Abstract: The present invention provides a method for identifying a subject having or at risk of having a metabolic disease, such as diabetes or obesity. The invention is based on an approach to identify candidate genes involved in metabolic diseases, such as obesity and type 2 diabetes (T2D) through epigenetic mechanisms. The method includes identifying in the subject genetic markers correlating differentially methylated regions (DMRs) in the genome with genetic risk loci for the subject and comparing methylation patterns of the markers with a control sample from a subject not having the disease. In another embodiment, the invention also provides a method of treating a subject having or at risk of having a metabolic disease. In another embodiment, the invention provides a method of providing a prognostic evaluation of a subject having or at risk of having a metabolic disease.