APOE and Alzheimer disease: We observed that the association of rs11666329 with AD risk is still highly significant after conditioning on APOE (before conditioning: P=1.52×10-66; after conditioning: P=7.12×10-32; Table S16), indicating this association is independent of APOE. Using the same analyses, the association of rs11666329 with NECTIN2 expression in cortex is also independent of APOE (before conditioning: P=2.78×10-5; after conditioning: P=3.32×10-5; Table S16).