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, PNPLA3 is linked to Sjogren syndrome.