The methylation frequency of serum SCAND3, Myo1g, and SCAND3 + Myo1g in the HCC, HBV (hepatitis B virus)-related liver cirrhosis (LC), benign liver disease (BLD), and healthy controls (HC) groups. (A) The SCAND3 methylation ratio among HCC patients (73.33%) was significantly higher than that of LC patients (5.7%), BLD cases (6%), and HC (4.1%) (χ2 = 151.12, p < 0.0001). There were no significant differences between the SCAND3 methylation levels in LC patients, BLD cases, and HC (χ2 = 0.217, p = 0.897). (B) The Myo1g methylation ratio among the HCC patients (78.79%) was significantly higher than that of the LC patients (32.69%), BLD cases (6%), and HC (2%) (χ2 = 137.8, p < 0.001). The methylation levels in the LC patients were higher than that in the BLD cases (χ2 = 7.76, p < 0.05) and HC (χ2 = 16.18, p < 0.001). (C) The “SCAND3 + Myo1g” methylation ratio among the HCC patients (92.73%) was significantly higher than that of the LC patients (36.53%), BLD cases (12%), and HC (8%) respectively, (χ2 = 132.47, p < 0.001). The “SCAND3 + Myo1g” methylation levels in the LC patients were higher than those in the BLD cases (χ2 = 5.524, p < 0.05) and HC (χ2 = 11.55, p < 0.001). * p < 0.05, ** p < 0.01.