According to DNA methylation profiles of NAFLD&NASH and HCC, we found three genes that had undergone hypermethylation, i.e., ALDOB (p value ≤ 8.50 × 10−1), HSPB1 (p value ≤ 1.00 × 10−3), and RPL30 (p value ≤ 1.00 × 10−3), and two genes that had undergone hypomethylation, i.e., TUBA1C (p value ≤ 1.00 × 10−3) and FRAT2 (p value ≤ 1.00 × 10−3) in a comparison of NAFLD&NASH with HCC cells. Here, FRAT2 is linked to metabolic dysfunction-associated steatotic liver disease.