Thus, our study suggested that CT and dominant model (CT + TT) genotypes and T allele of rs3731249 C > T (CDKN2A) variant were linked with a higher risk of childhood ALL (CT vs CC: OR = 9.56, 95% CI = 1.14–79.64, P = 0.037; Dominant model, CT + TT vs CC: OR = 10.76, 95% CI = 1.31–88.46, P = 0.004; and T allele vs C allele: OR = 11.00, 95% CI = 1.38–87.64, P = 0.024). The gene discussed is CDKN2A; the disease is acute lymphoblastic leukemia.