A missense single nucleotide polymorphism (SNP) known as rs2476601 in PTPN22 has been consistently associated with a variety of autoimmune diseases in populations of European ancestry, including rheumatoid arthritis (RA), type I diabetes, and systemic lupus erythematosus (SLE)14, 15, 16, 17, 18, but this functional SNP was non-polymorphic and no relationships were found in studies from Japan19, 20, 21, 22. Here, PTPN22 is linked to autoimmune disease.