Best TWAS P=7.44e-32 · Best GWAS P=2.33e-25 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 | CommonMind | Brain Pre-frontal Cortex | CNN2 | 0.14 | 0.07 | bslmm | 472 | 0.08 | 1.2e-09 | -10.4 | -10.7 | 1.3e-26 | 0.81 | 0.00 | 1.00 | FALSE |
| 2 | GTEx | Adipose Subcutaneous | CNN2 | 0.12 | 0.00 | enet | 3 | 0.00 | 6.4e-01 | -10.4 | -10.8 | 2.3e-27 | 0.98 | 0.00 | 0.98 | TRUE |
| 3 | GTEx | Adipose Subcutaneous | AC011558.5 | 0.19 | 0.01 | enet | 7 | 0.01 | 5.1e-02 | -7.2 | -9.1 | 1.3e-19 | 0.65 | 0.07 | 0.90 | FALSE |
| 4 | GTEx | Artery Aorta | AP3D1 | 0.27 | 0.12 | lasso | 3 | 0.13 | 1.3e-07 | 5.0 | -5.3 | 8.6e-08 | -0.02 | 0.00 | 0.99 | FALSE |
| 5 | GTEx | Artery Aorta | POLR2E | 0.36 | 0.10 | lasso | 5 | 0.30 | 3.7e-17 | -4.0 | -8.2 | 3.4e-16 | 0.04 | 0.99 | 0.00 | TRUE |
| 6 | GTEx | Artery Tibial | AP3D1 | 0.17 | 0.16 | lasso | 3 | 0.16 | 2.1e-12 | 5.4 | -5.3 | 1.5e-07 | -0.04 | 0.00 | 1.00 | FALSE |
| 7 | GTEx | Artery Tibial | POLR2E | 0.35 | 0.26 | enet | 19 | 0.27 | 2.5e-21 | -6.2 | -8.2 | 3.2e-16 | 0.06 | 1.00 | 0.00 | FALSE |
| 8 | GTEx | Brain Caudate basal ganglia | TMEM259 | 0.34 | 0.14 | lasso | 7 | 0.07 | 4.3e-03 | -10.4 | -9.8 | 8.1e-23 | 0.96 | 0.00 | 0.91 | FALSE |
| 9 | GTEx | Brain Cerebellar Hemisphere | ABCA7 | 0.46 | 0.02 | enet | 52 | 0.06 | 1.2e-02 | -2.9 | -7.9 | 2.3e-15 | 0.35 | 0.06 | 0.07 | TRUE |
| 10 | GTEx | Brain Cerebellum | ABCA7 | 0.46 | 0.23 | lasso | 8 | 0.19 | 3.0e-06 | -7.2 | -7.3 | 3.4e-13 | 0.44 | 0.26 | 0.04 | TRUE |
| 11 | GTEx | Brain Cerebellum | HMHA1 | 0.45 | 0.07 | lasso | 8 | 0.04 | 1.9e-02 | -7.3 | -8.2 | 3.3e-16 | 0.10 | 0.06 | 0.05 | FALSE |
| 12 | GTEx | Breast Mammary Tissue | ABCA7 | 0.20 | 0.04 | lasso | 3 | 0.08 | 4.6e-05 | -7.6 | -6.1 | 1.1e-09 | 0.44 | 0.07 | 0.60 | FALSE |
| 13 | GTEx | Breast Mammary Tissue | POLR2E | 0.39 | 0.06 | lasso | 8 | 0.16 | 2.1e-08 | 4.3 | -8.4 | 4.8e-17 | -0.03 | 0.48 | 0.02 | TRUE |
| 14 | GTEx | Breast Mammary Tissue | TMEM259 | 0.21 | 0.06 | enet | 23 | 0.08 | 9.5e-05 | 5.9 | -6.1 | 1.2e-09 | 0.22 | 0.12 | 0.20 | FALSE |
| 15 | GTEx | Cells Transformed fibroblasts | CNN2 | 0.22 | 0.18 | lasso | 2 | 0.16 | 2.7e-12 | -10.4 | -10.4 | 2.0e-25 | 1.00 | 0.00 | 1.00 | FALSE |
| 16 | GTEx | Cells Transformed fibroblasts | AC011558.5 | 0.27 | 0.05 | enet | 30 | 0.11 | 1.5e-08 | -10.4 | -9.5 | 3.2e-21 | 0.73 | 0.00 | 1.00 | FALSE |
| 17 | GTEx | Esophagus Mucosa | AP3D1 | 0.18 | 0.21 | lasso | 3 | 0.21 | 2.4e-14 | 5.0 | -5.4 | 8.0e-08 | -0.02 | 0.01 | 0.99 | FALSE |
| 18 | GTEx | Esophagus Muscularis | CNN2 | 0.38 | 0.03 | lasso | 9 | 0.08 | 1.9e-05 | -10.4 | -8.1 | 4.9e-16 | 0.68 | 0.00 | 0.99 | FALSE |
| 19 | GTEx | Esophagus Muscularis | AP3D1 | 0.32 | 0.24 | lasso | 3 | 0.24 | 5.7e-15 | 5.4 | -5.2 | 1.5e-07 | -0.03 | 0.00 | 1.00 | FALSE |
| 20 | GTEx | Esophagus Muscularis | POLR2E | 0.38 | 0.18 | enet | 38 | 0.20 | 3.9e-12 | -6.2 | -7.1 | 9.0e-13 | 0.07 | 1.00 | 0.00 | FALSE |
| 21 | GTEx | Esophagus Muscularis | AC011558.5 | 0.26 | 0.00 | enet | 32 | 0.02 | 1.4e-02 | -10.4 | -8.6 | 7.9e-18 | 0.49 | 0.00 | 0.96 | FALSE |
| 22 | GTEx | Lung | AP3D1 | 0.14 | 0.11 | lasso | 3 | 0.12 | 1.6e-09 | 5.4 | -5.3 | 1.1e-07 | -0.03 | 0.00 | 1.00 | FALSE |
| 23 | GTEx | Muscle Skeletal | AP3D1 | 0.11 | 0.07 | lasso | 5 | 0.07 | 2.9e-07 | 5.4 | -5.2 | 2.6e-07 | -0.04 | 0.00 | 1.00 | FALSE |
| 24 | GTEx | Nerve Tibial | ABCA7 | 0.20 | 0.06 | lasso | 5 | 0.05 | 1.3e-04 | -7.2 | -7.2 | 5.0e-13 | 0.41 | 0.85 | 0.05 | FALSE |
| 25 | GTEx | Nerve Tibial | POLR2E | 0.25 | 0.06 | lasso | 4 | 0.13 | 1.6e-09 | -6.2 | -7.9 | 3.7e-15 | 0.05 | 0.70 | 0.01 | FALSE |
| 26 | GTEx | Prostate | TMEM259 | 0.32 | 0.01 | lasso | 7 | 0.05 | 2.8e-02 | 4.7 | -6.3 | 2.3e-10 | 0.34 | 0.07 | 0.16 | FALSE |
| 27 | GTEx | Skin Sun Exposed Lower leg | ABCA7 | 0.30 | 0.14 | enet | 31 | 0.23 | 4.1e-19 | -7.6 | -8.4 | 6.2e-17 | 0.52 | 1.00 | 0.00 | FALSE |
| 28 | GTEx | Testis | HMHA1 | 0.26 | 0.15 | lasso | 2 | 0.14 | 1.1e-06 | -7.3 | 7.3 | 2.0e-13 | -0.11 | 0.92 | 0.00 | FALSE |
| 29 | GTEx | Thyroid | CNN2 | 0.22 | 0.11 | lasso | 4 | 0.09 | 2.1e-07 | -8.5 | -8.7 | 4.1e-18 | 0.69 | 0.09 | 0.90 | FALSE |
| 30 | GTEx | Thyroid | AC011558.5 | 0.34 | 0.10 | lasso | 9 | 0.14 | 1.0e-10 | -8.5 | -9.3 | 1.1e-20 | 0.69 | 0.02 | 0.98 | FALSE |
| 31 | GTEx | Whole Blood | POLR2E | 0.10 | 0.00 | enet | 21 | 0.00 | 2.3e-01 | 1.4 | -5.7 | 1.1e-08 | 0.17 | 0.05 | 0.04 | FALSE |
| 32 | GTEx | Whole Blood | AC011558.5 | 0.15 | 0.02 | enet | 22 | 0.02 | 1.2e-02 | -7.2 | -8.8 | 8.7e-19 | 0.36 | 0.08 | 0.39 | TRUE |
| 33 | ROSMAP | Brain Pre-frontal Cortex | AP3D1 | 0.39 | 0.40 | enet | 12 | 0.43 | 8.8e-60 | 5.4 | -5.2 | 2.1e-07 | -0.02 | 0.00 | 1.00 | FALSE |
| 34 | ROSMAP | Brain Pre-frontal Cortex | POLR2E | 0.29 | 0.27 | lasso | 4 | 0.29 | 6.6e-38 | -7.4 | -7.5 | 5.1e-14 | 0.10 | 1.00 | 0.00 | FALSE |
| 35 | YFS | Blood | CNN2 | 0.26 | 0.05 | bslmm | 341 | 0.14 | 4.3e-45 | 4.7 | -7.8 | 7.6e-15 | 0.35 | 1.00 | 0.00 | FALSE |
| 36 | YFS | Blood | POLR2E | 0.20 | 0.13 | bslmm | 337 | 0.16 | 7.8e-50 | 5.0 | 5.6 | 1.8e-08 | -0.17 | 1.00 | 0.00 | FALSE |
| 37 | The Cancer Genome Atlas | Bladder Urothelial Carcinoma | AP3D1 | 0.05 | 0.00 | blup | 49 | 0.02 | 1.7e-02 | 5.4 | -5.7 | 1.2e-08 | -0.02 | 0.00 | 0.85 | FALSE |
| 38 | The Cancer Genome Atlas | Bladder Urothelial Carcinoma | GPX4 | 0.08 | 0.01 | lasso | 7 | 0.02 | 4.7e-03 | 5.0 | 6.0 | 1.9e-09 | 0.10 | 0.11 | 0.03 | FALSE |
| 39 | The Cancer Genome Atlas | Breast Invasive Carcinoma | AP3D1 | 0.01 | 0.01 | blup | 52 | 0.01 | 5.4e-03 | 5.4 | -6.8 | 1.1e-11 | 0.01 | 0.00 | 0.90 | TRUE |
| 40 | The Cancer Genome Atlas | Breast Invasive Carcinoma | GRIN3B | 0.03 | 0.02 | blup | 70 | 0.01 | 5.6e-04 | 5.0 | -7.3 | 3.1e-13 | 0.29 | 0.27 | 0.06 | FALSE |
| 41 | The Cancer Genome Atlas | Colon Adenocarcinoma | GRIN3B | 0.11 | 0.01 | enet | 8 | 0.06 | 2.3e-04 | 5.0 | -6.5 | 8.7e-11 | 0.22 | 0.10 | 0.06 | TRUE |
| 42 | The Cancer Genome Atlas | Head and Neck Squamous Cell Carcinoma | GRIN3B | 0.05 | 0.00 | blup | 69 | 0.01 | 8.7e-03 | -8.5 | -8.0 | 1.3e-15 | 0.56 | 0.01 | 0.25 | FALSE |
| 43 | The Cancer Genome Atlas | Kidney Renal Clear Cell Carcinoma | ABCA7 | 0.05 | 0.02 | blup | 71 | 0.04 | 4.7e-05 | -6.2 | -9.6 | 8.5e-22 | 0.28 | 0.44 | 0.04 | TRUE |
| 44 | The Cancer Genome Atlas | Kidney Renal Clear Cell Carcinoma | AP3D1 | 0.04 | 0.04 | lasso | 2 | 0.04 | 6.1e-05 | 5.4 | -5.4 | 5.7e-08 | -0.04 | 0.00 | 0.99 | FALSE |
| 45 | The Cancer Genome Atlas | Kidney Renal Clear Cell Carcinoma | HMHA1 | 0.06 | 0.06 | lasso | 2 | 0.05 | 3.1e-06 | -6.2 | -6.6 | 3.2e-11 | 0.11 | 0.87 | 0.00 | FALSE |
| 46 | The Cancer Genome Atlas | Brain Lower Grade Glioma | CNN2 | 0.05 | 0.04 | blup | 63 | 0.03 | 2.0e-04 | -8.5 | -10.6 | 4.7e-26 | 0.63 | 0.01 | 0.92 | FALSE |
| 47 | The Cancer Genome Atlas | Brain Lower Grade Glioma | POLR2E | 0.06 | 0.02 | blup | 53 | 0.02 | 4.2e-03 | -4.0 | -7.7 | 1.9e-14 | 0.21 | 0.01 | 0.22 | FALSE |
| 48 | The Cancer Genome Atlas | Lung Adenocarcinoma | ABCA7 | 0.06 | 0.03 | blup | 71 | 0.04 | 3.9e-05 | 1.7 | -6.5 | 8.7e-11 | 0.17 | 0.92 | 0.00 | FALSE |
| 49 | The Cancer Genome Atlas | Prostate Adenocarcinoma | ABCA7 | 0.09 | 0.03 | lasso | 7 | 0.03 | 4.5e-04 | -6.2 | -8.7 | 3.1e-18 | 0.29 | 0.44 | 0.03 | TRUE |
| 50 | The Cancer Genome Atlas | Prostate Adenocarcinoma | AP3D1 | 0.06 | 0.05 | enet | 7 | 0.04 | 5.7e-05 | 5.4 | -5.5 | 4.7e-08 | -0.03 | 0.00 | 1.00 | FALSE |
| 51 | The Cancer Genome Atlas | Prostate Adenocarcinoma | POLR2E | 0.06 | 0.00 | blup | 53 | 0.03 | 2.3e-04 | -6.8 | -8.7 | 4.0e-18 | 0.08 | 0.01 | 0.87 | FALSE |
| 52 | The Cancer Genome Atlas | Stomach Adenocarcinoma | AP3D1 | 0.09 | 0.07 | lasso | 5 | 0.08 | 3.2e-06 | 5.4 | -5.5 | 3.6e-08 | -0.03 | 0.00 | 1.00 | FALSE |
| 53 | The Cancer Genome Atlas | Thyroid Carcinoma | ABCA7 | 0.10 | 0.06 | lasso | 2 | 0.05 | 8.1e-06 | -7.4 | -7.7 | 1.8e-14 | 0.12 | 0.70 | 0.03 | FALSE |
| 54 | The Cancer Genome Atlas | Thyroid Carcinoma | AP3D1 | 0.05 | 0.05 | lasso | 3 | 0.04 | 1.0e-04 | 5.4 | -5.4 | 5.7e-08 | -0.04 | 0.00 | 0.99 | FALSE |
| 55 | The Cancer Genome Atlas | Thyroid Carcinoma | CNN2 | 0.09 | 0.03 | blup | 63 | 0.07 | 5.4e-07 | -10.4 | -11.7 | 7.4e-32 | 0.74 | 0.00 | 1.00 | TRUE |