It was found that SNPs within two T1D-associated genes, PTPN22 and CTLA4, alter the predicted diabetes risk of various HLA haplotypes, partly confirming earlier reports that the effect of a susceptibility allele at PTPN22 is greater in individuals expressing low-risk than high-risk HLA class II genotypes (56–58). Here, CTLA4 is linked to type 1 diabetes mellitus.