Our pleiotropy analysis of all pairwise combinations of these traits identified GWS associations with APOE and three regions not previously reported with any neuropathologic traits or AD risk, including C2orf40 for the joint model comprising NP and NFT, as well as HDAC9 and TRAPPC12/TRAPPC12-AS1/ADI1 for the joint model comprising NFT and CAA. The gene discussed is HDAC9; the disease is Alzheimer disease.