Using single-SNP testing and conditional analysis, evidence for multiple independent association signals with high-density lipoprotein cholesterol was found in the 15q21 region (Holmen et al., 2014; Surakka et al., 2015). A conditional analysis using genotype data on 19 115 individuals from the National FINRISK study (Borodulin et al., 2015) revealed three independent associations at rs2043085, rs1800588 and rs113298164. We extracted a 6 megabase region centered on rs2043085 with 8612 polymorphic SNPs and pairwise absolute correlations less than 0.99 from the original genotype data. Single-SNP testing using a linear model implemented in SNPTEST was performed to compute z-scores. The dataset was then analyzed with FINEMAP using 100 iterations allowing for at most five causal variants and prior parameter value of sλ2=0.052. Top panel of Figure 7 shows that the functional lipid SNPs rs113298164 (missense variant, Durstenfeld et al., 1994) and rs1800588 (affecting hepatic lipase activity, Deeb and Peng, 2000) are among the variants with largest evidence of being causal. Rs2043085 that had the lowest P-value in single-SNP testing showed less evidence of being causal than rs7350789 (r2=0.81). Indeed, there is substantial
