Among the 31 genes annotated from these significant risk variants, eight were reported to be associated with NAFLD, including BPTF, BUD13, FTO, GCKR, LPL, SIK3, TRIB1AL, and ZNF512. In addition, we identified FLI-defined FLD risk variants that have previously been associated with lipid profiles that are highly correlated with fatty liver progression (Additional File 3–9). Here, GCKR is linked to fatty liver disease.