In summary, in a case–control study with 1100 CAD patients and 1069 controls, we have identified that two SNPs (HNF1A rs1169288, MADD-FOLH1 rs7395662) as well as the GRS were significantly associated with TC, HDL-c levels and CAD risk, and correlation may exist between the HNF1A rs1169288 and severity of coronary atherosclerosis. This evidence concerns the gene HNF1A and coronary atherosclerosis.