The noteworthy finding in the present study was that there was a significant gene–gene interaction observed in IL1A rs1609682, ITGA2 rs1991013, and HABP2 rs7923349 using the GMDR approach, and the high-risk interactive genotypes in the three variants were independently risk factors of carotid atherosclerosis. The gene discussed is HABP2; the disease is carotid atherosclerosis.