Table 1.
Notable enrichments from analyses of cell type, disease-dependent and cellular process gene programs.
| Cell type programs | ||||||
|---|---|---|---|---|---|---|
| GWAS disease/trait | Tissue (scRNA-seq) | Cell Type | E-score | p(E-score) | q-value | Top genes |
| Ulcerative colitis | Blood | B cells | 3.2 | 1.50E-05 | 2.33E-05 | REL,GPX1,LSP1 |
| Celiac disease | Blood | T cells | 4.5 | 2.30E-07 | 7.16E-07 | ETS1,CD247,CD28 |
| MDD | Brain | GABAergic | 4 | 1.00E-04 | 3.39E-04 | TCF4,BEND4,TMX2 |
| Atrial fibrillation | Heart | Atrial cardiomyocyte | 5.6 | 3.2E-09 | 2.2E-08 | CAV2,PKD2L2,FAM13B |
| Blood pressure(dia) | Heart | Smooth muscle | 3.4 | 2.9E-06 | 1.2E-05 | CACNB2,TMEM165,MRVI1 |
| Eczema | Skin | Langerhans cells | 3.7 | 0.004 | 0.03 | IL1R1,RUNX3,FCER1G |
| IBD | Colon | Endothelial | 2.8 | 0.002 | 0.01 | RHOA,PDLIM4,STARD3 |
| Disease-dependent programs | ||||||
| GWAS disease/trait | Tissue (scRNA-seq) | Cell Type | E-score | p (E-score) | q-value | Top genes |
| Multiple sclerosis | MS Brain | Microglia | 11.6 | 5.70E-06 | 3.66E-05 | PRDX5,RPL5,SKP1, |
| Alzheimer’s disease | AD Brain | Microglia | 9.1 | 7.10E-05 | 6.82E-04 | PICALM, APOE, APOC1 |
| Ulcerative colitis | UC Colon | Enterocytes | 2.6 | 2.70E-07 | 1.66E-06 | RNF186,APEH,DLD |
| IBD | UC Colon | M cells | 2.2 | 1.07E-04 | 2.2E-04 | UQCR10,FERMT1,PPP1R1B |
| Asthma | Asthma Lung | T cells | 12.8 | 4.82E-05 | 3.99E-04 | FMNL1,RORA,GPR183 |
| Cellular process programs | ||||||
| GWAS disease/trait | Tissue (scRNA-seq) | Cellular process | E-score | p (E-score) | q-value | Top genes |
| Eczema | Blood | CD4+ T cells | 3.8 | 1.32E-07 | 4.83E-07 | IL7R,STMN3,NDFIP1 |
| Celiac disease | Blood | Complement cascade | 2.8 | 4.84E-08 | 1.92E-07 | DCC,PDIA5,PPCDC |
| Alzheimer’s disease | Blood | MHC-II antigen processing | 4.9 | 7.11E-0 | 2.08E-06 | MS4A6A,MS4A4A,CD33 |
| BMI | Brain | LAMP5 | 2.7 | 6.33E-08 | 7.01E-07 | FLRT1,COL4A2,SBF2 |
| MDD | Brain | SST | 3.9 | 4.37E-05 | 1,22E-04 | TCF4,PCLO,ZNF462 |
| Years of education | Brain | Electron Transport | 3.5 | 4.42E-08 | 5.49E-07 | ATP6V0B,NSF,GPX1 |
| Multiple sclerosis | MS Brain | Complement cascade** | 4.9 | 5.49E-11 | 9.62E-10 | CD37,RGS14,NCF4 |
| Alzheimer’s disease | AD Brain | Apelin signaling* | 1.5 | 9.27E-07 | 6.50E-06 | MS4A6A,SORL1,SYK |
| Ulcerative colitis | UC Colon | EGFR1 pathway* | 3.0 | 8.81E-04 | 2.14E-03 | C1orf106,SLC26A3,NXPE4 |
| Asthma | Asthma Lung | Mac-neutrophil trans.* | 6.6 | 0.002 | 0.006 | CCL20,IL6,GPR183 |
For each notable enrichment, we report the GWAS disease/trait, tissue source for scRNA-seq data, cell type, enrichment score (E-score), 1-sided stratified LD score regression p-value for positive E-score, and top genes driving the enrichment. Multiple testing correction was performed across cell types and traits at the level of each tissue. MDD is an abbreviation for major depressive disorder, blood pressure (dia.) is an abbreviation for diastolic blood pressure, mac-neutrophil trans. is an abbreviation for macrophage-neutrophil transition.
denotes cellular process programs shared across healthy and disease states.
denotes cellular process programs specific to disease states.
The full list of genes driving these associations is provided in Supplementary Data 4.