Not only the most well-known polymorphism of PTPN22 at position 1858 called the PTPN22 C1858T SNP has significant variant characteristics, but also new variants in a variety of genes, such as cytotoxic T-lymphocyte-associated protein 4 (CTLA4), tumor necrosis factor (TNF), interferon regulatory factor 5 (IRF5), etc., are recently reported to be associated with autoimmune disorders (Table 1). Here, CTLA4 is linked to autoimmune disease.