Five SNPs (GCKR rs1260326, CDKN2A/B rs10811661, MTNR1B rs1387153, rs2166706, and rs10830963) were significantly associated with IFG and type 2 diabetes (p = 9.0 × 10−6, 1.0 × 10−5, 1.09 × 10−4, 4.1 × 10−5, and 8.9 × 10−5, respectively) after adjusting for age, sex, and body mass index (BMI), and rs1260326 in GCKR exhibited the strongest association in the Korean sample. Here, GCKR is linked to type 2 diabetes mellitus.