Best TWAS P=4.48e-18 · Best GWAS P=1.31e-15 conditioned to 0.00413
| # | Study | Tissue | Gene | h2 | eQTL R2 | model | # weights | model R2 | model R2 P | eQTL GWAS Z | TWAS Z | TWAS P | Top SNP corr | PP3 | PP4 | joint |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | CommonMind | Brain Pre-frontal Cortex | NAPA | 0.06 | 0.00 | bslmm | 381 | 0.01 | 7.2e-03 | 0.92 | 6.7 | 2.1e-11 | 0.47 | 0.03 | 0.52 | FALSE |
| 2 | GTEx | Adipose Subcutaneous | CCDC9 | 0.18 | 0.16 | lasso | 5 | 0.16 | 5.0e-13 | 7.96 | -7.9 | 2.6e-15 | -1.00 | 0.01 | 0.99 | FALSE |
| 3 | GTEx | Adipose Visceral Omentum | CCDC9 | 0.19 | 0.10 | enet | 11 | 0.11 | 3.1e-06 | 7.97 | -6.8 | 8.5e-12 | -0.95 | 0.01 | 0.99 | FALSE |
| 4 | GTEx | Artery Tibial | CCDC9 | 0.09 | 0.03 | lasso | 5 | 0.03 | 3.7e-03 | 7.97 | -7.4 | 1.5e-13 | -0.95 | 0.01 | 0.97 | FALSE |
| 5 | GTEx | Brain Caudate basal ganglia | KPTN | 0.24 | -0.01 | enet | 14 | -0.01 | 7.3e-01 | 3.46 | -7.0 | 2.6e-12 | -0.51 | 0.02 | 0.69 | FALSE |
| 6 | GTEx | Brain Frontal Cortex BA9 | KPTN | 0.26 | 0.01 | lasso | 4 | 0.00 | 4.1e-01 | 7.74 | -7.5 | 9.6e-14 | -0.95 | 0.01 | 0.81 | FALSE |
| 7 | GTEx | Cells EBV-transformed lymphocytes | CCDC9 | 0.32 | 0.22 | enet | 15 | 0.15 | 1.2e-05 | 7.99 | -7.4 | 1.4e-13 | -0.91 | 0.01 | 0.99 | FALSE |
| 8 | GTEx | Cells Transformed fibroblasts | CCDC9 | 0.16 | 0.13 | lasso | 3 | 0.14 | 2.0e-10 | 7.97 | -7.6 | 2.2e-14 | -0.96 | 0.01 | 0.99 | FALSE |
| 9 | GTEx | Esophagus Mucosa | CCDC9 | 0.18 | 0.13 | lasso | 3 | 0.12 | 2.7e-08 | 7.99 | -7.9 | 3.1e-15 | -1.00 | 0.01 | 0.99 | FALSE |
| 10 | GTEx | Esophagus Muscularis | CCDC9 | 0.14 | 0.11 | lasso | 3 | 0.11 | 3.9e-07 | 7.99 | -6.7 | 3.0e-11 | -0.88 | 0.01 | 0.99 | FALSE |
| 11 | GTEx | Heart Atrial Appendage | CCDC9 | 0.20 | 0.03 | enet | 21 | 0.05 | 2.2e-03 | 7.99 | -5.3 | 9.1e-08 | -0.71 | 0.01 | 0.88 | FALSE |
| 12 | GTEx | Nerve Tibial | CCDC9 | 0.28 | 0.17 | enet | 23 | 0.16 | 1.6e-11 | 7.99 | -6.8 | 9.5e-12 | -0.88 | 0.01 | 0.99 | FALSE |
| 13 | GTEx | Skin Sun Exposed Lower leg | CCDC9 | 0.13 | 0.00 | lasso | 5 | 0.00 | 2.2e-01 | 7.97 | -6.0 | 1.7e-09 | -0.89 | 0.01 | 0.93 | FALSE |
| 14 | GTEx | Thyroid | CCDC9 | 0.22 | 0.09 | lasso | 4 | 0.16 | 3.6e-12 | 7.97 | -5.7 | 1.5e-08 | -0.78 | 0.01 | 0.99 | FALSE |
| 15 | METSIM | Adipose | SAE1 | 0.12 | 0.04 | lasso | 5 | 0.07 | 1.7e-10 | 4.78 | 6.7 | 2.6e-11 | 0.38 | 0.99 | 0.01 | FALSE |
| 16 | YFS | Blood | SAE1 | 0.07 | 0.02 | enet | 18 | 0.05 | 3.6e-16 | 6.89 | 5.2 | 2.6e-07 | 0.31 | 0.97 | 0.03 | FALSE |
| 17 | YFS | Blood | SPHK2 | 0.07 | 0.04 | enet | 6 | 0.06 | 4.4e-18 | -6.85 | -5.8 | 5.2e-09 | 0.06 | 0.00 | 1.00 | FALSE |
| 18 | The Cancer Genome Atlas | Breast Invasive Carcinoma | SEC1 | 0.05 | 0.05 | enet | 5 | 0.05 | 2.2e-11 | -6.02 | 6.2 | 4.8e-10 | 0.00 | 0.01 | 0.99 | FALSE |
| 19 | The Cancer Genome Atlas | Breast Invasive Carcinoma | SPACA4 | 0.02 | 0.01 | blup | 59 | 0.01 | 1.1e-02 | -6.85 | 5.4 | 5.3e-08 | -0.02 | 0.00 | 0.80 | FALSE |
| 20 | The Cancer Genome Atlas | Cervical Squamous Cell Carcinoma | CCDC9 | 0.09 | 0.00 | enet | 12 | 0.03 | 7.9e-03 | 5.31 | -8.7 | 4.5e-18 | -0.65 | 0.01 | 0.77 | TRUE |
| 21 | The Cancer Genome Atlas | Cervical Squamous Cell Carcinoma | DBP | 0.09 | 0.01 | blup | 50 | 0.03 | 1.1e-02 | -6.02 | 5.9 | 3.8e-09 | -0.04 | 0.01 | 0.81 | FALSE |
| 22 | The Cancer Genome Atlas | Kidney Renal Clear Cell Carcinoma | CCDC9 | 0.04 | 0.01 | blup | 30 | 0.03 | 1.2e-04 | 7.99 | -6.0 | 1.9e-09 | -0.85 | 0.01 | 0.93 | FALSE |
| 23 | The Cancer Genome Atlas | Kidney Renal Clear Cell Carcinoma | SEC1 | 0.14 | 0.13 | lasso | 2 | 0.13 | 1.6e-14 | -6.98 | 7.1 | 1.6e-12 | -0.04 | 0.00 | 1.00 | TRUE |
| 24 | The Cancer Genome Atlas | Kidney Renal Papillary Cell Carcinoma | SEC1 | 0.12 | 0.05 | blup | 61 | 0.07 | 1.1e-04 | -6.85 | 6.1 | 1.2e-09 | -0.04 | 0.00 | 0.98 | FALSE |
| 25 | The Cancer Genome Atlas | Brain Lower Grade Glioma | SEC1 | 0.16 | 0.11 | lasso | 4 | 0.11 | 2.1e-12 | -6.85 | 6.7 | 1.9e-11 | -0.04 | 0.00 | 1.00 | FALSE |
| 26 | The Cancer Genome Atlas | Lung Squamous Cell Carcinoma | GRLF1 | 0.04 | 0.04 | blup | 51 | 0.03 | 7.0e-05 | -5.00 | -6.0 | 2.6e-09 | -0.08 | 0.01 | 0.97 | TRUE |
| 27 | The Cancer Genome Atlas | Prostate Adenocarcinoma | CCDC9 | 0.02 | 0.03 | lasso | 7 | 0.03 | 2.8e-04 | 7.97 | -8.2 | 2.1e-16 | -0.99 | 0.01 | 0.93 | FALSE |
| 28 | The Cancer Genome Atlas | Prostate Adenocarcinoma | SEC1 | 0.06 | 0.05 | enet | 2 | 0.06 | 1.9e-06 | -6.85 | 7.0 | 2.4e-12 | -0.04 | 0.00 | 1.00 | FALSE |
| 29 | The Cancer Genome Atlas | Rectum Adenocarcinoma | CCDC9 | 0.12 | 0.12 | lasso | 4 | 0.10 | 1.9e-03 | 7.97 | -7.1 | 1.2e-12 | -0.94 | 0.01 | 0.73 | FALSE |
| 30 | The Cancer Genome Atlas | Soft Tissue Sarcoma | SEC1 | 0.31 | 0.17 | lasso | 6 | 0.17 | 1.4e-10 | -6.85 | 7.0 | 1.9e-12 | -0.07 | 0.00 | 1.00 | FALSE |
| 31 | The Cancer Genome Atlas | Testicular Germ Cell Tumors | PRR24 | 0.08 | -0.01 | blup | 31 | 0.02 | 8.8e-02 | 7.97 | 5.8 | 5.7e-09 | 0.93 | 0.01 | 0.59 | FALSE |
| 32 | The Cancer Genome Atlas | Thyroid Carcinoma | SEC1 | 0.23 | 0.15 | blup | 64 | 0.14 | 6.7e-14 | -6.85 | 6.3 | 2.9e-10 | -0.01 | 0.00 | 1.00 | FALSE |
| 33 | The Cancer Genome Atlas | Thyroid Carcinoma | SPHK2 | 0.06 | 0.06 | lasso | 5 | 0.06 | 1.0e-06 | -6.85 | -6.9 | 6.6e-12 | 0.04 | 0.00 | 1.00 | FALSE |