Based on these observations, we hypothesized that cis-eQTL effects of some AD-associated alleles may be specific to myeloid cells and thus not easily detectable in cis-eQTL datasets obtained from brain homogenates where myeloid cells (microglia and other brain-resident macrophages) represent a minor fraction of the tissue. Therefore, we analyzed cis-eQTL effects of the AAOS-associated SNPs and their tagging SNPs in human cis-eQTL datasets composed of 738 monocyte and 593 macrophage samples from the Cardiogenics consortium27. We identified 14 genes with cis-eQTLs significantly associated with these SNPs (Table 3). Notably, the protective rs1057233G allele, located within the 3′ UTR of SPI1, was strongly associated with lower expression of SPI1 in both monocytes (P=1.50×10−105) and macrophages (P=6.41×10−87) (Fig. 1a, 1b, 2a). This allele was also associated with lower expression of MYBPC3 (monocytes: P=5.58×10−23; macrophages: P=4.99×10−51), higher expression of CELF1 in monocytes (P=3.95×10−8) and lower NUP160 expression in macrophages (P=5.35×10−22). Each of these genes lies within the SPI1/CELF1 locus, suggesting complex regulation of gene expression in this region. Within the MS4A locus, which contains many gene family members, the minor allele (C) of
