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Gaulton, Pediatrics, University of California San Diegohttps://www.ebi.ac.uk/ena/browser/view/PRJNA819065Homo sapiensGene regulation is highly cell type-specific and understanding the function of non-coding genetic variants associated with complex traits requires molecular phenotyping at cell type resolution. In this study we performed single nucleus ATAC-seq (snATAC-seq) and genotyping in peripheral blood mononuclear cells from 13 individuals. Clustering chromatin accessibility profiles of 96,002 total nuclei identified 17 immune cell types and sub-types. We mapped chromatin accessibility QTLs (caQTLs) in each immune cell type and sub-type which identified ~6,000 total caQTL peaks, including those obscured from assays of bulk tissue such as with divergent effects on different cell types. For ~3,000 caQTLs we further annotated putative target genes of variant activity using single cell co-accessibility, and caQTL variants were significantly correlated with the accessibility level of linked gene promoters. We fine-mapped loci associated with 16 complex immune traits and identified immune cell caQTLs, including those with cell type-specific effects. At the 6q15 locus associated with type 1 diabetes, in line with previous reports, variant rs72928038 was a naïve CD4+ T cell caQTL linked to BACH2 and we validated the allelic effects of this variant on regulatory activity in Jurkat T cells. These results highlight the utility of snATAC-seq for mapping genetic effects on accessible chromatin in specific cell types and provide a resource for annotating complex immune trait loci. Overall design: Single nucleus ATAC-seq (10x) of peripheral mononuclear blood cells from human donorsxref:PubMed:37289818ENAfalseMapping genetic effects on cell type-specific chromatin accessibility and annotating complex trait variants using single nucleus ATAC-seqMapping genetic effects on cell type-specific chromatin accessibility and annotating complex trait variants using single nucleus ATAC-seq2025-09-242022-10-07PRJNA819065GSE199253960637289818