In an allelic association analysis, rs2383207, rs3731245, and rs1537378 were significantly associated with CI; the odd ratios were 1.18 (95 % confidence interval (CI) = 1.01-1.37, P = 0.04), 1.29 (95 % CI = 1.06-1.56, P = 0.01), and 1.30 (95 % CI = 1.05-1.60, P = 0.02), respectively. rs1537378 remains significantly associated with CI independent of traditional cerebrovascular risk factors in a recessive model (odds ratio (OR) = 1.35, 95 % CI = 1.06-1.71, P = 0.013, Q = 0.03) and in an additive model (OR = 1.38, 95 % CI = 1.11-1.71, P = 0.004, Q = 0.02); conversely, rs2383207 (OR = 1.28, 95 % CI = 1.03-1.59, P = 0.02, Q = 0.03) and rs3731245 (OR = 1.31, 95 % CI = 1.05-1.65, P = 0.02, Q = 0.03) were significantly different in a recessive model.