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Background  Diabetes mellitus (DM) is a complex metabolic disease that is caused by a complex interplay between genetic and environmental factors. This research aimed to investigate the association of genetic polymorphisms in  PDX1  and  MC4R  with T2DM risk.    Methods  The genotypes of 10 selected SNPs in  PDX1  and  MC4R  were identified using the Agena MassARRAY platform. We utilized odds ratio (OR) and 95% confidence intervals (CIs) to assess the correlation between genetic polymorphisms and T2DM risk.    Results  We found that  PDX1 -rs9581943 decreased susceptibility to T2DM among in a Chinese Han population (OR = 0.76,  p  = 0.045). We also found that selected genetic polymorphisms in  PDX1  and  MC4R  could modify the risk of T2DM, which might also be influenced by age, sex, BMI, smoking status, and drinking status ( p  < 0.05).    Conclusions  We concluded that  PDX1  and  MC4R  genetic variants were significantly associated with T2DM risk in a Chinese Han population. These single polymorphic markers may be considered to be new targets in the assessment and prevention of T2DM among Chinese Han people.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12920-021-01037-3.

PDX1 and MC4R genetic polymorphisms are associated with type 2 diabetes mellitus risk in the Chinese Han population