Cell type specificity is mainly represented by enhancers, rather than promoters. A microglial specific enhancer depicting a chromatin loop to BIN1 promoter and bearing a high score AD risk variant was deleted with CRISPR-Cas9 in pluripotent stem cells. These cells were differentiated into microglia, neurons, and astrocytes and BIN1 expression was depleted only in microglia. Here, BIN1 is linked to Alzheimer disease.