Among them, we identified a methylation site located 2 kb upstream of the CpG island, which not only showed a causal association with FLOT1 (Probe ID cg23423329, beta_SMR = −0.3607, p_SMR = 2.38 × 10−11, FDR = 6.94 × 10−11, p_⁣HEIDI = 0.81; Figure 4d) but also acted as a protective factor against SLE (beta_SMR = −0.00024, p_SMR_multi = 4.04 × 10−10, FDR = 8.74 × 10−9, p_⁣HEIDI = 0.51; Figure 4c). The gene discussed is FLOT1; the disease is systemic lupus erythematosus.