We validated several previously-reported variant-nonalcoholic fatty liver disease associations (PNPLA3, TM6SF2, GCKR), and also identified new associations between variants in/near APOB and hepatic steatosis and between primary sclerosing cholangitis and a variant near VN1R10P, which is involved in regulation of innate and adaptive immunity including in diseases such as rheumatoid arthritis and Sjogren syndrome. Here, GCKR is linked to fatty liver disease.