In summary, this study identified RNAm-SNPs in many reported RA susceptibility genes (e.g., PADI2, SPRED2, PLCL2, HLA-A, HLA-B, HLA-DRB1, HLA-DPB1, TRAF1 and TXNDC11) and elucidated the relationships between RNAm-SNPs, gene expression and protein levels and RA. Here, PADI2 is linked to rheumatoid arthritis.