The results suggest that the SNPs may influence cerebral atherosclerosis risk partially through CNOT3 (rs6664221: mean indirect effect = −0.05, 95% CI = (−0.0952, −0.01), bootstrap p < 0.004; rs10881463: mean indirect effect = −0.05, 95% CI = (−0.0959, −0.02), bootstrap p < 2 × 10−16; N = 352). This evidence concerns the gene CNOT3 and cerebral atherosclerosis.