We then sought evidence of replication in an independent dataset of primary CD14+ human monocytes from 432 individuals28. We replicated cis-eQTL associations with expression of SPI1, MYBPC3, MS4A4A, MS4A6A, and SELL (Bonferroni-corrected threshold: P=0.05/15421 probes = 3.24×10−6). We found strong evidence for the association between rs1057233 and SPI1 expression (P=6.39×10−102) as well as MYBPC3 expression (P=5.95×10−33, Supplementary Table 7). Rs1530914 and rs7929589, both in high LD with rs7930318 (R2 = 0.99 and 0.87, respectively), were associated with expression of MS4A4A and MS4A6A (P=3.60×10−8, 6.37×10−15), respectively. Finally, rs2272918, tagging rs10919252, was significantly associated with expression of SELL (P=8.43×10−16). Interestingly, the minor allele of all of these SNPs showed protective effects in both AD risk and survival analyses, as well as lower expression of the associated genes. Further, SPI1, MS4A4A, MS4A6A, and SELL are specifically expressed in microglia based on RNA-Seq data29–31 (Fig. 2b, Supplementary Fig. 4). However, MYBPC3/Mybpc3 (a myosin binding protein expressed at high levels in cardiac muscle cells) is either not expressed or expressed at low levels in human and mouse microglia, respectively. Amongst all genes probed, MYBPC3 (ILMN_1781184)
