Best TWAS P=7.96e-20 · Best GWAS P=5.21e-20 conditioned to 1
| # | 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 | GTEx | Adipose Subcutaneous | TGOLN2 | 0.07 | 0.09 | lasso | 2 | 0.08 | 6.7e-07 | 6.7 | -6.6 | 5.5e-11 | 0.53 | 0.83 | 0.14 | FALSE |
| 2 | GTEx | Adipose Visceral Omentum | TGOLN2 | 0.18 | 0.06 | lasso | 5 | 0.06 | 7.0e-04 | -6.3 | -7.1 | 1.5e-12 | 0.63 | 0.07 | 0.81 | FALSE |
| 3 | GTEx | Adrenal Gland | MRPL35 | 0.19 | 0.10 | enet | 9 | 0.14 | 1.0e-05 | -4.4 | 5.9 | 4.1e-09 | 0.05 | 0.08 | 0.84 | FALSE |
| 4 | GTEx | Artery Tibial | CAPG | 0.56 | 0.38 | enet | 38 | 0.43 | 1.7e-36 | -4.8 | -5.6 | 1.8e-08 | 0.56 | 1.00 | 0.00 | FALSE |
| 5 | GTEx | Brain Caudate basal ganglia | REEP1 | 0.14 | 0.11 | lasso | 3 | 0.04 | 2.1e-02 | 4.9 | 5.3 | 1.3e-07 | 0.08 | 0.05 | 0.72 | FALSE |
| 6 | GTEx | Brain Cerebellum | REEP1 | 0.29 | 0.14 | enet | 22 | 0.15 | 3.0e-05 | -5.0 | 6.3 | 3.2e-10 | 0.02 | 0.04 | 0.96 | FALSE |
| 7 | GTEx | Brain Cerebellum | IMMT | 0.26 | 0.16 | enet | 14 | 0.22 | 2.8e-07 | -4.2 | -5.3 | 1.0e-07 | -0.04 | 0.74 | 0.03 | FALSE |
| 8 | GTEx | Brain Cerebellum | MAT2A | 0.41 | 0.08 | enet | 40 | 0.15 | 4.5e-05 | 8.4 | 6.2 | 6.4e-10 | -0.59 | 0.02 | 0.95 | FALSE |
| 9 | GTEx | Brain Cortex | GGCX | 0.38 | 0.17 | enet | 30 | 0.02 | 1.1e-01 | 3.2 | 5.2 | 2.3e-07 | -0.09 | 0.56 | 0.03 | FALSE |
| 10 | GTEx | Brain Hippocampus | REEP1 | 0.33 | 0.22 | lasso | 3 | 0.21 | 9.6e-06 | -5.0 | 5.3 | 1.2e-07 | 0.10 | 0.06 | 0.89 | FALSE |
| 11 | GTEx | Brain Nucleus accumbens basal ganglia | CAPG | 0.27 | 0.19 | lasso | 2 | 0.10 | 9.4e-04 | -9.1 | -9.0 | 1.5e-19 | 1.00 | 0.00 | 0.98 | FALSE |
| 12 | GTEx | Brain Putamen basal ganglia | REEP1 | 0.20 | 0.18 | lasso | 7 | 0.18 | 5.0e-05 | 5.7 | 5.7 | 1.1e-08 | 0.08 | 0.04 | 0.88 | FALSE |
| 13 | GTEx | Breast Mammary Tissue (Male) | TGOLN2 | 0.15 | -0.01 | lasso | 1 | 0.00 | 3.8e-01 | -6.3 | -6.3 | 3.4e-10 | 0.67 | 0.04 | 0.18 | FALSE |
| 14 | GTEx | Breast Mammary Tissue (Female) | TCF7L1 | 0.13 | -0.01 | enet | 8 | 0.01 | 1.7e-01 | -1.4 | -7.1 | 1.0e-12 | 0.59 | 0.02 | 0.72 | FALSE |
| 15 | GTEx | Breast Mammary Tissue (Female) | TGOLN2 | 0.10 | 0.01 | lasso | 2 | 0.02 | 8.7e-02 | -9.1 | -9.1 | 8.0e-20 | 1.00 | 0.02 | 0.43 | TRUE |
| 16 | GTEx | Cells EBV-transformed lymphocytes | CAPG | 0.23 | 0.02 | enet | 10 | 0.12 | 1.2e-04 | -4.5 | -5.9 | 3.8e-09 | 0.67 | 0.01 | 0.96 | FALSE |
| 17 | GTEx | Cells EBV-transformed lymphocytes | TGOLN2 | 0.49 | 0.15 | enet | 50 | 0.32 | 3.0e-11 | -4.9 | -6.9 | 5.2e-12 | 0.52 | 0.16 | 0.79 | FALSE |
| 18 | GTEx | Cells Transformed fibroblasts | CAPG | 0.26 | 0.13 | lasso | 8 | 0.20 | 1.1e-14 | -7.3 | -5.5 | 2.9e-08 | 0.69 | 0.51 | 0.49 | FALSE |
| 19 | GTEx | Cells Transformed fibroblasts | TGOLN2 | 0.22 | 0.26 | enet | 15 | 0.27 | 2.4e-20 | -6.9 | -6.9 | 5.6e-12 | 0.59 | 1.00 | 0.00 | FALSE |
| 20 | GTEx | Colon Transverse | TGOLN2 | 0.18 | 0.13 | enet | 16 | 0.12 | 2.8e-06 | -7.0 | -6.7 | 2.7e-11 | 0.53 | 0.89 | 0.08 | FALSE |
| 21 | GTEx | Colon Transverse | AC093162.5 | 0.20 | 0.01 | lasso | 4 | 0.05 | 1.6e-03 | -7.1 | 6.1 | 1.3e-09 | -0.48 | 0.50 | 0.08 | FALSE |
| 22 | GTEx | Esophagus Mucosa | CAPG | 0.28 | 0.20 | enet | 13 | 0.24 | 5.8e-16 | -6.1 | -6.3 | 2.8e-10 | 0.37 | 0.96 | 0.04 | FALSE |
| 23 | GTEx | Esophagus Mucosa | TGOLN2 | 0.17 | 0.19 | enet | 15 | 0.18 | 3.0e-12 | -6.9 | -7.6 | 3.9e-14 | 0.61 | 1.00 | 0.00 | FALSE |
| 24 | GTEx | Esophagus Muscularis | CAPG | 0.17 | 0.16 | lasso | 4 | 0.14 | 8.2e-09 | -7.3 | -7.8 | 4.5e-15 | 0.91 | 0.01 | 0.99 | FALSE |
| 25 | GTEx | Esophagus Muscularis | AC093162.5 | 0.14 | 0.09 | lasso | 2 | 0.06 | 1.3e-04 | -7.1 | 7.1 | 1.2e-12 | -0.57 | 0.56 | 0.12 | FALSE |
| 26 | GTEx | Liver | TGOLN2 | 0.29 | 0.28 | lasso | 3 | 0.27 | 4.2e-08 | -4.9 | -6.3 | 3.5e-10 | 0.71 | 0.29 | 0.56 | FALSE |
| 27 | GTEx | Lung | RETSAT | 0.17 | 0.08 | enet | 29 | 0.11 | 8.4e-09 | -4.1 | 5.8 | 5.0e-09 | -0.23 | 0.72 | 0.01 | FALSE |
| 28 | GTEx | Lung | GNLY | 0.41 | 0.15 | lasso | 7 | 0.15 | 1.9e-11 | 7.1 | 6.5 | 6.0e-11 | 0.07 | 1.00 | 0.00 | TRUE |
| 29 | GTEx | Lung | TGOLN2 | 0.07 | 0.04 | enet | 9 | 0.04 | 6.4e-04 | 6.7 | -7.3 | 4.0e-13 | 0.64 | 0.50 | 0.48 | FALSE |
| 30 | GTEx | Muscle Skeletal | CAPG | 0.12 | 0.04 | lasso | 6 | 0.04 | 4.8e-05 | -6.6 | -7.9 | 2.1e-15 | 0.61 | 0.48 | 0.50 | FALSE |
| 31 | GTEx | Nerve Tibial | AC093162.5 | 0.14 | 0.10 | enet | 11 | 0.07 | 1.6e-05 | -6.5 | 6.9 | 5.0e-12 | -0.57 | 0.97 | 0.01 | FALSE |
| 32 | GTEx | Ovary | USP39 | 0.40 | 0.02 | lasso | 6 | 0.05 | 2.8e-02 | 2.8 | -6.4 | 1.6e-10 | 0.09 | 0.07 | 0.06 | TRUE |
| 33 | GTEx | Pancreas | TGOLN2 | 0.30 | 0.00 | enet | 36 | 0.07 | 7.3e-04 | 5.6 | -5.6 | 1.9e-08 | 0.44 | 0.17 | 0.12 | FALSE |
| 34 | GTEx | Skin Not Sun Exposed Suprapubic | CAPG | 0.18 | 0.14 | lasso | 4 | 0.10 | 6.5e-06 | 7.9 | -7.1 | 1.4e-12 | 0.46 | 0.84 | 0.08 | FALSE |
| 35 | GTEx | Skin Not Sun Exposed Suprapubic | TGOLN2 | 0.27 | 0.18 | enet | 19 | 0.15 | 2.1e-08 | -4.9 | -6.1 | 1.1e-09 | 0.65 | 0.70 | 0.30 | FALSE |
| 36 | GTEx | Skin Sun Exposed Lower leg | CAPG | 0.24 | 0.22 | lasso | 5 | 0.21 | 4.1e-17 | 8.4 | -8.3 | 8.4e-17 | 0.60 | 0.64 | 0.36 | FALSE |
| 37 | GTEx | Skin Sun Exposed Lower leg | REEP1 | 0.09 | 0.00 | enet | 16 | 0.02 | 1.2e-02 | 5.8 | 7.0 | 1.8e-12 | 0.06 | 0.02 | 0.90 | TRUE |
| 38 | GTEx | Skin Sun Exposed Lower leg | TGOLN2 | 0.26 | 0.15 | lasso | 7 | 0.18 | 6.0e-15 | -7.0 | -7.5 | 4.3e-14 | 0.65 | 1.00 | 0.00 | FALSE |
| 39 | GTEx | Skin Sun Exposed Lower leg | AC093162.5 | 0.08 | 0.05 | lasso | 3 | 0.06 | 5.0e-06 | 8.4 | -7.9 | 2.3e-15 | 0.57 | 0.73 | 0.23 | FALSE |
| 40 | GTEx | Stomach | TGOLN2 | 0.20 | 0.11 | enet | 14 | 0.11 | 5.4e-06 | -7.1 | -6.6 | 3.4e-11 | 0.60 | 0.96 | 0.01 | FALSE |
| 41 | GTEx | Testis | CAPG | 0.49 | 0.48 | enet | 20 | 0.49 | 2.6e-24 | -9.1 | -8.8 | 9.9e-19 | 0.94 | 0.00 | 1.00 | FALSE |
| 42 | GTEx | Testis | REEP1 | 0.15 | 0.04 | enet | 37 | 0.02 | 4.3e-02 | -5.0 | 5.9 | 2.8e-09 | 0.08 | 0.17 | 0.66 | FALSE |
| 43 | GTEx | Thyroid | CAPG | 0.17 | 0.10 | lasso | 6 | 0.10 | 3.7e-08 | 7.9 | -8.4 | 4.9e-17 | 0.56 | 0.74 | 0.25 | FALSE |
| 44 | GTEx | Thyroid | ELMOD3 | 0.10 | 0.01 | enet | 10 | 0.02 | 7.7e-03 | -6.3 | 9.0 | 1.8e-19 | -0.78 | 0.01 | 0.95 | FALSE |
| 45 | GTEx | Thyroid | IMMT | 0.11 | 0.09 | lasso | 13 | 0.11 | 6.9e-09 | -5.0 | -5.3 | 1.3e-07 | -0.06 | 0.99 | 0.00 | FALSE |
| 46 | GTEx | Thyroid | TGOLN2 | 0.09 | 0.04 | lasso | 3 | 0.07 | 8.7e-06 | -6.3 | -7.5 | 7.0e-14 | 0.70 | 0.22 | 0.69 | FALSE |
| 47 | GTEx | Thyroid | AC093162.5 | 0.23 | 0.19 | enet | 22 | 0.20 | 6.5e-15 | -6.5 | 6.2 | 4.5e-10 | -0.57 | 1.00 | 0.00 | FALSE |
| 48 | GTEx | Whole Blood | RETSAT | 0.13 | 0.08 | lasso | 5 | 0.14 | 8.0e-13 | -4.1 | 6.1 | 1.3e-09 | -0.64 | 0.98 | 0.02 | FALSE |
| 49 | GTEx | Whole Blood | AC093162.5 | 0.11 | 0.03 | lasso | 2 | 0.01 | 4.0e-02 | -7.1 | 7.0 | 3.5e-12 | -0.58 | 0.42 | 0.25 | FALSE |
| 50 | GTEx | Whole Blood | RP11-301O19.1 | 0.04 | 0.05 | enet | 20 | 0.04 | 5.4e-05 | 4.6 | 5.2 | 2.4e-07 | 0.04 | 0.71 | 0.24 | FALSE |
| 51 | NTR | Blood | RETSAT | 0.07 | 0.09 | enet | 21 | 0.09 | 2.9e-28 | -6.5 | 7.2 | 7.3e-13 | -0.63 | 1.00 | 0.00 | FALSE |
| 52 | ROSMAP | Brain Pre-frontal Cortex | RETSAT | 0.24 | 0.13 | bslmm | 442 | 0.17 | 7.3e-22 | -6.3 | 6.4 | 2.0e-10 | -0.46 | 1.00 | 0.00 | FALSE |
| 53 | ROSMAP | Brain Pre-frontal Cortex | CAPG | 0.27 | 0.15 | bslmm | 456 | 0.23 | 1.4e-29 | -9.2 | -7.1 | 1.6e-12 | 0.74 | 0.00 | 1.00 | FALSE |
| 54 | ROSMAP | Brain Pre-frontal Cortex | REEP1 | 0.11 | 0.12 | lasso | 11 | 0.14 | 3.7e-17 | -4.4 | 5.3 | 9.1e-08 | 0.06 | 0.84 | 0.16 | FALSE |
| 55 | ROSMAP | Brain Pre-frontal Cortex | SH2D6 | 0.10 | 0.08 | lasso | 6 | 0.14 | 1.5e-17 | 7.4 | 9.1 | 9.4e-20 | -0.74 | 0.02 | 0.98 | FALSE |
| 56 | YFS | Blood | GGCX | 0.25 | 0.08 | bslmm | 474 | 0.16 | 1.2e-50 | 5.4 | 5.3 | 1.1e-07 | -0.17 | 1.00 | 0.00 | TRUE |
| 57 | YFS | Blood | RNF181 | 0.20 | 0.19 | bslmm | 474 | 0.20 | 4.4e-62 | 5.7 | -5.7 | 9.6e-09 | 0.00 | 1.00 | 0.00 | FALSE |
| 58 | The Cancer Genome Atlas | Bladder Urothelial Carcinoma | SH2D6 | 0.04 | 0.02 | lasso | 2 | 0.03 | 2.6e-03 | -6.2 | -7.0 | 2.3e-12 | 0.43 | 0.06 | 0.04 | FALSE |
| 59 | The Cancer Genome Atlas | Breast Invasive Carcinoma | GNLY | 0.19 | 0.11 | blup | 56 | 0.14 | 6.5e-28 | 3.9 | 5.5 | 3.1e-08 | -0.08 | 1.00 | 0.00 | FALSE |
| 60 | The Cancer Genome Atlas | Breast Invasive Carcinoma | SH2D6 | 0.05 | 0.06 | lasso | 2 | 0.05 | 8.2e-11 | -7.3 | -7.6 | 3.8e-14 | 0.86 | 0.48 | 0.52 | FALSE |
| 61 | The Cancer Genome Atlas | Breast Invasive Carcinoma | TGOLN2 | 0.05 | 0.10 | lasso | 5 | 0.11 | 5.5e-21 | -7.0 | -6.5 | 7.4e-11 | 0.61 | 0.02 | 0.98 | FALSE |
| 62 | The Cancer Genome Atlas | Cervical Squamous Cell Carcinoma | TGOLN2 | 0.15 | 0.17 | enet | 8 | 0.15 | 6.4e-08 | -6.6 | -6.3 | 3.2e-10 | 0.55 | 0.05 | 0.94 | FALSE |
| 63 | The Cancer Genome Atlas | Colon Adenocarcinoma | TGOLN2 | 0.26 | 0.18 | enet | 14 | 0.15 | 5.1e-09 | -6.9 | -6.0 | 2.6e-09 | 0.55 | 0.01 | 0.99 | FALSE |
| 64 | The Cancer Genome Atlas | Esophageal Carcinoma | CAPG | 0.24 | 0.08 | lasso | 3 | 0.14 | 3.6e-05 | -4.9 | -7.2 | 6.6e-13 | 0.27 | 0.09 | 0.06 | FALSE |
| 65 | The Cancer Genome Atlas | Esophageal Carcinoma | TGOLN2 | 0.15 | 0.07 | blup | 64 | 0.14 | 3.1e-05 | -6.9 | -5.5 | 2.9e-08 | 0.51 | 0.02 | 0.94 | FALSE |
| 66 | The Cancer Genome Atlas | Head and Neck Squamous Cell Carcinoma | TGOLN2 | 0.13 | 0.18 | enet | 18 | 0.20 | 1.5e-22 | -6.6 | -7.1 | 1.1e-12 | 0.55 | 0.03 | 0.97 | FALSE |
| 67 | The Cancer Genome Atlas | Kidney Renal Clear Cell Carcinoma | TGOLN2 | 0.05 | 0.10 | lasso | 1 | 0.09 | 1.1e-10 | -6.9 | -6.9 | 4.7e-12 | 0.58 | 0.01 | 0.99 | FALSE |
| 68 | The Cancer Genome Atlas | Kidney Renal Papillary Cell Carcinoma | MRPL35 | 0.04 | 0.02 | blup | 61 | 0.02 | 2.9e-02 | 4.7 | 5.5 | 4.5e-08 | 0.05 | 0.03 | 0.63 | FALSE |
| 69 | The Cancer Genome Atlas | Kidney Renal Papillary Cell Carcinoma | TGOLN2 | 0.09 | 0.09 | lasso | 9 | 0.08 | 2.8e-05 | -6.6 | -6.7 | 1.8e-11 | 0.55 | 0.02 | 0.97 | FALSE |
| 70 | The Cancer Genome Atlas | Brain Lower Grade Glioma | MAT2A | 0.05 | 0.03 | blup | 37 | 0.03 | 5.3e-04 | 4.5 | 6.2 | 6.7e-10 | -0.15 | 0.03 | 0.11 | FALSE |
| 71 | The Cancer Genome Atlas | Brain Lower Grade Glioma | RETSAT | 0.29 | 0.15 | enet | 27 | 0.17 | 3.5e-19 | -6.3 | 7.5 | 5.1e-14 | -0.71 | 1.00 | 0.00 | FALSE |
| 72 | The Cancer Genome Atlas | Brain Lower Grade Glioma | SH2D6 | 0.07 | 0.06 | lasso | 3 | 0.06 | 9.3e-08 | -6.1 | 7.8 | 8.7e-15 | -0.62 | 0.11 | 0.88 | FALSE |
| 73 | The Cancer Genome Atlas | Brain Lower Grade Glioma | TGOLN2 | 0.02 | 0.02 | enet | 9 | 0.02 | 7.1e-04 | 6.7 | -6.9 | 5.9e-12 | 0.55 | 0.02 | 0.94 | FALSE |
| 74 | The Cancer Genome Atlas | Liver Hepatocellular Carcinoma | SH2D6 | 0.21 | 0.08 | lasso | 6 | 0.18 | 1.2e-08 | -2.3 | -6.4 | 1.3e-10 | 0.75 | 0.00 | 0.99 | FALSE |
| 75 | The Cancer Genome Atlas | Lung Adenocarcinoma | SH2D6 | 0.12 | 0.09 | enet | 7 | 0.09 | 3.1e-10 | -7.3 | -7.5 | 5.8e-14 | 0.79 | 0.95 | 0.05 | FALSE |
| 76 | The Cancer Genome Atlas | Lung Adenocarcinoma | TGOLN2 | 0.08 | 0.08 | blup | 64 | 0.12 | 2.0e-13 | -7.0 | -6.7 | 2.8e-11 | 0.50 | 0.02 | 0.98 | FALSE |
| 77 | The Cancer Genome Atlas | Lung Squamous Cell Carcinoma | TGOLN2 | 0.06 | 0.09 | lasso | 2 | 0.08 | 8.6e-10 | -6.6 | -6.6 | 4.0e-11 | 0.55 | 0.04 | 0.96 | FALSE |
| 78 | The Cancer Genome Atlas | Ovarian Serous Cystadenocarcinoma | TGOLN2 | 0.18 | 0.16 | lasso | 6 | 0.16 | 3.5e-11 | -6.6 | -6.5 | 7.9e-11 | 0.56 | 0.03 | 0.97 | FALSE |
| 79 | The Cancer Genome Atlas | Pancreatic Adenocarcinoma | RETSAT | 0.07 | 0.04 | blup | 56 | 0.05 | 4.8e-03 | -6.3 | 7.0 | 2.5e-12 | -0.73 | 0.07 | 0.18 | FALSE |
| 80 | The Cancer Genome Atlas | Pancreatic Adenocarcinoma | TGOLN2 | 0.08 | 0.05 | blup | 64 | 0.08 | 4.2e-04 | 6.0 | -6.1 | 8.6e-10 | 0.56 | 0.02 | 0.95 | FALSE |
| 81 | The Cancer Genome Atlas | Prostate Adenocarcinoma | CAPG | 0.08 | 0.03 | blup | 43 | 0.08 | 2.0e-08 | -7.0 | -8.8 | 2.0e-18 | 0.66 | 0.08 | 0.92 | FALSE |
| 82 | The Cancer Genome Atlas | Prostate Adenocarcinoma | MRPL35 | 0.11 | 0.08 | lasso | 3 | 0.07 | 7.4e-08 | 5.9 | 5.9 | 3.3e-09 | 0.06 | 0.01 | 0.99 | FALSE |
| 83 | The Cancer Genome Atlas | Prostate Adenocarcinoma | REEP1 | 0.16 | 0.17 | blup | 109 | 0.19 | 2.1e-19 | 6.0 | 5.5 | 3.4e-08 | 0.06 | 0.02 | 0.98 | FALSE |
| 84 | The Cancer Genome Atlas | Prostate Adenocarcinoma | SH2D6 | 0.05 | 0.01 | blup | 44 | 0.02 | 1.1e-03 | -7.3 | -6.0 | 2.4e-09 | 0.67 | 0.02 | 0.49 | FALSE |
| 85 | The Cancer Genome Atlas | Prostate Adenocarcinoma | TGOLN2 | 0.13 | 0.20 | enet | 10 | 0.22 | 3.1e-22 | 6.7 | -7.3 | 2.1e-13 | 0.60 | 0.01 | 0.99 | FALSE |
| 86 | The Cancer Genome Atlas | Rectum Adenocarcinoma | TGOLN2 | 0.31 | 0.19 | enet | 10 | 0.15 | 1.8e-04 | 6.7 | -6.8 | 1.2e-11 | 0.53 | 0.03 | 0.93 | FALSE |
| 87 | The Cancer Genome Atlas | Soft Tissue Sarcoma | REEP1 | 0.05 | 0.07 | lasso | 4 | 0.05 | 8.1e-04 | 6.2 | 6.3 | 3.2e-10 | 0.06 | 0.01 | 0.96 | FALSE |
| 88 | The Cancer Genome Atlas | Stomach Adenocarcinoma | TGOLN2 | 0.09 | 0.08 | lasso | 9 | 0.08 | 1.1e-06 | -6.6 | -6.4 | 1.4e-10 | 0.59 | 0.03 | 0.97 | FALSE |
| 89 | The Cancer Genome Atlas | Testicular Germ Cell Tumors | REEP1 | 0.10 | 0.04 | blup | 109 | 0.07 | 2.0e-03 | -4.1 | 5.4 | 5.7e-08 | 0.06 | 0.06 | 0.87 | FALSE |
| 90 | The Cancer Genome Atlas | Thyroid Carcinoma | TGOLN2 | 0.09 | 0.13 | blup | 64 | 0.13 | 7.6e-13 | -7.0 | -7.4 | 1.1e-13 | 0.47 | 0.01 | 0.99 | FALSE |