PTPN22 and rheumatoid arthritis: High-risk RA polymorphisms in non-HLA genes are: PTPN22 [rs2476601] allele T OR = 2.3 [CI: 1.7–3.2], p = 0.0001; TNF [rs1800629] allele G OR = 2.25 [CI: 1.4–3.5], p = 0.0001; TPMT [rs2842934] allele G OR = 1.55 [CI: 1.2–2], p = 0.002; IL4 [rs2243250] allele T OR = 1.6 [CI: 1.2–2.1], p = 0.0025, etc. The highest OR values among the genotypes of non-HLA genes are shown for the homozygous TT genotype of the PTPN22 gene OR = 8.5 [CI: 4.6–15.56], p = 0.001 and the GG genotype of TPMT OR = 2.5 [CI: 1.4–4.5], p = 0.0016.