This analysis showed that DRB1*13:02 and D70 were negatively associated with ACPA(+) RA in both SE-positive and -negative subjects (SE-negative: P = 0.0212, OR 0.59, 95% CI 0.38–0.92; SE-positive: P = 0.0144, OR 0.53, 95% CI 0.32–0.87 and SE-negative: P = 0.0011, OR 0.59, 95% CI 0.43–0.81: SE-positive, P = 0.0001, OR 0.56, 95% CI 0.42–0.75, respectively). The gene discussed is PRTN3; the disease is rheumatoid arthritis.