Fig. 4

Overlap between genome-wide significant AD risk variants and transcription factor motif-containing open chromatin sites from the consolidated macrophage (a) and microglia (b) data. AD risk variants and 10,000 sets of matched SNPs were intersected with transcription factor motif-containing open chromatin region sets and one no-motif-containing set for each cell type. The x-axis is the z score and the y-axis is the transcription factor motif. Box plots indicate the distribution of overlap from the 10,000 background matched SNP sets. Red circles are the z scores for the AD risk variant set. P values were calculated from the observed overlap of the 10,000 background matched sets. P values have been adjusted within each cell type using the Bonferroni correction for the number of motif sets tested. AD Alzheimer’s disease, SNP single-nucleotide polymorphism. ***P < 0.005, *P < 0.05