Best TWAS P=2.19e-37 · Best GWAS P=3.08e-31 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 | PCGF2 | 0.14 | 0.12 | lasso | 2 | 0.12 | 6.1e-10 | -11.62 | -11.7 | 7.5e-32 | 0.98 | 0.00 | 1.00 | FALSE |
| 2 | GTEx | Adipose Subcutaneous | PSMB3 | 0.11 | 0.01 | enet | 8 | 0.03 | 2.7e-03 | 6.29 | 6.8 | 1.0e-11 | -0.31 | 0.24 | 0.04 | FALSE |
| 3 | GTEx | Adipose Subcutaneous | THRA | 0.12 | 0.00 | enet | 23 | 0.02 | 1.6e-02 | 5.11 | -5.3 | 1.2e-07 | -0.01 | 0.06 | 0.42 | TRUE |
| 4 | GTEx | Adipose Subcutaneous | PIP4K2B | 0.15 | 0.07 | lasso | 5 | 0.07 | 2.2e-06 | 7.11 | 7.3 | 3.4e-13 | -0.17 | 0.98 | 0.00 | TRUE |
| 5 | GTEx | Adipose Subcutaneous | MSL1 | 0.15 | 0.12 | lasso | 2 | 0.12 | 3.9e-10 | -8.69 | 8.7 | 4.2e-18 | -0.01 | 0.00 | 1.00 | FALSE |
| 6 | GTEx | Adrenal Gland | PCGF2 | 0.34 | 0.09 | lasso | 6 | 0.11 | 8.5e-05 | -11.62 | -12.5 | 9.0e-36 | 0.87 | 0.00 | 0.99 | FALSE |
| 7 | GTEx | Artery Aorta | PCGF2 | 0.51 | 0.32 | enet | 27 | 0.37 | 1.2e-21 | -11.62 | -12.1 | 8.0e-34 | 0.82 | 0.00 | 1.00 | FALSE |
| 8 | GTEx | Artery Aorta | PSMB3 | 0.23 | 0.17 | enet | 26 | 0.22 | 2.1e-12 | 7.11 | 6.2 | 6.9e-10 | -0.17 | 1.00 | 0.00 | FALSE |
| 9 | GTEx | Artery Tibial | LASP1 | 0.11 | 0.00 | enet | 13 | 0.04 | 6.9e-04 | -7.88 | -5.3 | 1.3e-07 | 0.37 | 0.08 | 0.11 | FALSE |
| 10 | GTEx | Artery Tibial | PCGF2 | 0.38 | 0.27 | lasso | 8 | 0.31 | 4.3e-25 | -11.62 | -12.4 | 4.6e-35 | 0.95 | 0.00 | 1.00 | TRUE |
| 11 | GTEx | Artery Tibial | PSMB3 | 0.10 | 0.02 | enet | 12 | 0.03 | 1.2e-03 | 7.11 | 5.7 | 1.5e-08 | -0.21 | 0.59 | 0.05 | FALSE |
| 12 | GTEx | Artery Tibial | PIP4K2B | 0.37 | 0.16 | enet | 49 | 0.22 | 2.1e-17 | 7.11 | 6.1 | 1.2e-09 | -0.06 | 1.00 | 0.00 | FALSE |
| 13 | GTEx | Artery Tibial | MSL1 | 0.19 | 0.14 | lasso | 2 | 0.15 | 4.9e-12 | -8.69 | 9.2 | 2.7e-20 | -0.01 | 0.00 | 1.00 | TRUE |
| 14 | GTEx | Brain Cerebellum | PCGF2 | 0.25 | 0.29 | lasso | 3 | 0.26 | 2.4e-08 | -9.66 | 10.4 | 2.2e-25 | -0.83 | 0.01 | 0.99 | FALSE |
| 15 | GTEx | Brain Cerebellum | CWC25 | 0.30 | 0.01 | enet | 9 | 0.02 | 1.0e-01 | 3.22 | 6.4 | 1.4e-10 | -0.24 | 0.06 | 0.06 | TRUE |
| 16 | GTEx | Brain Nucleus accumbens basal ganglia | RAPGEFL1 | 0.16 | 0.06 | lasso | 4 | 0.07 | 7.7e-03 | 4.82 | 5.7 | 1.6e-08 | 0.01 | 0.07 | 0.51 | FALSE |
| 17 | GTEx | Breast Mammary Tissue | ORMDL3 | 0.17 | 0.04 | enet | 27 | 0.06 | 7.2e-04 | 3.24 | 5.9 | 4.1e-09 | 0.04 | 0.45 | 0.12 | TRUE |
| 18 | GTEx | Breast Mammary Tissue | MSL1 | 0.20 | 0.06 | lasso | 6 | 0.07 | 2.2e-04 | -8.69 | 8.6 | 1.1e-17 | -0.03 | 0.00 | 1.00 | FALSE |
| 19 | GTEx | Breast Mammary Tissue (Female) | MSL1 | 0.09 | 0.00 | enet | 9 | 0.03 | 5.8e-02 | -8.69 | 7.6 | 3.3e-14 | -0.04 | 0.01 | 0.80 | FALSE |
| 20 | GTEx | Cells Transformed fibroblasts | PCGF2 | 0.34 | 0.28 | lasso | 4 | 0.30 | 3.2e-23 | -11.62 | -12.8 | 2.2e-37 | 0.94 | 0.00 | 1.00 | TRUE |
| 21 | GTEx | Cells Transformed fibroblasts | GSDMB | 0.11 | 0.02 | enet | 18 | 0.06 | 4.9e-05 | -4.87 | -6.8 | 1.1e-11 | -0.01 | 0.84 | 0.08 | FALSE |
| 22 | GTEx | Colon Transverse | PCGF2 | 0.29 | 0.21 | lasso | 5 | 0.20 | 6.2e-10 | -11.62 | -11.9 | 1.5e-32 | 1.00 | 0.00 | 1.00 | FALSE |
| 23 | GTEx | Colon Transverse | MSL1 | 0.18 | 0.11 | lasso | 3 | 0.05 | 2.1e-03 | -8.69 | 9.1 | 1.0e-19 | -0.01 | 0.00 | 0.99 | FALSE |
| 24 | GTEx | Esophagus Mucosa | PCGF2 | 0.32 | 0.24 | lasso | 7 | 0.23 | 1.8e-15 | -11.62 | -12.4 | 2.0e-35 | 0.97 | 0.00 | 1.00 | FALSE |
| 25 | GTEx | Esophagus Muscularis | PCGF2 | 0.21 | 0.15 | lasso | 8 | 0.13 | 3.3e-08 | -11.62 | -11.1 | 1.9e-28 | 0.96 | 0.00 | 1.00 | FALSE |
| 26 | GTEx | Esophagus Muscularis | MSL1 | 0.25 | 0.18 | lasso | 8 | 0.22 | 1.7e-13 | -8.25 | 8.3 | 7.8e-17 | 0.00 | 0.01 | 0.99 | TRUE |
| 27 | GTEx | Heart Atrial Appendage | PCGF2 | 0.18 | 0.13 | lasso | 3 | 0.09 | 6.1e-05 | -11.62 | -11.5 | 1.1e-30 | 1.00 | 0.00 | 1.00 | FALSE |
| 28 | GTEx | Lung | PCGF2 | 0.25 | 0.17 | lasso | 7 | 0.17 | 4.8e-13 | -11.62 | -11.9 | 1.9e-32 | 0.97 | 0.00 | 1.00 | FALSE |
| 29 | GTEx | Nerve Tibial | PCGF2 | 0.20 | 0.07 | lasso | 4 | 0.13 | 3.1e-09 | 4.14 | -10.2 | 1.2e-24 | 0.74 | 0.00 | 1.00 | FALSE |
| 30 | GTEx | Nerve Tibial | MSL1 | 0.33 | 0.25 | lasso | 4 | 0.24 | 6.3e-17 | -8.69 | 9.1 | 7.9e-20 | -0.01 | 0.00 | 1.00 | FALSE |
| 31 | GTEx | Pancreas | PCGF2 | 0.29 | 0.12 | lasso | 5 | 0.07 | 5.3e-04 | -11.62 | -12.1 | 6.9e-34 | 0.96 | 0.00 | 0.98 | FALSE |
| 32 | GTEx | Pituitary | MSL1 | 0.40 | 0.27 | lasso | 7 | 0.24 | 1.3e-06 | -8.00 | 8.3 | 6.6e-17 | 0.00 | 0.03 | 0.88 | FALSE |
| 33 | GTEx | Skin Not Sun Exposed Suprapubic | PCGF2 | 0.39 | 0.23 | lasso | 4 | 0.21 | 6.9e-12 | -11.62 | -11.7 | 2.1e-31 | 1.00 | 0.00 | 1.00 | FALSE |
| 34 | GTEx | Skin Not Sun Exposed Suprapubic | MSL1 | 0.18 | 0.15 | lasso | 4 | 0.15 | 2.1e-08 | -8.69 | 8.2 | 3.5e-16 | -0.02 | 0.00 | 1.00 | FALSE |
| 35 | GTEx | Skin Sun Exposed Lower leg | PCGF2 | 0.36 | 0.30 | lasso | 7 | 0.32 | 1.3e-26 | -11.62 | -12.0 | 4.8e-33 | 0.97 | 0.00 | 1.00 | FALSE |
| 36 | GTEx | Skin Sun Exposed Lower leg | MSL1 | 0.08 | 0.04 | lasso | 2 | 0.05 | 8.1e-05 | -7.19 | 8.6 | 7.4e-18 | 0.00 | 0.00 | 0.99 | FALSE |
| 37 | GTEx | Spleen | GSDMB | 0.50 | 0.45 | enet | 14 | 0.43 | 1.9e-12 | -5.19 | -5.9 | 3.1e-09 | -0.03 | 1.00 | 0.00 | TRUE |
| 38 | GTEx | Spleen | ORMDL3 | 0.40 | 0.44 | enet | 11 | 0.39 | 5.7e-11 | -5.19 | -5.3 | 1.1e-07 | -0.04 | 0.99 | 0.00 | FALSE |
| 39 | GTEx | Testis | LASP1 | 0.35 | 0.20 | lasso | 5 | 0.20 | 2.4e-09 | -7.53 | -7.8 | 7.3e-15 | 0.40 | 1.00 | 0.00 | FALSE |
| 40 | GTEx | Testis | PSMB3 | 0.30 | 0.24 | lasso | 4 | 0.21 | 8.9e-10 | 7.11 | 7.2 | 7.7e-13 | -0.19 | 1.00 | 0.00 | FALSE |
| 41 | GTEx | Testis | MSL1 | 0.23 | 0.05 | enet | 9 | 0.15 | 2.9e-07 | -8.69 | 8.0 | 1.0e-15 | 0.04 | 0.00 | 1.00 | TRUE |
| 42 | GTEx | Testis | RP1-56K13.3 | 0.27 | 0.10 | lasso | 8 | 0.08 | 1.7e-04 | -7.53 | -7.7 | 1.3e-14 | 0.41 | 0.72 | 0.02 | FALSE |
| 43 | GTEx | Thyroid | CTB-58E17.3 | 0.11 | 0.00 | enet | 45 | 0.02 | 2.3e-02 | 0.25 | -5.6 | 1.7e-08 | 0.36 | 0.10 | 0.43 | FALSE |
| 44 | GTEx | Whole Blood | ORMDL3 | 0.18 | 0.12 | lasso | 5 | 0.14 | 1.8e-12 | -5.19 | -5.3 | 1.3e-07 | -0.02 | 1.00 | 0.00 | FALSE |
| 45 | METSIM | Adipose | MSL1 | 0.12 | 0.06 | lasso | 10 | 0.06 | 1.8e-09 | -8.69 | 8.6 | 7.4e-18 | 0.00 | 0.00 | 1.00 | FALSE |
| 46 | METSIM | Adipose | PCGF2 | 0.05 | 0.04 | lasso | 4 | 0.02 | 3.7e-04 | -10.97 | -11.5 | 1.8e-30 | 0.63 | 0.01 | 0.98 | FALSE |
| 47 | METSIM | Adipose | PIP4K2B | 0.06 | 0.01 | blup | 360 | 0.02 | 7.0e-04 | 5.42 | 5.2 | 1.6e-07 | -0.19 | 0.47 | 0.04 | FALSE |
| 48 | NTR | Blood | GSDMB | 0.09 | 0.10 | enet | 16 | 0.12 | 3.8e-36 | -5.05 | -5.4 | 5.2e-08 | 0.00 | 1.00 | 0.00 | FALSE |
| 49 | NTR | Blood | IKZF3 | 0.04 | 0.03 | blup | 319 | 0.02 | 1.5e-08 | 4.85 | 6.1 | 1.2e-09 | 0.02 | 1.00 | 0.00 | TRUE |
| 50 | NTR | Blood | PIP4K2B | 0.02 | 0.01 | lasso | 3 | 0.01 | 6.4e-04 | 7.11 | -6.7 | 1.8e-11 | 0.18 | 0.27 | 0.03 | FALSE |
| 51 | YFS | Blood | GSDMB | 0.36 | 0.41 | lasso | 12 | 0.49 | 4.0e-186 | -4.75 | -5.2 | 1.5e-07 | 0.00 | 1.00 | 0.00 | FALSE |
| 52 | YFS | Blood | ORMDL3 | 0.31 | 0.36 | lasso | 9 | 0.45 | 2.2e-165 | -4.75 | -5.3 | 1.0e-07 | 0.01 | 1.00 | 0.00 | TRUE |
| 53 | YFS | Blood | PCGF2 | 0.03 | 0.02 | enet | 7 | 0.03 | 2.1e-11 | -11.62 | -11.3 | 2.0e-29 | 0.79 | 0.00 | 1.00 | FALSE |
| 54 | YFS | Blood | PIP4K2B | 0.03 | 0.00 | bslmm | 348 | 0.01 | 6.5e-03 | 1.44 | -5.7 | 1.6e-08 | 0.27 | 0.06 | 0.27 | FALSE |
| 55 | YFS | Blood | PSMB3 | 0.14 | 0.11 | enet | 31 | 0.16 | 7.2e-49 | 7.59 | 5.9 | 3.9e-09 | -0.13 | 1.00 | 0.00 | FALSE |
| 56 | The Cancer Genome Atlas | Bladder Urothelial Carcinoma | PCGF2 | 0.14 | 0.06 | blup | 35 | 0.11 | 1.1e-09 | -9.66 | -12.3 | 7.8e-35 | 0.82 | 0.00 | 1.00 | FALSE |
| 57 | The Cancer Genome Atlas | Bladder Urothelial Carcinoma | PSMB3 | 0.04 | 0.00 | blup | 37 | 0.02 | 6.7e-03 | 5.42 | 5.7 | 1.1e-08 | -0.18 | 0.04 | 0.05 | FALSE |
| 58 | The Cancer Genome Atlas | Breast Invasive Carcinoma | PCGF2 | 0.06 | 0.06 | blup | 37 | 0.05 | 4.4e-11 | -11.62 | -11.9 | 1.2e-32 | 0.85 | 0.00 | 1.00 | FALSE |
| 59 | The Cancer Genome Atlas | Colon Adenocarcinoma | GSDMB | 0.10 | 0.15 | blup | 40 | 0.14 | 1.2e-08 | 4.72 | -5.6 | 1.8e-08 | -0.01 | 0.03 | 0.96 | TRUE |
| 60 | The Cancer Genome Atlas | Colon Adenocarcinoma | PCGF2 | 0.23 | 0.23 | lasso | 3 | 0.22 | 9.8e-13 | -11.62 | -11.7 | 8.5e-32 | 0.99 | 0.00 | 1.00 | FALSE |
| 61 | The Cancer Genome Atlas | Head and Neck Squamous Cell Carcinoma | PCGF2 | 0.13 | 0.06 | blup | 37 | 0.09 | 7.0e-10 | -11.62 | -10.7 | 1.2e-26 | 0.85 | 0.00 | 1.00 | FALSE |
| 62 | The Cancer Genome Atlas | Head and Neck Squamous Cell Carcinoma | PIP4K2B | 0.04 | 0.01 | blup | 56 | 0.03 | 6.3e-04 | 7.59 | 8.9 | 3.6e-19 | -0.43 | 0.05 | 0.05 | FALSE |
| 63 | The Cancer Genome Atlas | Kidney Renal Clear Cell Carcinoma | ORMDL3 | 0.01 | 0.01 | blup | 36 | 0.00 | 8.5e-02 | 4.72 | -5.4 | 5.9e-08 | -0.02 | 0.02 | 0.60 | FALSE |
| 64 | The Cancer Genome Atlas | Kidney Renal Clear Cell Carcinoma | PCGF2 | 0.24 | 0.15 | lasso | 5 | 0.18 | 2.2e-19 | -11.62 | -11.9 | 9.9e-33 | 0.93 | 0.00 | 1.00 | FALSE |
| 65 | The Cancer Genome Atlas | Kidney Renal Papillary Cell Carcinoma | RAPGEFL1 | 0.13 | 0.02 | enet | 9 | 0.06 | 4.3e-04 | -6.77 | 6.2 | 7.0e-10 | -0.03 | 0.04 | 0.21 | FALSE |
| 66 | The Cancer Genome Atlas | Liver Hepatocellular Carcinoma | PCGF2 | 0.11 | 0.00 | blup | 37 | 0.03 | 1.0e-02 | 4.96 | -10.7 | 7.0e-27 | 0.57 | 0.00 | 0.51 | FALSE |
| 67 | The Cancer Genome Atlas | Lung Adenocarcinoma | PCGF2 | 0.08 | 0.05 | enet | 11 | 0.08 | 3.8e-09 | -9.61 | -11.8 | 2.2e-32 | 0.78 | 0.04 | 0.96 | FALSE |
| 68 | The Cancer Genome Atlas | Lung Squamous Cell Carcinoma | PCGF2 | 0.05 | 0.03 | lasso | 3 | 0.04 | 1.0e-05 | -9.61 | -11.7 | 1.3e-31 | 0.89 | 0.00 | 1.00 | FALSE |
| 69 | The Cancer Genome Atlas | Ovarian Serous Cystadenocarcinoma | CISD3 | 0.11 | 0.06 | blup | 33 | 0.04 | 1.9e-03 | -9.66 | 10.1 | 5.3e-24 | -0.78 | 0.01 | 0.95 | FALSE |
| 70 | The Cancer Genome Atlas | Ovarian Serous Cystadenocarcinoma | PCGF2 | 0.08 | 0.00 | blup | 37 | 0.01 | 3.8e-02 | -9.61 | -10.0 | 1.2e-23 | 0.71 | 0.00 | 0.69 | TRUE |
| 71 | The Cancer Genome Atlas | Pancreatic Adenocarcinoma | PCGF2 | 0.28 | 0.16 | lasso | 4 | 0.13 | 3.4e-06 | -11.62 | -12.5 | 6.0e-36 | 0.97 | 0.00 | 1.00 | FALSE |
| 72 | The Cancer Genome Atlas | Prostate Adenocarcinoma | PCGF2 | 0.18 | 0.14 | lasso | 4 | 0.16 | 2.4e-16 | -11.62 | -12.0 | 5.9e-33 | 0.94 | 0.00 | 1.00 | FALSE |
| 73 | The Cancer Genome Atlas | Prostate Adenocarcinoma | PIP4K2B | 0.05 | 0.04 | blup | 56 | 0.05 | 5.3e-06 | 6.82 | 6.5 | 1.1e-10 | -0.18 | 0.57 | 0.02 | FALSE |
| 74 | The Cancer Genome Atlas | Rectum Adenocarcinoma | GSDMB | 0.14 | 0.09 | blup | 39 | 0.17 | 7.0e-05 | 5.08 | -5.3 | 1.3e-07 | -0.03 | 0.02 | 0.85 | FALSE |
| 75 | The Cancer Genome Atlas | Soft Tissue Sarcoma | PCGF2 | 0.18 | 0.05 | blup | 36 | 0.11 | 7.3e-07 | -9.41 | -11.6 | 6.2e-31 | 0.71 | 0.00 | 0.99 | FALSE |
| 76 | The Cancer Genome Atlas | Stomach Adenocarcinoma | GSDMB | 0.06 | 0.08 | enet | 7 | 0.08 | 1.1e-06 | -5.12 | -5.3 | 1.4e-07 | -0.03 | 0.02 | 0.97 | FALSE |
| 77 | The Cancer Genome Atlas | Stomach Adenocarcinoma | PCGF2 | 0.14 | 0.04 | enet | 8 | 0.16 | 6.8e-12 | 4.14 | -11.3 | 8.3e-30 | 0.76 | 0.00 | 1.00 | FALSE |
| 78 | The Cancer Genome Atlas | Testicular Germ Cell Tumors | PSMB3 | 0.12 | 0.09 | lasso | 3 | 0.06 | 3.0e-03 | 7.59 | 7.6 | 3.9e-14 | -0.22 | 0.05 | 0.06 | FALSE |
| 79 | The Cancer Genome Atlas | Thyroid Carcinoma | PCGF2 | 0.27 | 0.22 | enet | 9 | 0.25 | 1.4e-24 | -11.62 | -11.7 | 2.2e-31 | 0.88 | 0.00 | 1.00 | FALSE |
| 80 | The Cancer Genome Atlas | Thyroid Carcinoma | PSMB3 | 0.05 | 0.06 | lasso | 1 | 0.05 | 2.4e-05 | 7.11 | 7.1 | 1.2e-12 | -0.19 | 0.50 | 0.03 | FALSE |