The APOE and TM6SF2 variants were associated with increased markers of inflammation, glycemia and kidney markers, and increased risk of CLD, but negatively associated with LDL cholesterol, triglycerides, and apolipoprotein B. The TM6SF2 rs8107974 and PNPLA3 variants were associated with an increased risk of MASLD. Here, APOE is linked to metabolic dysfunction-associated steatotic liver disease.