These TWAS significant genes included some established JIA-associated genes that have been reported previously, such as CCDC101 (p = 5.82 × 10−8 and FDR = 1.64 × 10−4 for Muscle Skeletal), CLN3 (p = 5.82 × 10−8 and FDR= 2.53 × 10−4 for Whole Blood), ERAP2 (p = 5.49 × 10−6 and FDR = 2.16 × 10−3 for Cells EBV-transformed lymphocytes), LNPEP (p = 3.53 × 10−6 and FDR = 2.36 × 10−3 for Artery Tibial). Here, LNPEP is linked to juvenile idiopathic arthritis.