For five brain regions, BLNK (OR = 1.16, 95% CI: 1.09–1.23, P = 6.2 × 10− 7) and CD2AP (OR = 1.28, 95% CI: 1.20–1.36, P = 4.0 × 10− 13) presented consistent associations with higher AD risk in the cortex, and GRN demonstrated consistent protective associations with AD in the cerebellum (OR = 0.87, 95% CI: 0.84–0.90, P = 2.2 × 10− 12), cortex (OR = 0.87, 95% CI: 0.84–0.90, P = 2.2 × 10− 12) and hippocampus (OR = 0.94, 95% CI: 0.92–0.97, P = 1.2 × 10− 5): these associations were supported by strong colocalization evidence (Fig. 4; Additional File 1: Tables S7, S8). This evidence concerns the gene CD2AP and Alzheimer disease.