The full Methods are in Supplementary Information and provide information about: (1) study samples and phenotypes; (2) genotyping and imputation; (3) genome-wide association analyses; (4) meta-analyses of directly typed and imputed SNPs; (5) estimation of effect sizes; (6) conditional analyses of top signals; (7) sex-specific analyses; (8) cis-expression quantitative trait locus analyses; (9) analyses of lipid-associated SNPs in European and non-European samples; (10) analyses of lipid-associated SNPs in individuals with and without CAD; (11) analyses of associated SNPs in patients with extreme LDL-C, HDL-C, or TG levels; (12) simulation studies to assess overlap between GWAS signals and Mendelian disease loci; and (13) details of mouse studies.