BackgroundEpigenome, genetic variants, and other environmental factors involved in gene regulation are highly inter-dependent in several chronic diseases, including obesity, cardiovascular disease, and diabetes. The present study aimed at testing the associations and the mechanism involved in silencing of CYP2R1 gene in normal and obese Saudi women patients. Height, weight, BMI, 25-hydroxy vitamin D, parathyroid hormone, glycemic status, and lipid profile (TG, LDL, HDL, and TC) of CYP2R1 were measured in 100 women (31 normal and 69 obese patients).ResultsOur result shows that hypermethylation in site 2 of the CYP2R1 gene with body weight (p< 0.004), BMI (p< 0.002), waist circumference (p< 0.002), total-LDL (p< 0.027), total cholesterol (p< 0.022), and vitamin D (VD) (close to borderline significancep< 0.06) and site 4 of CYP2R1 with LDL (p< 0.041) in the four tested sites among normal and obese women was significantly associated. Moreover, we tested five different CpG sites in the CYP27B1 gene where site 5 correlated significantly with VD levels.ConclusionOur present study clearly indicates that hypermethylation of specific sites in the CYP2R1 and CYP27B1 genes might regulate gene expression with special reference to the risk of obesity and vitamin D metabolism.Supplementary InformationThe online version contains supplementary material available at 10.1186/s43141-023-00508-7.