In the present study, we found that several SNPs identified in GWAS to associate with type 1 diabetes (e.g. PTPN2[15], INS[15] and HLA[86]), type 2 diabetes (e.g. ADCY5[60], [64], [87] and KCNJ11[25], [26], [29], [79]) and glucose-traits (GRB10[64] and PDX1[64]) were also associated with differential DNA methylation between genotype groups in human pancreatic islets. This evidence concerns the gene PTPN2 and type 1 diabetes mellitus.