In this study, we aimed to investigate the relationship of IKBKE rs15672 and BANK1 rs12640056 gene polymorphisms with systemic lupus erythematosus (SLE) susceptibility in China. A case-control study was performed on 567 SLE patients and 345 healthy controls. Six single nucleotide polymorphisms (rs15672, rs2296164, rs12640056, rs6842661, rs1957106 and rs2274064) and clinical features were analyzed. Genotyping was executed with improved multiplex ligation detection reaction assay. SNP rs15672 increased the risk (P = 0.028, OR = 1.25, 95%CI = 1.02–1.52) but rs12640056 decreased the risk of SLE (P = 0.015, OR = 0.78, 95%CI = 0.64–0.95). For rs15672, patients carrying allele A assumed high-level IL-6 (25.36 ± 4.64 vs 16.56 ± 2.95, P = 0.036) and IL-4 (12.06 ± 4.51 vs 4.88 ± 1.76, P = 0.047), but low-level granzyme B (14.07 ± 1.86 vs 18.38 ± 3.85, P = 0.023), IL-18 (267.39 ± 14.67 vs 348.57 ± 44.25, P = 0.002) and IL-33 (0.91 ± 0.26 vs 2.19 ± 1.35, P = 0.029). Organ injury showed that mutant genotype at rs15672 had high-prevalence of arthritis (32.02%) and serositis (34.78%), but low in neuropathy (9.09%). For rs12640056, patients carrying allele T assumed low-level IL-33 (0.46 ± 0.17 vs 2.16 ± 1.00, P = 0.009). In conclusion, gene polymorphisms of rs15672 and rs12640056 present relevant with susceptibility of SLE, and affect the expression of cytokine and organ injury.

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