Best TWAS P=1.67e-13 · Best GWAS P=7.33e-32 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 | LACTB2 | 0.07 | 0.09 | lasso | 5 | 0.08 | 3.7e-10 | 6.0 | -5.8 | 8.5e-09 | -0.01 | 0.19 | 0.81 | FALSE |
2 | CommonMind | Brain Pre-frontal Cortex | XKR9 | 0.26 | 0.52 | lasso | 13 | 0.51 | 1.6e-72 | 5.6 | 5.8 | 6.8e-09 | 0.01 | 0.74 | 0.26 | FALSE |
3 | GTEx | Artery Tibial | LACTB2 | 0.17 | 0.02 | enet | 26 | 0.06 | 1.0e-05 | -5.5 | -5.4 | 6.6e-08 | 0.04 | 0.09 | 0.90 | FALSE |
4 | GTEx | Cells Transformed fibroblasts | TRAM1 | 0.06 | 0.03 | enet | 17 | 0.03 | 3.0e-03 | -6.5 | -5.7 | 1.3e-08 | 0.03 | 0.03 | 0.96 | TRUE |
5 | GTEx | Cells Transformed fibroblasts | LACTB2 | 0.05 | 0.00 | enet | 4 | 0.02 | 1.6e-02 | 5.4 | -5.7 | 1.4e-08 | -0.03 | 0.20 | 0.48 | FALSE |
6 | GTEx | Nerve Tibial | LACTB2 | 0.07 | 0.06 | lasso | 2 | 0.04 | 1.5e-03 | 5.3 | -5.2 | 1.7e-07 | 0.00 | 0.41 | 0.54 | FALSE |
7 | GTEx | Pancreas | LACTB2 | 0.13 | 0.11 | enet | 19 | 0.05 | 3.3e-03 | 5.3 | -5.6 | 2.8e-08 | -0.02 | 0.21 | 0.72 | FALSE |
8 | GTEx | Skin Not Sun Exposed Suprapubic | LACTB2 | 0.07 | 0.07 | lasso | 2 | 0.07 | 7.5e-05 | 6.0 | -6.1 | 1.1e-09 | -0.01 | 0.13 | 0.85 | TRUE |
9 | GTEx | Skin Sun Exposed Lower leg | LACTB2 | 0.05 | 0.03 | lasso | 3 | 0.04 | 4.6e-04 | 6.0 | -5.3 | 8.8e-08 | -0.01 | 0.18 | 0.79 | FALSE |
10 | METSIM | Adipose | XKR9 | 0.17 | 0.37 | enet | 33 | 0.38 | 8.6e-60 | 5.6 | -5.4 | 7.6e-08 | -0.02 | 0.75 | 0.25 | FALSE |
11 | ROSMAP | Brain Pre-frontal Cortex | EYA1 | 0.13 | 0.05 | blup | 567 | 0.08 | 5.1e-10 | 11.7 | 7.4 | 1.7e-13 | 0.62 | 0.00 | 1.00 | TRUE |
12 | ROSMAP | Brain Pre-frontal Cortex | XKR9 | 0.22 | 0.38 | bslmm | 366 | 0.40 | 1.0e-54 | 5.6 | -6.5 | 7.1e-11 | 0.00 | 0.72 | 0.28 | TRUE |
13 | YFS | Blood | TRAM1 | 0.02 | 0.01 | enet | 22 | 0.02 | 8.1e-07 | 6.0 | -5.9 | 4.0e-09 | 0.06 | 0.15 | 0.80 | TRUE |
14 | The Cancer Genome Atlas | Breast Invasive Carcinoma | XKR9 | 0.25 | 0.51 | lasso | 8 | 0.51 | 2.4e-123 | 5.3 | -5.3 | 1.4e-07 | -0.01 | 0.07 | 0.93 | FALSE |
15 | The Cancer Genome Atlas | Cervical Squamous Cell Carcinoma | XKR9 | 0.35 | 0.42 | enet | 12 | 0.42 | 3.5e-22 | 5.6 | -5.7 | 1.1e-08 | -0.01 | 0.05 | 0.95 | FALSE |
16 | The Cancer Genome Atlas | Colon Adenocarcinoma | XKR9 | 0.32 | 0.44 | lasso | 12 | 0.45 | 7.9e-29 | 5.3 | -5.3 | 9.3e-08 | -0.01 | 0.06 | 0.94 | FALSE |
17 | The Cancer Genome Atlas | Glioblastoma Multiforme | XKR9 | 0.18 | 0.15 | enet | 19 | 0.20 | 1.1e-06 | 5.6 | -5.8 | 5.0e-09 | -0.01 | 0.05 | 0.94 | FALSE |
18 | The Cancer Genome Atlas | Head and Neck Squamous Cell Carcinoma | XKR9 | 0.21 | 0.38 | lasso | 6 | 0.38 | 4.6e-45 | 5.6 | -5.2 | 2.6e-07 | -0.01 | 0.06 | 0.94 | FALSE |
19 | The Cancer Genome Atlas | Kidney Renal Clear Cell Carcinoma | XKR9 | 0.34 | 0.51 | enet | 16 | 0.51 | 9.7e-66 | 5.3 | -5.7 | 1.3e-08 | -0.01 | 0.06 | 0.94 | FALSE |
20 | The Cancer Genome Atlas | Kidney Renal Papillary Cell Carcinoma | XKR9 | 0.45 | 0.55 | lasso | 3 | 0.57 | 1.2e-38 | 5.3 | -5.4 | 6.7e-08 | -0.01 | 0.07 | 0.93 | FALSE |
21 | The Cancer Genome Atlas | Brain Lower Grade Glioma | XKR9 | 0.18 | 0.35 | enet | 13 | 0.34 | 7.7e-40 | 5.6 | -5.2 | 1.5e-07 | -0.01 | 0.05 | 0.95 | FALSE |
22 | The Cancer Genome Atlas | Liver Hepatocellular Carcinoma | XKR9 | 0.40 | 0.46 | lasso | 5 | 0.46 | 5.5e-24 | 5.6 | -5.4 | 5.1e-08 | -0.01 | 0.06 | 0.94 | FALSE |
23 | The Cancer Genome Atlas | Lung Squamous Cell Carcinoma | XKR9 | 0.28 | 0.46 | lasso | 9 | 0.46 | 1.7e-57 | 5.6 | -5.3 | 1.5e-07 | -0.01 | 0.06 | 0.94 | FALSE |
24 | The Cancer Genome Atlas | Ovarian Serous Cystadenocarcinoma | XKR9 | 0.32 | 0.53 | lasso | 7 | 0.52 | 6.5e-40 | 5.6 | -5.5 | 3.7e-08 | -0.01 | 0.06 | 0.94 | FALSE |
25 | The Cancer Genome Atlas | Pheochromocytoma and Paraganglioma | XKR9 | 0.47 | 0.58 | enet | 13 | 0.59 | 1.5e-28 | 5.3 | -5.3 | 1.1e-07 | -0.02 | 0.06 | 0.94 | FALSE |
26 | The Cancer Genome Atlas | Prostate Adenocarcinoma | XKR9 | 0.51 | 0.62 | lasso | 7 | 0.64 | 4.7e-86 | 5.5 | -5.2 | 2.4e-07 | -0.01 | 0.06 | 0.94 | FALSE |
27 | The Cancer Genome Atlas | Stomach Adenocarcinoma | XKR9 | 0.22 | 0.26 | enet | 13 | 0.24 | 1.8e-17 | 5.6 | -5.5 | 4.2e-08 | 0.00 | 0.05 | 0.95 | FALSE |
28 | The Cancer Genome Atlas | Testicular Germ Cell Tumors | XKR9 | 0.33 | 0.33 | enet | 21 | 0.34 | 9.6e-13 | 5.6 | -5.6 | 1.6e-08 | -0.01 | 0.06 | 0.94 | FALSE |
29 | The Cancer Genome Atlas | Thyroid Carcinoma | LACTB2 | 0.03 | 0.01 | enet | 5 | 0.01 | 6.1e-02 | 5.6 | -6.7 | 2.9e-11 | -0.01 | 0.02 | 0.64 | FALSE |
30 | The Cancer Genome Atlas | Thyroid Carcinoma | XKR9 | 0.38 | 0.55 | lasso | 9 | 0.56 | 2.5e-65 | 5.6 | -5.6 | 2.4e-08 | -0.01 | 0.06 | 0.94 | FALSE |
31 | The Cancer Genome Atlas | Uterine Corpus Endometrial Carcinoma | XKR9 | 0.24 | 0.24 | lasso | 4 | 0.25 | 1.3e-07 | 5.6 | -5.9 | 4.7e-09 | -0.01 | 0.03 | 0.97 | TRUE |