We found two susceptibility loci in MRPS6/SLC5A3 genes associated with 2hPG, six loci in LINC01648, MATN1, CRAT37, and SLCO3A1 genes associated with HbA1C, and five loci in TRPM3/TMEM2 and MLYCD/OSGIN1 correlated to BMI in Hainan prediabetes. Here, LINC01648 is linked to prediabetes syndrome.