These regions contain prototypical lipid/lipoprotein regulating genes, such as APOE, CETP, LDLR, and PCSK9. Interestingly, for all lead SNPs with marginal association with coronary atherosclerosis (P < 1.0 × 10−3; with and without conditioning on clinical lipids), 43 (81%) were associated with lipid endophenotypes for CAD. Here, PCSK9 is linked to coronary atherosclerosis.