Further gender stratification showed that older age (OR = 1.070, 95% CI [1.029–1.112]) and longer disease duration (OR = 1.004, 95% CI [1.000–1.007]) were independently associated with malignancy in male Chinese patients with RA, while older age (OR = 1.041, 95% CI [1.021–1.061]), positive RF (OR = 2.047, 95% CI [1.032–4.060]) and positive ACPA (OR = 2.677, 95% CI [1.312–5.463]) were associated with malignancy in female Chinese patients with RA. Here, PRTN3 is linked to rheumatoid arthritis.