Best TWAS P=9.55e-41 · Best GWAS P=6.71e-39 conditioned to 0.00356
| # | 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 | LPA | 0.10 | 0.02 | lasso | 5 | 0.04 | 3.2e-06 | 2.44 | -6.8 | 1.0e-11 | -0.62 | 0.04 | 0.92 | TRUE |
| 2 | CommonMind | Brain Pre-frontal Cortex | LPAL2 | 0.08 | 0.02 | bslmm | 575 | 0.03 | 2.1e-04 | -4.80 | 6.2 | 4.8e-10 | 0.48 | 0.38 | 0.05 | FALSE |
| 3 | CommonMind | Brain Pre-frontal Cortex | SLC22A3 | 0.10 | 0.02 | blup | 582 | 0.05 | 4.4e-07 | -9.04 | -7.0 | 2.0e-12 | -0.63 | 0.60 | 0.39 | FALSE |
| 4 | CommonMind | Brain Pre-frontal Cortex | TULP4 | 0.16 | 0.08 | bslmm | 596 | 0.12 | 2.9e-14 | -9.71 | -10.9 | 1.8e-27 | -0.04 | 0.00 | 1.00 | FALSE |
| 5 | GTEx | Adipose Visceral Omentum | SLC22A3 | 0.13 | 0.06 | enet | 7 | 0.09 | 1.3e-05 | -8.51 | -8.7 | 3.0e-18 | -0.63 | 0.52 | 0.47 | FALSE |
| 6 | GTEx | Artery Aorta | SNX9 | 0.14 | 0.00 | lasso | 3 | 0.00 | 1.9e-01 | 12.89 | 9.1 | 1.0e-19 | 0.00 | 0.01 | 0.97 | FALSE |
| 7 | GTEx | Artery Tibial | RP11-288H12.3 | 0.17 | 0.01 | lasso | 8 | 0.06 | 2.3e-05 | -3.15 | -5.6 | 1.9e-08 | -0.37 | 0.21 | 0.13 | TRUE |
| 8 | GTEx | Brain Caudate basal ganglia | SLC22A3 | 0.15 | 0.10 | enet | 39 | 0.11 | 5.6e-04 | -11.33 | -10.8 | 3.0e-27 | -0.71 | 0.04 | 0.90 | FALSE |
| 9 | GTEx | Brain Cerebellar Hemisphere | TULP4 | 0.44 | 0.37 | lasso | 12 | 0.32 | 4.3e-09 | 8.04 | 7.3 | 3.3e-13 | 0.00 | 0.93 | 0.04 | FALSE |
| 10 | GTEx | Brain Cerebellum | TULP4 | 0.46 | 0.32 | lasso | 15 | 0.28 | 7.6e-09 | 6.18 | 6.1 | 8.1e-10 | -0.02 | 0.98 | 0.00 | FALSE |
| 11 | GTEx | Brain Cortex | TMEM181 | 0.32 | -0.01 | enet | 72 | 0.04 | 2.8e-02 | -0.87 | 5.9 | 2.9e-09 | -0.06 | 0.07 | 0.09 | TRUE |
| 12 | GTEx | Brain Frontal Cortex BA9 | SLC22A3 | 0.26 | 0.08 | lasso | 6 | 0.05 | 1.5e-02 | -5.45 | -8.5 | 2.6e-17 | -0.62 | 0.16 | 0.56 | FALSE |
| 13 | GTEx | Cells EBV-transformed lymphocytes | SERAC1 | 0.24 | 0.31 | lasso | 8 | 0.30 | 1.4e-10 | -5.88 | -6.9 | 4.4e-12 | -0.02 | 0.92 | 0.03 | TRUE |
| 14 | GTEx | Colon Transverse | SLC22A3 | 0.18 | 0.00 | enet | 11 | 0.00 | 5.2e-01 | 5.92 | -6.3 | 3.8e-10 | -0.40 | 0.09 | 0.41 | FALSE |
| 15 | GTEx | Esophagus Mucosa | SLC22A3 | 0.19 | 0.08 | enet | 47 | 0.12 | 1.7e-08 | 7.92 | -11.8 | 3.9e-32 | -0.58 | 0.67 | 0.32 | TRUE |
| 16 | GTEx | Muscle Skeletal | TULP4 | 0.08 | 0.01 | enet | 20 | 0.02 | 1.9e-03 | -9.03 | 6.6 | 5.2e-11 | 0.06 | 0.22 | 0.39 | FALSE |
| 17 | GTEx | Muscle Skeletal | IGF2R | 0.34 | 0.26 | lasso | 3 | 0.26 | 6.8e-26 | -5.04 | -5.2 | 2.0e-07 | -0.01 | 1.00 | 0.00 | TRUE |
| 18 | GTEx | Nerve Tibial | SLC22A3 | 0.20 | 0.10 | lasso | 7 | 0.13 | 3.2e-09 | -8.61 | -8.1 | 4.8e-16 | -0.56 | 0.99 | 0.00 | FALSE |
| 19 | GTEx | Ovary | SLC22A3 | 0.33 | 0.29 | lasso | 6 | 0.23 | 2.8e-06 | -6.76 | -7.4 | 1.9e-13 | -0.65 | 0.11 | 0.81 | FALSE |
| 20 | GTEx | Pancreas | SLC22A3 | 0.17 | 0.04 | enet | 36 | 0.04 | 8.7e-03 | 7.77 | -5.2 | 1.6e-07 | -0.27 | 0.26 | 0.09 | FALSE |
| 21 | GTEx | Skin Not Sun Exposed Suprapubic | SLC22A3 | 0.15 | 0.05 | lasso | 9 | 0.05 | 9.9e-04 | -4.42 | -8.3 | 1.1e-16 | -0.65 | 0.24 | 0.68 | FALSE |
| 22 | GTEx | Skin Sun Exposed Lower leg | SLC22A3 | 0.29 | 0.14 | lasso | 10 | 0.20 | 3.7e-16 | 4.71 | -7.0 | 1.8e-12 | -0.48 | 1.00 | 0.00 | FALSE |
| 23 | GTEx | Small Intestine Terminal Ileum | SLC22A3 | 0.24 | 0.13 | lasso | 5 | 0.10 | 3.3e-03 | 5.91 | -5.2 | 1.7e-07 | -0.31 | 0.12 | 0.07 | FALSE |
| 24 | GTEx | Stomach | TULP4 | 0.25 | 0.18 | lasso | 7 | 0.16 | 2.6e-08 | 6.27 | 6.3 | 3.8e-10 | 0.06 | 1.00 | 0.00 | FALSE |
| 25 | GTEx | Stomach | IGF2R | 0.25 | 0.00 | enet | 41 | 0.00 | 6.6e-01 | 3.71 | -6.0 | 1.6e-09 | -0.28 | 0.10 | 0.05 | FALSE |
| 26 | GTEx | Testis | SLC22A3 | 0.19 | 0.01 | lasso | 14 | 0.05 | 2.6e-03 | -12.34 | -7.5 | 6.6e-14 | -0.66 | 0.43 | 0.52 | FALSE |
| 27 | GTEx | Thyroid | TULP4 | 0.09 | 0.02 | lasso | 4 | 0.03 | 1.4e-03 | 12.89 | 9.4 | 6.0e-21 | 0.08 | 0.01 | 0.94 | FALSE |
| 28 | METSIM | Adipose | SERAC1 | 0.12 | 0.09 | bslmm | 584 | 0.09 | 5.5e-14 | -4.70 | -5.8 | 4.8e-09 | -0.05 | 1.00 | 0.00 | TRUE |
| 29 | ROSMAP | Brain Pre-frontal Cortex | TULP4 | 0.07 | 0.02 | lasso | 3 | 0.03 | 1.2e-04 | 12.89 | -8.1 | 4.2e-16 | 0.02 | 0.00 | 0.99 | FALSE |
| 30 | ROSMAP | Brain Pre-frontal Cortex | SLC22A3 | 0.14 | 0.20 | lasso | 10 | 0.19 | 2.4e-24 | -8.98 | -9.3 | 1.7e-20 | -0.67 | 1.00 | 0.00 | FALSE |
| 31 | The Cancer Genome Atlas | Colon Adenocarcinoma | SLC22A3 | 0.17 | 0.06 | lasso | 5 | 0.04 | 2.8e-03 | -4.26 | 5.6 | 2.8e-08 | 0.45 | 0.07 | 0.20 | FALSE |
| 32 | The Cancer Genome Atlas | Kidney Renal Clear Cell Carcinoma | TULP4 | 0.09 | 0.05 | blup | 148 | 0.04 | 2.0e-05 | 9.42 | -13.4 | 9.5e-41 | 0.05 | 0.67 | 0.15 | TRUE |
| 33 | The Cancer Genome Atlas | Brain Lower Grade Glioma | SERAC1 | 0.09 | 0.03 | lasso | 4 | 0.02 | 3.0e-03 | -4.70 | -5.2 | 1.6e-07 | -0.04 | 0.01 | 0.50 | FALSE |
| 34 | The Cancer Genome Atlas | Brain Lower Grade Glioma | SLC22A3 | 0.12 | 0.07 | enet | 24 | 0.07 | 4.0e-08 | -8.91 | 6.0 | 2.0e-09 | 0.32 | 1.00 | 0.00 | FALSE |
| 35 | The Cancer Genome Atlas | Brain Lower Grade Glioma | TULP4 | 0.03 | 0.03 | lasso | 3 | 0.02 | 5.1e-03 | 8.04 | -8.3 | 9.8e-17 | 0.01 | 0.21 | 0.09 | FALSE |
| 36 | The Cancer Genome Atlas | Ovarian Serous Cystadenocarcinoma | LPAL2 | 0.07 | 0.00 | blup | 74 | 0.04 | 1.1e-03 | -4.80 | 9.0 | 2.3e-19 | 0.75 | 0.05 | 0.46 | FALSE |