This study aimed to accomplish three main objectives: first, to identify genetic risk factors associated with JIA in a Swedish cohort through a Genome-Wide Association Study (GWAS) analysis; second, to enhance the understanding of HLA associations by imputing classical HLA alleles within all JIA patients as one group and within specific subtypes; and third, to investigate the association between these HLA alleles and autoantibodies such as ANA, RF, ACPA, along with patient clinical parameters. Here, BTG3 is linked to juvenile idiopathic arthritis.