Best TWAS P=6.56e-23 · Best GWAS P=5.65e-26 conditioned to NaN
# | 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 | INTS12 | 0.06 | 0.06 | enet | 5 | 0.05 | 2.9e-07 | 9.4 | -9.4 | 8.2e-21 | 0.08 | 0.75 | 0.25 | FALSE |
2 | GTEx | Adipose Subcutaneous | PPA2 | 0.15 | 0.02 | enet | 36 | 0.06 | 7.0e-06 | 5.4 | -5.7 | 9.4e-09 | 0.35 | 0.26 | 0.14 | FALSE |
3 | GTEx | Adipose Subcutaneous | GSTCD | 0.08 | 0.07 | lasso | 8 | 0.07 | 2.9e-06 | 7.5 | 8.8 | 9.0e-19 | -0.13 | 0.89 | 0.08 | TRUE |
4 | GTEx | Adipose Visceral Omentum | PPA2 | 0.15 | 0.04 | lasso | 6 | 0.05 | 9.1e-04 | 5.6 | -6.2 | 5.3e-10 | 0.37 | 0.12 | 0.19 | FALSE |
5 | GTEx | Adrenal Gland | INTS12 | 0.23 | 0.02 | enet | 21 | 0.04 | 1.4e-02 | 2.7 | -7.5 | 5.7e-14 | 0.06 | 0.18 | 0.07 | TRUE |
6 | GTEx | Artery Aorta | PPA2 | 0.11 | -0.01 | enet | 24 | 0.01 | 1.6e-01 | -10.5 | -9.4 | 8.1e-21 | 0.68 | 0.01 | 0.86 | FALSE |
7 | GTEx | Artery Aorta | INTS12 | 0.13 | 0.14 | lasso | 3 | 0.14 | 6.5e-08 | 8.4 | -8.6 | 9.7e-18 | 0.09 | 0.69 | 0.28 | FALSE |
8 | GTEx | Brain Cerebellum | PPA2 | 0.22 | 0.01 | lasso | 4 | 0.03 | 3.7e-02 | -7.0 | -5.3 | 8.8e-08 | 0.56 | 0.08 | 0.16 | FALSE |
9 | GTEx | Brain Cortex | PPA2 | 0.14 | 0.09 | lasso | 9 | 0.09 | 1.6e-03 | -7.9 | -8.0 | 1.1e-15 | 0.79 | 0.06 | 0.60 | FALSE |
10 | GTEx | Cells EBV-transformed lymphocytes | GSTCD | 0.16 | 0.07 | lasso | 17 | 0.03 | 4.3e-02 | 8.5 | 8.9 | 4.2e-19 | -0.08 | 0.36 | 0.12 | TRUE |
11 | GTEx | Cells Transformed fibroblasts | PPA2 | 0.11 | 0.03 | lasso | 3 | 0.01 | 6.5e-02 | -4.6 | -5.2 | 2.2e-07 | 0.59 | 0.28 | 0.38 | TRUE |
12 | GTEx | Cells Transformed fibroblasts | INTS12 | 0.15 | 0.16 | lasso | 9 | 0.17 | 9.5e-13 | 8.5 | -9.2 | 5.3e-20 | 0.08 | 0.84 | 0.16 | FALSE |
13 | GTEx | Esophagus Gastroesophageal Junction | PPA2 | 0.29 | 0.15 | lasso | 5 | 0.14 | 8.8e-06 | -10.5 | -9.8 | 6.6e-23 | 0.89 | 0.00 | 0.99 | TRUE |
14 | GTEx | Esophagus Mucosa | PPA2 | 0.18 | 0.06 | enet | 14 | 0.12 | 2.5e-08 | 7.4 | -9.1 | 7.8e-20 | 0.75 | 0.02 | 0.98 | FALSE |
15 | GTEx | Esophagus Muscularis | INTS12 | 0.12 | 0.10 | lasso | 15 | 0.10 | 1.3e-06 | 9.2 | -8.9 | 6.7e-19 | 0.06 | 0.81 | 0.17 | FALSE |
16 | GTEx | Heart Atrial Appendage | PPA2 | 0.15 | 0.05 | lasso | 7 | 0.06 | 7.4e-04 | -7.7 | -6.9 | 5.1e-12 | 0.65 | 0.19 | 0.50 | FALSE |
17 | GTEx | Lung | PPA2 | 0.09 | 0.02 | enet | 16 | 0.03 | 1.4e-03 | 3.1 | -6.4 | 1.8e-10 | 0.49 | 0.14 | 0.52 | FALSE |
18 | GTEx | Lung | NPNT | 0.07 | 0.02 | enet | 24 | 0.04 | 2.3e-04 | 9.2 | -5.7 | 1.0e-08 | 0.00 | 0.04 | 0.92 | FALSE |
19 | GTEx | Muscle Skeletal | PPA2 | 0.19 | 0.06 | enet | 28 | 0.11 | 8.7e-11 | -7.3 | -5.2 | 2.0e-07 | 0.60 | 0.69 | 0.30 | FALSE |
20 | GTEx | Nerve Tibial | PPA2 | 0.13 | 0.07 | enet | 23 | 0.07 | 2.1e-05 | -7.0 | -6.9 | 5.2e-12 | 0.59 | 0.24 | 0.63 | FALSE |
21 | GTEx | Nerve Tibial | GSTCD | 0.09 | 0.03 | enet | 16 | 0.02 | 1.3e-02 | 8.0 | 9.2 | 5.7e-20 | -0.13 | 0.56 | 0.05 | FALSE |
22 | GTEx | Ovary | PPA2 | 0.18 | 0.10 | lasso | 3 | 0.14 | 2.2e-04 | -7.0 | -7.3 | 2.6e-13 | 0.69 | 0.02 | 0.90 | FALSE |
23 | GTEx | Pituitary | GSTCD | 0.28 | 0.14 | lasso | 5 | 0.09 | 2.8e-03 | 8.4 | 7.8 | 5.7e-15 | -0.12 | 0.33 | 0.10 | FALSE |
24 | GTEx | Skin Sun Exposed Lower leg | PPA2 | 0.09 | 0.07 | lasso | 3 | 0.04 | 4.3e-04 | 5.6 | -5.4 | 5.9e-08 | 0.29 | 0.67 | 0.02 | FALSE |
25 | GTEx | Skin Sun Exposed Lower leg | GSTCD | 0.08 | 0.02 | lasso | 6 | 0.01 | 3.8e-02 | 7.8 | 9.1 | 9.0e-20 | -0.14 | 0.68 | 0.15 | FALSE |
26 | GTEx | Skin Sun Exposed Lower leg | TET2 | 0.09 | 0.01 | enet | 18 | 0.02 | 3.6e-03 | -10.0 | -6.4 | 1.3e-10 | 0.63 | 0.05 | 0.72 | FALSE |
27 | GTEx | Thyroid | INTS12 | 0.07 | 0.05 | lasso | 7 | 0.03 | 1.2e-03 | 9.2 | -9.2 | 2.3e-20 | 0.08 | 0.70 | 0.20 | FALSE |
28 | ROSMAP | Brain Pre-frontal Cortex | PPA2 | 0.32 | 0.38 | lasso | 2 | 0.38 | 1.1e-51 | 5.6 | -6.1 | 1.3e-09 | 0.38 | 1.00 | 0.00 | FALSE |
29 | YFS | Blood | PPA2 | 0.22 | 0.05 | lasso | 19 | 0.12 | 9.7e-38 | -3.5 | 5.2 | 2.3e-07 | -0.48 | 1.00 | 0.00 | FALSE |
30 | The Cancer Genome Atlas | Bladder Urothelial Carcinoma | INTS12 | 0.04 | 0.03 | blup | 51 | 0.04 | 3.9e-04 | 8.5 | -8.8 | 1.9e-18 | 0.13 | 0.01 | 0.96 | FALSE |
31 | The Cancer Genome Atlas | Breast Invasive Carcinoma | INTS12 | 0.04 | 0.03 | blup | 49 | 0.04 | 7.1e-08 | 8.4 | -9.6 | 5.2e-22 | 0.09 | 0.01 | 0.99 | FALSE |
32 | The Cancer Genome Atlas | Cervical Squamous Cell Carcinoma | INTS12 | 0.12 | 0.06 | blup | 50 | 0.08 | 1.2e-04 | 9.2 | -9.6 | 5.2e-22 | 0.10 | 0.01 | 0.98 | FALSE |
33 | The Cancer Genome Atlas | Head and Neck Squamous Cell Carcinoma | INTS12 | 0.03 | 0.02 | blup | 49 | 0.02 | 6.4e-03 | 9.2 | -9.7 | 2.5e-22 | 0.11 | 0.01 | 0.87 | TRUE |
34 | The Cancer Genome Atlas | Kidney Renal Clear Cell Carcinoma | INTS12 | 0.08 | 0.10 | lasso | 2 | 0.10 | 2.9e-11 | 9.2 | -9.2 | 2.8e-20 | 0.08 | 0.01 | 0.99 | FALSE |
35 | The Cancer Genome Atlas | Kidney Renal Clear Cell Carcinoma | PPA2 | 0.11 | 0.03 | blup | 84 | 0.03 | 4.7e-04 | -7.0 | -5.4 | 7.3e-08 | 0.55 | 0.22 | 0.61 | TRUE |
36 | The Cancer Genome Atlas | Kidney Renal Papillary Cell Carcinoma | INTS12 | 0.32 | 0.00 | blup | 49 | 0.06 | 1.8e-04 | 8.4 | -9.4 | 8.2e-21 | 0.09 | 0.01 | 0.80 | FALSE |
37 | The Cancer Genome Atlas | Brain Lower Grade Glioma | GSTCD | 0.07 | 0.05 | lasso | 4 | 0.04 | 6.6e-05 | 9.4 | 9.7 | 4.6e-22 | -0.09 | 0.01 | 0.99 | FALSE |
38 | The Cancer Genome Atlas | Lung Adenocarcinoma | INTS12 | 0.08 | 0.10 | enet | 11 | 0.10 | 9.9e-12 | 9.2 | -8.9 | 3.6e-19 | 0.10 | 0.01 | 0.99 | TRUE |
39 | The Cancer Genome Atlas | Ovarian Serous Cystadenocarcinoma | INTS12 | 0.03 | 0.01 | blup | 49 | 0.03 | 6.0e-03 | 5.4 | -7.5 | 8.5e-14 | 0.16 | 0.02 | 0.64 | FALSE |
40 | The Cancer Genome Atlas | Pancreatic Adenocarcinoma | INTS12 | 0.22 | 0.15 | lasso | 6 | 0.16 | 2.3e-07 | 8.5 | -8.8 | 1.3e-18 | 0.06 | 0.02 | 0.96 | FALSE |
41 | The Cancer Genome Atlas | Prostate Adenocarcinoma | INTS12 | 0.15 | 0.11 | lasso | 3 | 0.17 | 2.1e-17 | 4.8 | -7.8 | 6.8e-15 | 0.15 | 0.05 | 0.95 | FALSE |
42 | The Cancer Genome Atlas | Stomach Adenocarcinoma | GSTCD | 0.04 | 0.06 | lasso | 1 | 0.05 | 9.1e-05 | 9.1 | 9.1 | 1.0e-19 | -0.09 | 0.03 | 0.89 | FALSE |
43 | The Cancer Genome Atlas | Thyroid Carcinoma | INTS12 | 0.11 | 0.09 | blup | 49 | 0.11 | 1.3e-10 | 9.2 | -9.1 | 1.4e-19 | 0.13 | 0.01 | 0.99 | FALSE |
44 | The Cancer Genome Atlas | Thyroid Carcinoma | PPA2 | 0.04 | 0.02 | blup | 84 | 0.04 | 6.1e-05 | -7.3 | -6.8 | 1.5e-11 | 0.72 | 0.14 | 0.66 | FALSE |