Table 1: Single-cell epigenomic studies on human tissues and annotation of disease associated variants.
The listed studies showcase the diverse human tissue types profiled using single cell epigenomic assays, including the number of cells and modalities, to generate cCRE catalogs and analyze disease associated variants.
| Single-cell modality | Method | # cells | Summary of catalog | Genetic enrichment tests | Variant prioritization | Variant functional effects | Variant target gene links | Reference |
|---|---|---|---|---|---|---|---|---|
| Pan-tissue | ||||||||
| Chromatin accessibility | sciATAC-seq | 615,998 | 890k cCREs in 111 cell types from 30 adult tissues, and 1.15M cCREs in 222 cell types from 45 adult and fetal tissues when combined with Domcke et al 2020 | S-LDSC using cell type cCREs | Credible set variants identified in statistical fine-mapping overlapping cell type cCREs | - | ABC links in each cell type | 55 |
| Chromatin accessibility | sciATAC-seq3 | 790,957 | 1.05M cCREs in 124 cell types across 15 fetal tissues | S-LDSC using cell type cCREs | - | Allelic imbalance mapping of cell type cCREs | Cicero co-accessibility in cell type cCREs | 58 |
| Artery | ||||||||
| Chromatin accessibility | 10x scATAC-seq | 7,009 | 329k cCREs in 5 cell types in atherosclerotic lesions | Custom enrichment test based on permuted background sites | Variants in LD with index variants overlapping cell type cCREs | - | Cicero co-accessibility in cell type cCREs | 50 |
| Chromatin accessibility | 10x scATAC-seq | 28,316 | 324k cCREs in 14 coronary artery cell types | S-LDSC using cell type cCREs | Variants in LD with index variants overlapping cell type cCREs | Chromatin QTL mapping of cell type cCREs | Cicero co-accessibility in cell type cCREs, integrated cCRE and gene expression co-activity | 71 |
| Brain | ||||||||
| Chromatin accessibility | 10x scATAC-seq | 70,361 | 359k cCRES in 24 isocortex, hippocampus, striatum, and substantia nigra cell types | S-LDSC using cell type cCREs | Variants in LD with genome-wide significant variants overlapping cell type cCREs | Predicted effects on cell type cCREs using SVMs | Cicero co-accessibility in cell type cCREs | 51 |
| Chromatin accessibility | 10x scATAC-seq | 130,418 | cCREs in 7 prefrontal cortex cell types from control and late-stage Alzheimer’s disease samples | S-LDSC using cell type cCREs, gchromVAR in single microglia cells | Credible set variants from previous statistical fine-mapping overlapping cytokine-responsive cCREs | - | Cicero co-accessibility in cell type cCREs, integrated cCRE and gene expression co-activity | 52 |
| Chromatin accessibility | 10x scATAC-seq | 31,304 | 658K cCREs in prefrontal cortex developmental cell types | - | - | Predicted effects on cell type cCREs using BPNet | Integrated cCRE-gene expression co-activity | 60 |
| Chromatin accessibility | 10x scATAC-seq | 45,205 | cREs in 11 frontal cortex cell types from supranuclear palsy, corticobasal degeneration, and control donors | Custom enrichment tests | - | - | - | 62 |
| Chromatin accessibility | 10x scATAC-seq | 87,339 | 253k cCREs in 12 major prefrontal cortex cell types | No genetic analyses performed | 65 | |||
| Chromatin accessibility | 10x scATAC-seq, | 80,827 | cCREs in 31 cell types from stem cell-derived cerebral organoids | No genetic analyses performed | 72 | |||
| SHARE-seq | ||||||||
| DNA methylation | snmC-seq | 2,784 | 498k differentially methylated regions in 21 prefrontal cortex neuronal subtypes | No genetic analyses performed | 46 | |||
| DNA methylation, 3D interactions | sn-m3C-seq | 4,200 | 37k chromatin interactions in 14 prefrontal cortex cell types | No genetic analyses performed | 75 | |||
| Chromatin accessibility, DNA methylation, 3D interactions | snmCAT-seq, sn-m3C-seq, snmC-seq, snmC-seq2, sciATAC-seq | 27,587 | cCREs and DMRs in 63 cell types and sub-types from frontal cortex | S-LDSC using cell type cCREs and DMRs | - | - | - | 68 |
| Colon | ||||||||
| Chromatin accessibility | 10x scATAC-seq | 447,829 | cCREs in 34 colon cell types from normal, polyps, and colorectal cancer donors | No genetic analyses performed | 61 | |||
| Heart | ||||||||
| Chromatin accessibility | sciATAC-seq | 79,515 | 287k cCREs in 12 cell types from multiple regions of the adult human heart. | S-LDSC using cell type cCREs | Credible set variants in statistical fine-mapping overlapping cell type cCREs | - | Cicero co-accessibility in cell type cCREs | 49 |
| Chromatin accessibility | 10x scATAC-seq | 46,086 | cCREs in 8 heart cell types from control and myocardial infarction donors | No genetic analyses performed | 66 | |||
| Hematopoietic | ||||||||
| Chromatin accessibility | dsciATAC-seq | 136,463 | cCREs in 15 cell types in resting and stimulated bone marrow | - | Credible set variants in previous statistical fine-mapping overlapping differential cell type cCREs | - | - | 77 |
| Chromatin accessibility | 10x scATAC-seq | 35,038 | cCREs in 26 cell types from bone marrow and peripheral blood | No genetic analyses performed | 76 | |||
| Chromatin accessibility | 10x scATAC-seq | 63,882 | 571k cCREs in 31 peripheral blood cell types and sub-types | No genetic analyses performed | 54 | |||
| Chromatin accessibility | sciATAC-seq, 10x scATAC-seq | 131,554 | 448k cCREs in 28 pancreas and peripheral blood cell types and sub-types. | S-LDSC using cell type cCREs; fgwas using cell type-specific cCREs | Credible set variants from statistical fine-mapping overlapping cell type cCREs | - | Cicero co-accessibility in cell type cCREs | 47 |
| Kidney | ||||||||
| Chromatin accessibility | 10x scATAC-seq | 27,034 | 215k cCREs in 15 kidney cell types | No genetic analyses performed | 79 | |||
| Chromatin accessibility | 10x scATAC-seq | 50,986 | cCREs in 11 kidney cell types in control and polycystic kidney disease donors | No genetic analyses performed | 80 | |||
| Chromatin accessibility | 10x scATAC-seq | 68,456 | cCREs in 20 kidney cell types in control and diabetic kidney disease donors | S-LDSC using cell type cCREs and differentially accessible cCREs | - | Allelic imbalance mapping of single cells | Integrated cCRE-gene expression co-activity | 74 |
| Chromatin accessibility | 10x scATAC-seq | 57,229 | cCREs in 12 kidney cell types | S-LDSC using cell type cCREs, gchromVAR in single cells | Variants from GWAS overlapping cell type cCREs | - | Cicero co-accessibility in cell type cCREs; Priority scoring of genes based on multiple different datasets | 67 |
| Chromatin accessibility | 10x scATAC | 9,460 | cCREs in 20 kidney cell types | No genetic analyses performed | 73 | |||
| Lung | ||||||||
| Chromatin accessibility | sciATAC-seq | 90,980 | 398k cCREs in 19 lung cell types | - | Credible set variants from previous statistical fine-mapping overlapping cell type cCREs | Predicted effects on cell type cCREs using deltaSVM | Cicero co-accessibility in cell type cCREs | 53 |
| Chromatin accessibility | scTHS-seq | 40,427 | 427k cCREs in 20 lung cell types | gchromVAR using single cell profiles | - | - | - | 63 |
| Pancreas | ||||||||
| Chromatin accessibility | sciATAC-seq | 1,456 | cCREs in 3 pancreatic islet cell types | Enrichment of cell type cCREs using GREGOR and fGWAS | Credible set variants from previous statistical fine-mapping overlapping cell type cCREs | - | Cicero co-accessibility in cell type cCREs | 57 |
| Chromatin accessibility | sciATAC-seq | 15,298 | 229k cCREs in 12 pancreatic islet cell types | S-LDSC using cell type cCREs; fGWAS using cell type-specific cCREs, PolyTest using single cell profiles | Credible set variants from previous statistical fine-mapping overlapping cell type cCREs | Predicted effects on cell type cCREs using deltaSVM | Cicero co-accessibility in cell type cCREs | 48 |
| Chromatin accessibility | sciATAC-seq, 10x scATAC-seq | 131,554 | 448k cCREs in 28 pancreas and peripheral blood cell types | S-LDSC using cell type cCREs; fgwas using cell type-specific cCREs | Credible set variants from statistical fine-mapping overlapping cell type cCREs | - | Cicero co-accessibility in cell type cCREs | 47 |
| Chromatin accessibility | 10x scATAC-seq | 7,829 | cCREs in 7 cell types from cytokine-treated and untreated pancreatic islets | - | Credible set variants from previous statistical fine-mapping overlapping cytokine-responsive cCREs | - | Co-accessibility in cytokine-stimuated and baseline cell types | 69 |
| Chromatin accessibility | 10x scATAC-seq | 12,473 | cCREs in 9 pancreatic islet cell types | S-LDSC using cell type cCREs linked to a target gene | Variants in LD with index variants overlapping cell type cCREs | - | - | 70 |
| Retina | ||||||||
| Chromatin accessibility | 10x scATAC-seq | 102,802 | cCREs in 8 cell types from fetal retina and stem cell-derived retinal organoids | No genetic analyses performed | 64 | |||
| Skeletal muscle | ||||||||
| Chromatin accessibility | 10x scATAC-seq | 5,053 | cCREs in 7 skeletal muscle cell types | S-LDSC of 404 traits using cell type cCREs | Variants identified in previous statistical fine-mapping overlapping cell type cCREs | Predicted effects on cell type cCREs using SVMs | Cicero co-accessibility in cell type cCREs | 56 |
| scMultiome | ||||||||