To apply systems level understanding for the role of DNA methylation it is important to have the prevailing view to distinguish the sequence elements regulating gene expression. We have mapped the methylome of The Finnish Diabetic Nephropathy Study (FinnDiane) and show differential methylated regions (DMRs) of key transcription factor binding sites. In this cohort, we show DNA methylation changes derived from leukocytes for genes implicated in insulin signaling, integrin interactions and lipid metabolism. Methylation sequencing identified that mTOR (mechanistic target of rapamycin) gene regulation was subject to differential CpG methylation at CTCF binding sites. These clinical findings were tested ex vivo in primary diabetic HAECs that confirm transition to high glucose conditions increased mTOR gene expression. The significance of DNA methylation on mTOR was confirmed using the DNA methylation inhibitor, 5-aza-2'-deoxycytidine (5adC). We show exon-specific mTOR expression is DNA methylation dependent and hypothesize alternative splicing of mTOR is mediated by Pol II pausing conferred by DNA methylation. The result of Chromatin immunoprecipitation experiments implicate DNA methylation of mTOR regulates CTCF binding in primary HAECs stimulated by hyperglycemia and 5adC. These results highlight glucose-derived changes to CTCF binding sites are sensitive to loss-of-methylation with gain-of-function in diabetes. This strengthens the evidence base against methylation changes just being an epiphenomenon with the identification of gene targets that contribute to the pathogenesis of diabetic nephropathy.