We performed functional annotation and expression- and splicing-QTL mapping for these independent signals and several of these SNPs are either eQTL or sQTL for TOMM40 and NECTIN2, suggesting that these genes may also be contributing to amyloid deposition independently of APOE. Colocalization analysis with AD risk for all the hits from APOE conditional analyses (N = 50) with AD risk GWAS [4] suggests more than half of these signals to be colocalizing with H4 > 0.8 (Additional file 1: Table S10). The gene discussed is TOMM40; the disease is Alzheimer disease.