We found a higher frequency of SE alleles in ACPA-positive RA compared with healthy controls (67.8% versus 41.6%, OR 2.95, CI 1.93 to 4.53, P < 0.001), but we did not observe this relationship with ACPA-negative RA patients and controls (35.2% versus 41.6%, P = 0.31), indicating that SE alleles are associated with ACPA production in RA. Here, PRTN3 is linked to rheumatoid arthritis.