To explore the relationship between sequence variants affecting blood lipids and coronary artery disease (CAD), Helgadottir et al. examined rare and low-frequency variants for effects on non-HDL-cholesterol, HDL-cholesterol, LDL-cholesterol, and triglyceride levels in a large cohort. In total, 13 rare and low-frequency sequence variants with large effects on lipid levels were identified, in addition to 14 previously reported variants. The causality analysis using genetic risk scores demonstrated an effect of non-HDL cholesterol, but not HDL cholesterol or triglycerides, on the pathogenesis of CAD. Furthermore, the results indicate that non-HDL cholesterol confers an additional risk of CAD beyond that associated with LDL cholesterol.