To validate the results of the ImmGen analysis, we analyzed ATAC-seq peaks from 13 cell types spanning the hematopoietic hierarchy in humans64. The 13 cell types did not allow us to validate at very high resolution; instead, we classified all cell types from ImmGen and from the hematopoiesis data set using the classification for visualization of Figure 5 into five categories: B cells, T cells, NK cells, myeloid cells, and other cells. There were no stromal cells in the hematopoiesis data set and it was not possible to validate the enrichments for diastolic and systolic blood pressure; this left us with 14 phenotypes with an enrichment at FDR<5% in the ImmGen analysis where the top result fell into one of the first four categories (excluding “Other”). We considered one of these 14 results to be validated if any cell type in the same category from the hematopoiesis data set passed FDR<5%. The four phenotypes whose top results did not replicate were Lupus, schizophrenia, bipolar disorder, and neuroticism.
