We identified a SNP pair located in cis at the LPA locus, rs1800769 and rs9458001, to be jointly associated with risk for CAD [odds ratio (OR) = 1.37, P = 1.07 × 10−11], peripheral arterial disease (OR = 1.22, P = 2.32 × 10−4), aortic stenosis (OR = 1.47, P = 6.95 × 10−7), hepatic lipoprotein(a) (Lp(a)) transcript levels (beta = 0.39, P = 1.41 × 10−8), and Lp(a) serum levels (beta = 0.58, P = 8.7 × 10−32), while individual SNPs displayed no association. This evidence concerns the gene LPA and aortic stenosis.