According to the DNA methylation profiles of PBC&PSC and HCC for validation, we found four genes with hypermethylation, i.e., ALDOB (p value ≤ 8.30 × 10−1), TIMP1 (p value ≤ 1.00 × 10−3), RPL30 (p value ≤ 1.00 × 10−3), and IGF2 (p value ≤ 1.00 × 10−3), and two genes with hypomethylation, i.e., H3F3A (p value ≤ 1.00 × 10−3) and FRAT2 (p value ≤ 1.00 × 10−3) in a comparison between PBC&PSC and HCC. The gene discussed is H3-3A; the disease is hepatocellular carcinoma.