Supporting data for: Mapping genetic effects on cell type-specific chromatin accessibility and annotating complex immune trait variants using single nucleus ATAC-seq in peripheral blood

<strong>Summary</strong> 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 using individuals of European ancestry which identified 6,901 total caQTLs at FDR &lt;10%. For 3,941 caQTLs we further annotated putative target genes of variant activity using single cell co-accessibility. We fine-mapped loci associated with 16 complex immune traits and identified immune cell caQTLs at 622 candidate causal variants. Raw sequence data are available in NCBI GEO accession <strong>GSE199253</strong> and <strong>GSE163160</strong>. <strong>Description of processed data deposited here:</strong> <strong>0_snATAC_cluster_lables_and_qc.txt :</strong> Final list of barcodes, annotated with UMAP coordinates, sample and cell type labels and QC metrics. <strong>1_peaks_coordinates.zip</strong> : Output of MACS2 peak calling for individual cell subtypes (NARROW.PEAKS) act_cd4_t_peaks.narrowPeak adaptive_NK_peaks.narrowPeak cDC_peaks.narrowPeak cMono_peaks.narrowPeak cyto_cd8_t_peaks.narrowPeak cyto_nk_peaks.narrowPeak iMono_peaks.narrowPeak mem_b_peaks.narrowPeak mem_cd8_t_peaks.narrowPeak mkc_peaks.narrowPeak naive_b_peaks.narrowPeak naive_cd4_t_peaks.narrowPeak naive_cd8_t_peaks.narrowPeak ncMono_peaks.narrowPeak pDC_peaks.narrowPeak plasma_peaks.narrowPeak tReg_peaks.narrowPeak <strong>2_co-accessibility.zip</strong> : Co-accessibility results (Cicero) of snATAC in four major blood cell types (BEDPE) t.filtered_coaccessible_sites4s.txt nk.filtered_coaccessible_sites4s.txt mono.filtered_coaccessible_sites4s.txt b.filtered_coaccessible_sites4s.txt annotated.coaccessible.matrix4s <strong>3_genome_browser_tracks.zip</strong>: Genome browser tracks of PBMC cell types and subtypes (BIGWIG) pbmc1_15.tReg.scale_1e6.bw pbmc1_15.plasma.scale_1e6.bw pbmc1_15.naive_cd4_t.scale_1e6.bw pbmc1_15.naive_cd8_t.scale_1e6.bw pbmc1_15.ncMono.scale_1e6.bw pbmc1_15.mem_cd8_t.scale_1e6.bw pbmc1_15.naive_b.scale_1e6.bw pbmc1_15.mem_b.scale_1e6.bw pbmc1_15.cyto_nk.scale_1e6.bw pbmc1_15.iMono.scale_1e6.bw pbmc1_15.cyto_cd8_t.scale_1e6.bw pbmc1_15.cMono.scale_1e6.bw pbmc1_15.cDC.scale_1e6.bw pbmc1_15.adaptive_NK.scale_1e6.bw pbmc1_15.act_cd4_t.scale_1e6.bw <strong>4_summary_stats.zip</strong>: Summary statistics of caQTLs in PBMC cell types, subtypes, and “bulk” like data (TSV) ## Lead only combined EUR_caqtl_leads_run3.tsv ## Bulk-like bulk_caqtl_sumstats_run3.tsv ## Cell types b_caqtl_sumstats_run3.tsv t_caqtl_sumstats_run3.tsv nk_caqtl_sumstats_run3.tsv mono_caqtl_sumstats_run3.tsv ## Cell subtypes tReg_caqtl_sumstats_run3.tsv naive_cd4_t_caqtl_sumstats_run3.tsv naive_cd8_t_caqtl_sumstats_run3.tsv ncMono_caqtl_sumstats_run3.tsv naive_b_caqtl_sumstats_run3.tsv mem_cd8_t_caqtl_sumstats_run3.tsv mkc_caqtl_sumstats_run3.tsv mem_b_caqtl_sumstats_run3.tsv iMono_caqtl_sumstats_run3.tsv cyto_nk_caqtl_sumstats_run3.tsv cyto_cd8_t_caqtl_sumstats_run3.tsv cMono_caqtl_sumstats_run3.tsv cDC_caqtl_sumstats_run3.tsv cd8_t_caqtl_sumstats_run3.tsv cd4_t_caqtl_sumstats_run3.tsv adaptive_NK_caqtl_sumstats_run3.tsv act_cd4_t_caqtl_sumstats_run3.tsv <br> <strong>5_credible_sets.zip</strong>: Fine-mapping credible sets for loci associated with 16 complex immune traits (BED) Ulcerative_colitis.99credset.PPA.bed Type_1_diabetes.99credset.PPA.bed Systemic_lupus_erythematosus.99credset.PPA.bed Rheumatoid_arthritis.99credset.PPA.bed Selective_IgA_deficiency.99credset.PPA.bed Primary_sclerosing_cholangitis.99credset.PPA.bed Monocyte_count.99credset.PPA.bed Neutrophil_count.99credset.PPA.bed Lymphocyte_count.99credset.PPA.bed Gout.99credset.PPA.bed Eosinophil_count.99credset.PPA.bed Crohns_disease.99credset.PPA.bed Basophil_count.99credset.PPA.bed Autoimmune_vitiligo.99credset.PPA.bed Atopic_dermatitis.99credset.PPA.bed Asthma_child_onset.99credset.PPA.bed <br>