium with LIPC p.Thr405Met. Furthermore, the association signal at the variants discovered by GWAS as two independent signals (rs1532085 and rs261334) remain strongly associated after conditioning on p.Thr405Met, suggesting the association at these two SNPs is independent from p.Thr405Met.

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