We found that the three well-known CVD risk loci (CDKN2B-AS1, LPA-PLG and APOE) were associated with both coronary and carotid atherosclerosis, but there were also considerable differences in the genetic background for atherosclerosis between the two vascular beds: The majority of SIS-associated SNPs did not appear to colocalize with CarPlaq, and the overall genetic correlation between SIS and CarPlaq was relatively modest (r = 0.42). Here, APOE is linked to atherosclerosis.