Sites annotated to 10 candidate genes for type 2 diabetes, including DUSP9, BCL11A, HNF4A, and CDKN2B, and 7 candidate genes for related metabolic traits (for example, ATP11A, ADCY5 and IRS1) had differential DNA methylation in human pancreatic islets based on sex (Additional files 11 and 12). Here, ATP11A is linked to type 2 diabetes mellitus.