Best TWAS P=2.79e-11 · Best GWAS P=4.02e-13 conditioned to 0.000972
| # | 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 | 5.8 | -5.7 | 1.5e-08 | -0.78 | 0.83 | 0.17 | FALSE |
| 2 | CommonMind | Brain Pre-frontal Cortex | SNF8 | 0.08 | 0.07 | lasso | 5 | 0.08 | 9.3e-10 | -4.3 | 5.2 | 1.8e-07 | 0.07 | 0.16 | 0.84 | TRUE |
| 3 | GTEx | Brain Caudate basal ganglia | RP11-6N17.9 | 0.45 | -0.01 | enet | 28 | 0.16 | 3.3e-05 | -1.0 | -5.9 | 4.0e-09 | -0.48 | 0.06 | 0.13 | FALSE |
| 4 | GTEx | Brain Cerebellar Hemisphere | CDK5RAP3 | 0.22 | 0.10 | lasso | 6 | 0.09 | 2.6e-03 | 4.8 | -5.8 | 7.7e-09 | -0.74 | 0.08 | 0.40 | FALSE |
| 5 | GTEx | Brain Cerebellar Hemisphere | RP11-6N17.10 | 0.21 | 0.16 | lasso | 5 | 0.13 | 3.8e-04 | 4.8 | -5.3 | 8.9e-08 | -0.73 | 0.09 | 0.43 | FALSE |
| 6 | GTEx | Brain Nucleus accumbens basal ganglia | KPNB1 | 0.24 | 0.00 | lasso | 9 | 0.01 | 2.1e-01 | 1.1 | -5.2 | 2.5e-07 | -0.80 | 0.02 | 0.79 | FALSE |
| 7 | GTEx | Brain Nucleus accumbens basal ganglia | CDK5RAP3 | 0.21 | 0.04 | lasso | 4 | 0.02 | 7.2e-02 | 6.1 | -5.8 | 7.3e-09 | -0.78 | 0.08 | 0.36 | FALSE |
| 8 | GTEx | Brain Nucleus accumbens basal ganglia | RP11-6N17.9 | 0.47 | 0.05 | lasso | 17 | 0.11 | 8.3e-04 | 5.3 | -5.7 | 1.4e-08 | -0.65 | 0.11 | 0.39 | TRUE |
| 9 | GTEx | Esophagus Gastroesophageal Junction | RP11-6N17.9 | 0.18 | 0.14 | lasso | 3 | 0.09 | 4.9e-04 | -3.6 | -5.1 | 2.8e-07 | -0.49 | 0.03 | 0.73 | FALSE |
| 10 | GTEx | Heart Atrial Appendage | CDK5RAP3 | 0.13 | 0.00 | enet | 18 | 0.04 | 5.1e-03 | 2.0 | -5.4 | 6.0e-08 | -0.42 | 0.09 | 0.05 | FALSE |
| 11 | GTEx | Muscle Skeletal | AC003665.1 | 0.05 | 0.03 | enet | 8 | 0.03 | 1.4e-03 | 4.9 | 6.0 | 1.9e-09 | 0.63 | 0.12 | 0.72 | FALSE |
| 12 | GTEx | Pancreas | CDK5RAP3 | 0.11 | -0.01 | lasso | 4 | 0.02 | 5.1e-02 | 4.8 | -5.7 | 1.0e-08 | -0.48 | 0.09 | 0.18 | FALSE |
| 13 | GTEx | Pancreas | RP11-6N17.9 | 0.15 | 0.04 | lasso | 5 | 0.04 | 9.3e-03 | -1.6 | -5.4 | 7.1e-08 | -0.47 | 0.13 | 0.17 | FALSE |
| 14 | GTEx | Stomach | RP11-6N17.9 | 0.13 | 0.02 | lasso | 6 | 0.04 | 8.0e-03 | 5.4 | -6.2 | 5.8e-10 | -0.70 | 0.12 | 0.69 | FALSE |
| 15 | GTEx | Testis | RP11-6N17.4 | 0.14 | 0.02 | lasso | 10 | 0.02 | 4.8e-02 | 6.1 | 6.0 | 2.4e-09 | 0.78 | 0.18 | 0.66 | FALSE |
| 16 | GTEx | Thyroid | RP11-6N17.10 | 0.19 | 0.12 | lasso | 5 | 0.13 | 3.0e-10 | -3.6 | -5.3 | 1.1e-07 | -0.47 | 1.00 | 0.00 | FALSE |
| 17 | The Cancer Genome Atlas | Breast Invasive Carcinoma | CDK5RAP3 | 0.05 | 0.03 | lasso | 2 | 0.02 | 1.8e-05 | 5.4 | -5.5 | 4.9e-08 | -0.76 | 0.00 | 1.00 | FALSE |
| 18 | The Cancer Genome Atlas | Head and Neck Squamous Cell Carcinoma | CBX1 | 0.03 | 0.01 | lasso | 3 | 0.01 | 8.7e-03 | 6.1 | -5.3 | 1.4e-07 | -0.80 | 0.01 | 0.82 | FALSE |
| 19 | The Cancer Genome Atlas | Prostate Adenocarcinoma | CBX1 | 0.03 | 0.04 | lasso | 4 | 0.04 | 3.7e-05 | 6.1 | -6.0 | 1.7e-09 | -0.84 | 0.01 | 0.99 | FALSE |
| 20 | The Cancer Genome Atlas | Prostate Adenocarcinoma | CDK5RAP3 | 0.06 | 0.00 | blup | 62 | 0.03 | 1.0e-03 | -4.4 | -6.7 | 2.8e-11 | -0.35 | 0.00 | 0.80 | TRUE |