A genome-wide association study and meta-analysis for intrahepatic cholestasis of pregnancy (ICP) that included 1,138 patients and 153,642 individuals as controls revealed 11 ICP risk loci (P < 5 × 10–8), which might affect liver-specific genes. Coding variants were identified in SERPINA1, GCKR and HNF4A, whereas noncoding variants were identified in gene loci relevant to lipid and bile acid homeostasis (such as ABCG5/8, ABCB1/4, ABCB11, CYP7A1 and SULT2A1). Three ICP-related risk loci were not directly related to lipid and bile acid homeostasis.