By integrative analysis of TCGA bulk RNA-seq and methylomic datasets of HCC patients, we found that DNA methylation levels of MCM2 enhancer (cg08889930) was significantly negatively correlated with MCM2 mRNA expression (Pearson correlation test; r = − 0.548, p = 2.57e−33, Fig. 5C, D). This evidence concerns the gene MCM2 and hepatocellular carcinoma.