In the final model, the CDKN2A-rs10811661 polymorphism (OR per T allele = 1.22, 95 % CI = 1.04–1.44, P = 0.017), systolic blood pressure (OR per 10 mmHg = 1.14, 95 % CI = 1.08–1.20, P < 0.0001), waist-hip ratio (OR = 1.25, 95 % CI = 1.10–1.42, P < 0.0001), dyslipidemia (OR = 1.57, 95 % CI = 1.15–2.14, P = 0.004), and residence (OR = 1.93, 95 % CI = 2.82–4.14, P < 0.0001) were the most significant independent predictors of prediabetes, in which the power of the adjusted prediction model was 0.646. The gene discussed is CDKN2A; the disease is metabolic syndrome.