Using conditional Q–Q plots and conjFDR statistical framework, we found significant pleiotropic overlap between AD and cognition-related phenotypes and identified 11 shared risk loci: APOE, CCDC83, PICALM, HBEGF, PICALM, EED, VAC14, EFL1, CKM, SKA2, and NECTIN2. Although VAC14, EFL1, CKM, SKA2, and NECTIN2 were novel risk loci, most of them were reported to be associated with AD, the risk of cognitive decline, or other brain diseases. This evidence concerns the gene CKM and brain disorder.