At HLA class II loci, the frequencies of DPB1*04:01, DQB1*03:02, and DRB1*01:01 were increased by more than twofold in the JIA group (33.46%, 14.39%, and 10.29%) compared to in the control group (11.21%, 4.23%, and 4.17%), respectively (PDPB1*04:01 = 8.99 × 10−07, PDQB1*03:02 = 7.24 × 10−04, and PDRB1*01:01 = 1.83 × 10−02). Here, HLA-DPB1 is linked to juvenile idiopathic arthritis.