After adjusting with each SNP, the multivariate logistic regression (adjusted) model analysis showed that the CC genotype rs2162145 (CPA6) (AOR = 14.86; 95% CI 1.71–29.04; p = 0.014), GG (AOR = 7.91; 95% CI 1.67–37.27; p = 0.009) and GA (AOR = 5.27; 95% CI 1.19–23.19; p = 0.028) genotypes of rs889299 (SCNN1B) were significantly associated with uncontrolled T2DM. Here, SCNN1B is linked to type 2 diabetes mellitus.