Best TWAS P=1.06e-11 · Best GWAS P=2.01e-14 conditioned to 6.91e-05
| # | 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 | CDK5RAP3 | 0.15 | 0.12 | bslmm | 392 | 0.14 | 3.6e-16 | 6.16 | -6.1 | 1.4e-09 | -0.78 | 0.90 | 0.10 | FALSE |
| 2 | CommonMind | Brain Pre-frontal Cortex | SNF8 | 0.08 | 0.07 | lasso | 5 | 0.08 | 9.3e-10 | -4.48 | 5.3 | 9.5e-08 | 0.07 | 0.10 | 0.90 | FALSE |
| 3 | GTEx | Adipose Subcutaneous | RP11-6N17.9 | 0.10 | 0.05 | enet | 14 | 0.05 | 6.8e-05 | -3.31 | -5.6 | 2.2e-08 | -0.42 | 0.46 | 0.06 | FALSE |
| 4 | GTEx | Adipose Visceral Omentum | RP11-6N17.9 | 0.13 | 0.04 | enet | 16 | 0.05 | 8.4e-04 | -1.82 | -5.1 | 2.7e-07 | -0.47 | 0.26 | 0.30 | FALSE |
| 5 | GTEx | Artery Aorta | CDK5RAP3 | 0.26 | 0.22 | lasso | 11 | 0.25 | 5.8e-14 | -4.46 | -5.2 | 2.1e-07 | -0.35 | 1.00 | 0.00 | FALSE |
| 6 | GTEx | Artery Aorta | RP11-6N17.9 | 0.23 | 0.12 | enet | 19 | 0.19 | 9.5e-11 | -4.46 | -5.5 | 4.7e-08 | -0.42 | 0.99 | 0.00 | FALSE |
| 7 | GTEx | Artery Aorta | RP11-6N17.10 | 0.20 | 0.07 | enet | 24 | 0.14 | 3.5e-08 | -4.46 | -5.8 | 8.9e-09 | -0.43 | 0.50 | 0.12 | FALSE |
| 8 | GTEx | Artery Coronary | PNPO | 0.13 | 0.00 | lasso | 4 | -0.01 | 5.9e-01 | 4.72 | 5.1 | 2.7e-07 | 0.24 | 0.13 | 0.06 | FALSE |
| 9 | GTEx | Artery Tibial | ARL17A | 0.69 | 0.37 | lasso | 9 | 0.44 | 5.4e-38 | 5.08 | 5.1 | 2.8e-07 | -0.07 | 0.00 | 1.00 | FALSE |
| 10 | GTEx | Brain Caudate basal ganglia | RP11-6N17.9 | 0.45 | -0.01 | enet | 28 | 0.16 | 3.3e-05 | -0.74 | -6.0 | 1.6e-09 | -0.48 | 0.06 | 0.13 | FALSE |
| 11 | GTEx | Brain Cerebellar Hemisphere | CDK5RAP3 | 0.22 | 0.10 | lasso | 6 | 0.09 | 2.6e-03 | 5.20 | -6.4 | 1.4e-10 | -0.74 | 0.08 | 0.40 | FALSE |
| 12 | GTEx | Brain Cerebellar Hemisphere | RP11-6N17.10 | 0.21 | 0.16 | lasso | 5 | 0.13 | 3.8e-04 | 5.20 | -5.9 | 4.8e-09 | -0.73 | 0.09 | 0.43 | FALSE |
| 13 | GTEx | Brain Cortex | ARL17A | 0.35 | 0.20 | lasso | 6 | 0.25 | 1.7e-07 | 5.08 | 5.6 | 2.6e-08 | -0.05 | 0.00 | 0.95 | FALSE |
| 14 | GTEx | Brain Nucleus accumbens basal ganglia | KPNB1 | 0.24 | 0.00 | lasso | 9 | 0.01 | 2.1e-01 | 0.80 | -5.3 | 1.1e-07 | -0.80 | 0.02 | 0.79 | FALSE |
| 15 | GTEx | Brain Nucleus accumbens basal ganglia | CDK5RAP3 | 0.21 | 0.04 | lasso | 4 | 0.02 | 7.2e-02 | 6.45 | -6.3 | 3.6e-10 | -0.78 | 0.08 | 0.36 | FALSE |
| 16 | GTEx | Brain Nucleus accumbens basal ganglia | RP11-6N17.9 | 0.47 | 0.05 | lasso | 17 | 0.11 | 8.3e-04 | 5.62 | -6.1 | 1.3e-09 | -0.65 | 0.11 | 0.38 | FALSE |
| 17 | GTEx | Cells EBV-transformed lymphocytes | NSF | 0.20 | 0.07 | lasso | 2 | 0.10 | 3.4e-04 | 4.80 | -5.1 | 3.0e-07 | -0.04 | 0.03 | 0.70 | FALSE |
| 18 | GTEx | Esophagus Gastroesophageal Junction | CDK5RAP3 | 0.21 | 0.09 | lasso | 6 | 0.07 | 1.2e-03 | -4.46 | -5.9 | 3.2e-09 | -0.30 | 0.09 | 0.50 | FALSE |
| 19 | GTEx | Esophagus Gastroesophageal Junction | RP11-6N17.9 | 0.18 | 0.14 | lasso | 3 | 0.09 | 4.9e-04 | -4.46 | -6.0 | 2.6e-09 | -0.49 | 0.03 | 0.73 | FALSE |
| 20 | GTEx | Heart Atrial Appendage | CDK5RAP3 | 0.13 | 0.00 | enet | 18 | 0.04 | 5.1e-03 | 1.88 | -6.1 | 8.6e-10 | -0.42 | 0.09 | 0.05 | FALSE |
| 21 | GTEx | Liver | ARL17A | 0.34 | 0.18 | lasso | 9 | 0.18 | 9.8e-06 | 5.08 | 6.0 | 1.8e-09 | -0.04 | 0.00 | 0.90 | TRUE |
| 22 | GTEx | Muscle Skeletal | AC003665.1 | 0.05 | 0.03 | enet | 8 | 0.03 | 1.4e-03 | 5.29 | 6.8 | 1.1e-11 | 0.63 | 0.12 | 0.72 | TRUE |
| 23 | GTEx | Nerve Tibial | CDK5RAP3 | 0.41 | 0.35 | enet | 23 | 0.36 | 6.1e-27 | -4.46 | -5.4 | 7.6e-08 | -0.41 | 1.00 | 0.00 | FALSE |
| 24 | GTEx | Nerve Tibial | RP11-6N17.10 | 0.28 | 0.19 | lasso | 8 | 0.19 | 1.6e-13 | -4.46 | -5.3 | 1.3e-07 | -0.36 | 1.00 | 0.00 | FALSE |
| 25 | GTEx | Pancreas | CDK5RAP3 | 0.11 | -0.01 | lasso | 4 | 0.02 | 5.1e-02 | 5.20 | -6.2 | 4.9e-10 | -0.48 | 0.09 | 0.18 | FALSE |
| 26 | GTEx | Pancreas | RP11-6N17.9 | 0.15 | 0.04 | lasso | 5 | 0.04 | 9.3e-03 | -2.05 | -5.7 | 1.0e-08 | -0.47 | 0.13 | 0.17 | FALSE |
| 27 | GTEx | Stomach | RP11-6N17.9 | 0.13 | 0.02 | lasso | 6 | 0.04 | 8.0e-03 | 5.72 | -6.1 | 8.4e-10 | -0.70 | 0.12 | 0.69 | FALSE |
| 28 | GTEx | Testis | RP11-6N17.4 | 0.14 | 0.02 | lasso | 10 | 0.02 | 4.8e-02 | 6.45 | 6.3 | 2.3e-10 | 0.78 | 0.18 | 0.66 | FALSE |
| 29 | GTEx | Thyroid | CDK5RAP3 | 0.21 | 0.14 | lasso | 5 | 0.18 | 1.6e-13 | -4.46 | -5.7 | 1.3e-08 | -0.51 | 1.00 | 0.00 | FALSE |
| 30 | GTEx | Thyroid | RP11-6N17.9 | 0.22 | 0.14 | lasso | 5 | 0.14 | 5.2e-11 | -4.46 | -5.6 | 2.8e-08 | -0.44 | 1.00 | 0.00 | FALSE |
| 31 | GTEx | Thyroid | RP11-6N17.10 | 0.19 | 0.12 | lasso | 5 | 0.13 | 3.0e-10 | -4.46 | -5.7 | 1.0e-08 | -0.47 | 1.00 | 0.00 | FALSE |
| 32 | YFS | Blood | UBE2Z | 0.06 | 0.03 | enet | 19 | 0.06 | 1.5e-18 | 3.31 | 5.7 | 1.3e-08 | 0.10 | 1.00 | 0.00 | TRUE |
| 33 | The Cancer Genome Atlas | Breast Invasive Carcinoma | CDK5RAP3 | 0.05 | 0.03 | lasso | 2 | 0.02 | 1.8e-05 | 5.72 | -5.8 | 6.2e-09 | -0.76 | 0.00 | 1.00 | FALSE |
| 34 | The Cancer Genome Atlas | Head and Neck Squamous Cell Carcinoma | CBX1 | 0.03 | 0.01 | lasso | 3 | 0.01 | 8.7e-03 | 6.45 | -5.8 | 8.4e-09 | -0.80 | 0.01 | 0.81 | FALSE |
| 35 | The Cancer Genome Atlas | Prostate Adenocarcinoma | CBX1 | 0.03 | 0.04 | lasso | 4 | 0.04 | 3.7e-05 | 6.50 | -6.4 | 1.6e-10 | -0.84 | 0.01 | 0.99 | FALSE |
| 36 | The Cancer Genome Atlas | Prostate Adenocarcinoma | CDK5RAP3 | 0.06 | 0.00 | blup | 62 | 0.03 | 1.0e-03 | -3.42 | -6.5 | 6.3e-11 | -0.35 | 0.01 | 0.82 | FALSE |
| 37 | The Cancer Genome Atlas | Soft Tissue Sarcoma | LRRC37A2 | 0.43 | 0.26 | enet | 22 | 0.37 | 3.8e-23 | -3.30 | -5.3 | 1.2e-07 | -0.04 | 0.36 | 0.14 | FALSE |
| 38 | The Cancer Genome Atlas | Thyroid Carcinoma | ATP5G1 | 0.19 | 0.03 | lasso | 3 | 0.08 | 4.4e-08 | 4.21 | 5.4 | 6.6e-08 | 0.08 | 0.01 | 0.97 | FALSE |