PURPOSE OF STUDY: Environmental factors are pivotal in shaping disease outcomes for obesity, diabetes, and metabolic syndrome (MetS), especially in the Pakistani population. This study aimed to determine whether promoter methylation levels of 12 diabetes and obesity susceptibility genes are associated with MetS phenotypes and risk of T2DM in Pakistani individuals. STUDY DESIGN: A cross-sectional study was undertaken whereby methylation-specific PCR assays were conducted on 203 adult subjects recruited from the community in Karachi, Pakistan. Participants were stratified into four groups based on their metabolic health and BMI (MOU n = 39, MHO n = 43, MUHNW n = 51, MHNW n = 70). Biochemical and biophysical data were statistically analyzed to determine the association of methylation levels with MetS phenotypes. RESULTS: Low chemerin promoter methylation was observed in metabolically unhealthy participants, irrespective of BMI, while higher methylation levels were observed for POMC and PCSK1. Unsupervised machine learning showed that the methylation status of Chemerin, IGF2, POMC, PCSK1 (P <
.001), and FNDC (P <
.05) was independently linked with the risk of developing MetS. Hierarchical clustering analysis revealed distinct genetic clusters that partially aligned with the original MetS and BMI categories, indicating the presence of unique genetic profiles and the potential misdiagnosis of high-risk individuals. CONCLUSION: Chemerin, IGF2, POMC, PCSK1, and FNDC's methylation status shows independently linked trends with the risk of developing MetS and obesity. Distinct genetic clusters for MUHNW and MHO exhibit similar phenotypic profiles, implying misdiagnosis risks and comparable risks of developing cardiometabolic disorders in the future. Large-scale methylation studies are needed to confirm the association. Key message What is already known on this topic: Genetic susceptibility contributes significantly to complex disorders like obesity, diabetes, and MetS. Prior research has highlighted the role of genetic polymorphisms but hasn't extensively explored the influence of promoter methylation in Pakistani populations. Understanding genetic and epigenetic factors in disease etiology is crucial for tailored interventions, particularly in populations with diverse genetic backgrounds and environmental exposures. What this study adds: Distinct trends of methylation patterns were observed in genes like Chemerin, IGF2, POMC, PCSK1, and FNDC, independently linked with MetS and obesity risk. Potential misdiagnosis risks and comparable risks of developing cardiometabolic disorders in individuals with metabolically unhealthy normal weight individuals and metabolically healthy phenotypes were observed. How this study might affect research, practice, or policy: Incorporating epigenetic biomarkers into risk assessment algorithms could enhance disease prediction accuracy and facilitate early intervention strategies. Recognizing misdiagnosis risks associated with MUHNW and MHO phenotypes could inform clinical practice and public health policies for improved disease screening and management.