Haplotype analysis (Table 4) showed that CTLA4 Ars62182595Trs16840252 (OR = 0.042, 95% CI = 0.005–0.324, p < 0.001), Ars62182595Crs16840252 (OR = 0.042, 95% CI = 0.005–0.324, p < 0.001), and Grs62182595Trs16840252 (OR = 0.037, 95% CI = 0.005–0.286, p < 0.001), and TNFSF4 Grs1234314Grs45454293 (OR = 0.229, 95% CI = 0.091–0.579, p = 0.001) had a lower risk of SLE. This evidence concerns the gene CTLA4 and systemic lupus erythematosus.