Table 1.
Enrichment of eQTLs from Different Sources (GTEx, Geuvadis, and TwinsUK Cohort) among Functional Variants Predicted by FUN-LDA in Tissues and Cell Types in Roadmap Epigenomics
| Tissue | Roadmap Epigenomics Name | −log10(p) | −log10(FDR.p) | Enrichment Ratio |
|---|---|---|---|---|
| GTEx | ||||
| Whole blood | primary neutrophils from peripheral blood | 189.72 | 185.92 | 1.38 |
| Cells – transformed fibroblasts | muscle satellite cultured cells | 62.69 | 59.59 | 1.22 |
| Cells – EBV-transformed lymphocytes | GM12878 lymphoblastoid cells | 37.74 | 35.23 | 1.48 |
| Liver | liver | 31.82 | 29.45 | 1.68 |
| Muscle – skeletal | skeletal muscle male | 19.42 | 17.26 | 1.13 |
| Heart – left ventricle | fetal heart | 15.83 | 13.74 | 1.22 |
| Esophagus – mucosa | esophagus | 12.78 | 10.74 | 1.15 |
| Pancreas | pancreas | 10.84 | 8.89 | 1.25 |
| Colon – transverse | rectal mucosa donor 31 | 10.46 | 8.52 | 1.23 |
| Artery – tibial | stomach smooth muscle | 7.74 | 5.87 | 1.10 |
| Esophagus muscularis | stomach smooth muscle | 6.74 | 4.91 | 1.11 |
| Thyroid | fetal intestine small | 5.96 | 4.19 | 1.06 |
| Skin – sun exposed (lower leg) | foreskin keratinocyte primary cells skin03 | 5.47 | 3.73 | 1.07 |
| Spleen | primary B cells from peripheral blood | 5.35 | 3.61 | 1.22 |
| Artery – aorta | aorta | 5.28 | 3.57 | 1.14 |
| Brain – hippocampus | brain cingulate gyrus | 5.10 | 3.42 | 1.38 |
| Small intestine – terminal ileum | fetal intestine large | 5.04 | 3.37 | 1.37 |
| Heart – atrial appendage | fetal heart | 4.90 | 3.25 | 1.15 |
| Adipose – subcutaneous | adipose nuclei | 4.74 | 3.11 | 1.07 |
| Colon – sigmoid | colon smooth muscle | 4.62 | 2.99 | 1.19 |
| Brain – caudate (basal ganglia) | brain substantia nigra | 4.17 | 2.60 | 1.18 |
| Nerve – tibial | brain hippocampus middle | 4.11 | 2.56 | 1.05 |
| Adrenal gland | fetal adrenal gland | 3.94 | 2.42 | 1.14 |
| Skin – not sun exposed (suprapubic) | foreskin keratinocyte primary cells skin03 | 3.56 | 2.07 | 1.09 |
| Brain – putamen (basal ganglia) | brain substantia nigra | 3.36 | 1.90 | 1.23 |
| Brain – cerebellum | primary T cells from cord blood | 3.20 | 1.78 | 1.11 |
| Brain – cerebellar hemisphere | brain angular gyrus | 3.08 | 1.67 | 1.12 |
| Stomach | stomach mucosa | 3.02 | 1.63 | 1.13 |
| Lung | primary hematopoietic stem cells G-CSF-mobilized male | 2.42 | 1.13 | 1.05 |
| Adipose – visceral (omentum) | primary T helper cells from peripheral blood | 2.00 | 0.82 | 1.08 |
| Brain – nucleus accumbens (basal ganglia) | H9 cells | 1.80 | 0.67 | 1.17 |
| Pituitary | ES-I3 cells | 1.75 | 0.64 | 1.13 |
| Brain – cortex | primary natural killer cells from peripheral blood | 1.61 | 0.54 | 1.11 |
| Esophagus – gastresophageal junction | primary B cells from peripheral blood | 1.49 | 0.46 | 1.09 |
| Artery – coronary | primary B cells from peripheral blood | 1.35 | 0.38 | 1.10 |
| Brain – hypothalamus | primary natural killer cells from peripheral blood | 1.26 | 0.33 | 1.16 |
| Brain – frontal cortex (BA9) | H1 cells | 1.08 | 0.22 | 1.11 |
| Brain – anterior cingulate cortex (BA24) | primary natural killer cells from peripheral blood | 1.00 | 0.19 | 1.12 |
| Geuvadis | ||||
| Lymphoblastoid cell line | GM12878 lymphoblastoid cells | 9.27 | 7.35 | 1.13 |
| TwinsUK | ||||
| Blood | primary neutrophils from peripheral blood | 7.30 | 5.46 | 1.42 |
| Fat | mesenchymal stem cell derived adipocyte cultured cells | 6.26 | 4.45 | 1.21 |
| Skin | foreskin keratinocyte primary cells skin02 | 3.99 | 2.45 | 1.18 |
| Lymphoblastoid cell line | GM12878 lymphoblastoid cells | 3.08 | 1.67 | 1.08 |
The top Roadmap tissue (with smallest enrichment p value) is given for each eQTL tissue, along with the p value from a two-sample proportion test, the FDR-adjusted p value (FDR.p), and the enrichment ratio (see Material and Methods). Tests that are significant at an FDR of 0.05 have −log10(FDR.p) > 1.30.