We found that the minor allele (“C”) of rs7493 in PON2, the minor allele (“T”) of rs7593130 in ADCY3, and the minor allele (“C”) of rs11583680 in PCSK9 were associated with a reduced risk of NAFLD in the Chinese population, whereas the minor allele (“C”) of rs1260326 in GCKR was associated with a reduced risk of NAFLD. Here, PON2 is linked to metabolic dysfunction-associated steatotic liver disease.