Best TWAS P=2.1e-33 · Best GWAS P=3.57e-29 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 | GTEx | Adipose Subcutaneous | PRDX5 | 0.06 | 0.03 | lasso | 5 | 0.03 | 1.7e-03 | 6.19 | -7.8 | 7.1e-15 | -0.49 | 0.16 | 0.24 | TRUE |
2 | GTEx | Adipose Subcutaneous | RAD9A | 0.43 | 0.22 | lasso | 6 | 0.23 | 7.1e-19 | -5.87 | -5.6 | 2.7e-08 | -0.04 | 0.00 | 1.00 | FALSE |
3 | GTEx | Adipose Subcutaneous | RP11-554A11.9 | 0.34 | 0.13 | enet | 43 | 0.26 | 4.1e-21 | -4.74 | -5.5 | 4.6e-08 | 0.03 | 1.00 | 0.00 | TRUE |
4 | GTEx | Adrenal Gland | LRP5 | 0.25 | 0.14 | lasso | 4 | 0.06 | 2.5e-03 | 4.58 | 5.3 | 1.1e-07 | 0.02 | 0.06 | 0.62 | FALSE |
5 | GTEx | Artery Aorta | PPP1R14B | 0.12 | 0.03 | lasso | 4 | 0.08 | 3.0e-05 | -3.92 | 6.1 | 9.6e-10 | 0.30 | 0.51 | 0.15 | FALSE |
6 | GTEx | Artery Aorta | RP11-554A11.9 | 0.37 | 0.18 | enet | 23 | 0.27 | 3.3e-15 | -4.74 | -6.2 | 4.2e-10 | 0.02 | 1.00 | 0.00 | TRUE |
7 | GTEx | Artery Tibial | NDUFV1 | 0.04 | 0.07 | lasso | 3 | 0.04 | 2.4e-04 | -5.23 | -5.2 | 1.7e-07 | 0.00 | 0.04 | 0.92 | FALSE |
8 | GTEx | Artery Tibial | RAD9A | 0.39 | 0.26 | lasso | 2 | 0.24 | 3.5e-19 | -5.87 | -5.8 | 4.9e-09 | -0.05 | 0.00 | 1.00 | FALSE |
9 | GTEx | Artery Tibial | RP11-554A11.9 | 0.34 | 0.06 | enet | 35 | 0.22 | 4.0e-17 | 4.15 | -6.1 | 1.1e-09 | 0.00 | 1.00 | 0.00 | TRUE |
10 | GTEx | Brain Cerebellum | RP11-554A11.9 | 0.59 | 0.16 | enet | 29 | 0.33 | 1.4e-10 | -1.13 | -5.7 | 9.7e-09 | 0.03 | 0.39 | 0.06 | FALSE |
11 | GTEx | Brain Frontal Cortex BA9 | PACS1 | 0.17 | 0.14 | enet | 18 | 0.18 | 1.7e-05 | 3.12 | -5.1 | 3.1e-07 | 0.04 | 0.28 | 0.05 | FALSE |
12 | GTEx | Breast Mammary Tissue | KAT5 | 0.15 | 0.06 | lasso | 10 | 0.02 | 2.1e-02 | -8.16 | -8.7 | 3.7e-18 | 0.04 | 0.03 | 0.68 | TRUE |
13 | GTEx | Breast Mammary Tissue (Male) | KAT5 | 0.05 | -0.01 | lasso | 4 | -0.01 | 7.4e-01 | -8.27 | -6.5 | 6.7e-11 | 0.05 | 0.02 | 0.35 | FALSE |
14 | GTEx | Breast Mammary Tissue (Female) | PPP1R14B | 0.10 | 0.06 | lasso | 2 | 0.08 | 2.0e-03 | 7.58 | 7.0 | 2.3e-12 | 0.31 | 0.05 | 0.05 | FALSE |
15 | GTEx | Breast Mammary Tissue (Female) | RP11-554A11.9 | 0.40 | 0.25 | enet | 18 | 0.30 | 1.5e-09 | -4.74 | -6.8 | 9.2e-12 | 0.01 | 0.56 | 0.05 | TRUE |
16 | GTEx | Cells Transformed fibroblasts | RP11-554A11.9 | 0.25 | 0.06 | enet | 18 | 0.14 | 2.0e-10 | 3.34 | -7.4 | 1.6e-13 | -0.04 | 0.99 | 0.00 | TRUE |
17 | GTEx | Esophagus Mucosa | TPCN2 | 0.20 | 0.07 | lasso | 8 | 0.06 | 5.6e-05 | 4.21 | 5.7 | 9.4e-09 | 0.07 | 0.62 | 0.11 | FALSE |
18 | GTEx | Esophagus Mucosa | PACS1 | 0.08 | 0.01 | lasso | 5 | 0.01 | 7.9e-02 | 4.37 | -5.2 | 1.9e-07 | 0.05 | 0.38 | 0.09 | TRUE |
19 | GTEx | Esophagus Mucosa | SIPA1 | 0.34 | 0.17 | lasso | 6 | 0.20 | 1.6e-13 | -7.04 | 6.5 | 7.4e-11 | 0.00 | 0.96 | 0.04 | FALSE |
20 | GTEx | Esophagus Mucosa | DOC2GP | 0.16 | 0.14 | lasso | 5 | 0.11 | 1.0e-07 | -5.23 | 5.2 | 2.2e-07 | 0.00 | 0.04 | 0.96 | FALSE |
21 | GTEx | Esophagus Mucosa | RP11-554A11.9 | 0.23 | 0.18 | lasso | 3 | 0.18 | 4.0e-12 | -4.74 | -5.2 | 1.7e-07 | -0.02 | 1.00 | 0.00 | FALSE |
22 | GTEx | Esophagus Muscularis | NUDT8 | 0.07 | 0.05 | lasso | 2 | 0.03 | 9.9e-03 | -5.23 | -5.2 | 1.7e-07 | 0.01 | 0.03 | 0.90 | FALSE |
23 | GTEx | Esophagus Muscularis | RAD9A | 0.25 | 0.26 | lasso | 2 | 0.26 | 6.2e-16 | -5.87 | -5.9 | 3.3e-09 | -0.05 | 0.00 | 1.00 | TRUE |
24 | GTEx | Esophagus Muscularis | RP11-554A11.9 | 0.31 | 0.18 | lasso | 9 | 0.22 | 1.4e-13 | -4.74 | -5.5 | 3.9e-08 | 0.01 | 1.00 | 0.00 | FALSE |
25 | GTEx | Heart Atrial Appendage | VEGFB | 0.21 | 0.01 | enet | 21 | 0.07 | 3.0e-04 | 8.89 | -8.7 | 2.4e-18 | -0.65 | 0.01 | 0.93 | TRUE |
26 | GTEx | Heart Left Ventricle | RP11-554A11.9 | 0.16 | 0.11 | lasso | 3 | 0.09 | 2.2e-05 | -4.74 | -5.2 | 1.6e-07 | 0.00 | 0.38 | 0.05 | TRUE |
27 | GTEx | Muscle Skeletal | RP11-554A11.9 | 0.24 | 0.01 | lasso | 8 | 0.12 | 2.0e-11 | 4.15 | -5.5 | 3.6e-08 | 0.00 | 0.94 | 0.00 | FALSE |
28 | GTEx | Nerve Tibial | PRDX5 | 0.10 | 0.01 | lasso | 5 | 0.04 | 9.8e-04 | 6.43 | -5.3 | 1.4e-07 | -0.21 | 0.30 | 0.10 | FALSE |
29 | GTEx | Nerve Tibial | RAD9A | 0.53 | 0.24 | lasso | 10 | 0.23 | 5.6e-16 | -5.87 | -5.7 | 1.2e-08 | -0.05 | 0.00 | 1.00 | FALSE |
30 | GTEx | Skin Not Sun Exposed Suprapubic | PRDX5 | 0.13 | 0.12 | lasso | 2 | 0.11 | 1.5e-06 | 7.65 | -7.3 | 3.8e-13 | -0.35 | 0.59 | 0.06 | TRUE |
31 | GTEx | Skin Sun Exposed Lower leg | PRDX5 | 0.08 | 0.07 | enet | 16 | 0.05 | 1.0e-04 | 7.65 | -5.7 | 1.3e-08 | -0.22 | 0.75 | 0.01 | FALSE |
32 | GTEx | Spleen | CTD-3074O7.5 | 0.29 | 0.03 | enet | 27 | 0.05 | 2.6e-02 | -0.48 | -5.9 | 4.4e-09 | 0.00 | 0.05 | 0.08 | FALSE |
33 | GTEx | Testis | RAD9A | 0.72 | 0.50 | lasso | 4 | 0.49 | 1.1e-24 | -5.87 | -5.8 | 6.1e-09 | -0.05 | 0.00 | 1.00 | FALSE |
34 | GTEx | Vagina | RP11-755F10.1 | 0.39 | 0.02 | lasso | 6 | 0.09 | 3.9e-03 | 3.26 | 5.6 | 1.7e-08 | -0.11 | 0.08 | 0.23 | FALSE |
35 | METSIM | Adipose | BANF1 | 0.10 | 0.06 | bslmm | 343 | 0.07 | 4.9e-10 | -5.12 | 6.0 | 1.6e-09 | -0.02 | 1.00 | 0.00 | FALSE |
36 | METSIM | Adipose | LTBP3 | 0.03 | 0.00 | bslmm | 369 | 0.01 | 1.5e-02 | 0.15 | 5.2 | 1.7e-07 | -0.05 | 0.09 | 0.12 | FALSE |
37 | METSIM | Adipose | MYEOV | 0.30 | 0.24 | lasso | 8 | 0.25 | 1.1e-37 | 6.87 | -8.3 | 1.3e-16 | 0.04 | 1.00 | 0.00 | TRUE |
38 | METSIM | Adipose | SART1 | 0.08 | 0.05 | enet | 26 | 0.05 | 1.1e-07 | -5.04 | 6.8 | 9.0e-12 | 0.05 | 1.00 | 0.00 | FALSE |
39 | METSIM | Adipose | VEGFB | 0.12 | 0.06 | enet | 17 | 0.08 | 6.5e-12 | 10.19 | -11.7 | 8.4e-32 | -0.77 | 0.01 | 0.99 | FALSE |
40 | NTR | Blood | BANF1 | 0.03 | 0.00 | enet | 10 | 0.02 | 1.1e-06 | 3.19 | 5.3 | 1.1e-07 | 0.05 | 0.17 | 0.13 | TRUE |
41 | NTR | Blood | ORAOV1 | 0.04 | 0.02 | lasso | 2 | 0.02 | 2.3e-07 | 5.30 | -5.3 | 1.1e-07 | 0.07 | 1.00 | 0.00 | TRUE |
42 | ROSMAP | Brain Pre-frontal Cortex | DNAJC4 | 0.11 | 0.00 | enet | 31 | 0.02 | 4.2e-04 | 10.90 | -7.4 | 1.4e-13 | -0.51 | 0.00 | 0.94 | TRUE |
43 | ROSMAP | Brain Pre-frontal Cortex | PPP6R3 | 0.04 | 0.01 | blup | 421 | 0.02 | 3.2e-04 | 3.64 | -5.4 | 7.6e-08 | 0.07 | 0.69 | 0.07 | TRUE |
44 | ROSMAP | Brain Pre-frontal Cortex | PRDX5 | 0.10 | 0.05 | lasso | 6 | 0.08 | 2.8e-10 | 4.01 | -5.8 | 6.0e-09 | -0.13 | 1.00 | 0.00 | TRUE |
45 | ROSMAP | Brain Pre-frontal Cortex | CTSW | 0.06 | 0.03 | bslmm | 328 | 0.03 | 3.6e-05 | 1.53 | -5.8 | 6.1e-09 | 0.09 | 0.40 | 0.35 | FALSE |
46 | ROSMAP | Brain Pre-frontal Cortex | VEGFB | 0.10 | 0.07 | enet | 6 | 0.05 | 1.5e-07 | 10.90 | -12.0 | 2.1e-33 | -0.77 | 0.02 | 0.98 | TRUE |
47 | ROSMAP | Brain Pre-frontal Cortex | DOC2GP | 0.06 | 0.06 | lasso | 4 | 0.06 | 2.4e-08 | -5.23 | 5.3 | 1.1e-07 | -0.03 | 0.04 | 0.96 | FALSE |
48 | YFS | Blood | BANF1 | 0.14 | 0.19 | bslmm | 342 | 0.21 | 8.3e-67 | -4.95 | 5.5 | 4.3e-08 | 0.02 | 1.00 | 0.00 | FALSE |
49 | YFS | Blood | CCDC88B | 0.49 | 0.54 | bslmm | 346 | 0.59 | 1.9e-249 | -4.13 | 5.2 | 1.6e-07 | 0.21 | 1.00 | 0.00 | TRUE |
50 | YFS | Blood | GPR137 | 0.03 | 0.02 | lasso | 5 | 0.02 | 1.5e-08 | 7.58 | 6.8 | 7.7e-12 | 0.26 | 0.97 | 0.02 | FALSE |
51 | The Cancer Genome Atlas | Breast Invasive Carcinoma | EIF1AD | 0.02 | 0.03 | blup | 42 | 0.03 | 4.3e-07 | -5.11 | -5.4 | 7.8e-08 | 0.01 | 0.01 | 0.98 | FALSE |
52 | The Cancer Genome Atlas | Cervical Squamous Cell Carcinoma | TSGA10IP | 0.19 | 0.01 | lasso | 5 | 0.02 | 2.2e-02 | -5.11 | 5.2 | 2.6e-07 | 0.02 | 0.01 | 0.82 | FALSE |
53 | The Cancer Genome Atlas | Colon Adenocarcinoma | TBX10 | 0.11 | 0.08 | lasso | 2 | 0.07 | 7.5e-05 | -5.46 | -5.5 | 4.5e-08 | 0.03 | 0.00 | 0.99 | TRUE |
54 | The Cancer Genome Atlas | Head and Neck Squamous Cell Carcinoma | SIPA1 | 0.06 | 0.04 | blup | 43 | 0.05 | 4.6e-06 | -8.70 | 8.5 | 1.9e-17 | 0.00 | 0.00 | 0.99 | FALSE |
55 | The Cancer Genome Atlas | Kidney Renal Clear Cell Carcinoma | KCNK7 | 0.04 | 0.01 | blup | 42 | 0.01 | 1.2e-02 | 3.23 | -5.9 | 4.3e-09 | 0.03 | 0.35 | 0.23 | FALSE |
56 | The Cancer Genome Atlas | Kidney Renal Clear Cell Carcinoma | MAP3K11 | 0.06 | 0.03 | lasso | 4 | 0.03 | 2.1e-04 | -8.70 | 8.4 | 5.5e-17 | -0.01 | 0.00 | 0.97 | FALSE |
57 | The Cancer Genome Atlas | Kidney Renal Clear Cell Carcinoma | SIPA1 | 0.04 | 0.00 | blup | 43 | 0.02 | 6.2e-03 | -7.04 | 8.2 | 3.7e-16 | 0.02 | 0.01 | 0.40 | FALSE |
58 | The Cancer Genome Atlas | Brain Lower Grade Glioma | TRMT112 | 0.10 | 0.02 | blup | 28 | 0.05 | 4.7e-06 | 6.19 | -5.9 | 4.0e-09 | -0.41 | 0.00 | 1.00 | FALSE |
59 | The Cancer Genome Atlas | Lung Squamous Cell Carcinoma | EIF1AD | 0.03 | 0.00 | blup | 42 | 0.01 | 2.5e-02 | -4.12 | -5.1 | 3.0e-07 | 0.03 | 0.01 | 0.31 | FALSE |
60 | The Cancer Genome Atlas | Lung Squamous Cell Carcinoma | SIPA1 | 0.09 | 0.03 | blup | 43 | 0.06 | 1.2e-07 | -7.04 | 7.2 | 8.3e-13 | -0.03 | 0.00 | 0.99 | FALSE |
61 | The Cancer Genome Atlas | Lung Squamous Cell Carcinoma | VEGFB | 0.06 | 0.00 | blup | 47 | 0.02 | 3.9e-03 | 11.21 | -8.6 | 7.1e-18 | -0.48 | 0.00 | 0.81 | FALSE |
62 | The Cancer Genome Atlas | Prostate Adenocarcinoma | MAP3K11 | 0.06 | 0.02 | blup | 47 | 0.03 | 1.4e-04 | -7.04 | 5.6 | 2.6e-08 | 0.03 | 0.05 | 0.33 | FALSE |
63 | The Cancer Genome Atlas | Soft Tissue Sarcoma | EIF1AD | 0.05 | 0.06 | blup | 42 | 0.02 | 1.3e-02 | -5.00 | -5.2 | 2.5e-07 | 0.00 | 0.01 | 0.90 | FALSE |
64 | The Cancer Genome Atlas | Soft Tissue Sarcoma | NEAT1 | 0.09 | 0.04 | blup | 31 | 0.07 | 5.6e-05 | 3.86 | 5.3 | 1.1e-07 | -0.08 | 0.02 | 0.93 | FALSE |
65 | The Cancer Genome Atlas | Skin Cutaneous Melanoma | SNX32 | 0.51 | 0.26 | blup | 60 | 0.36 | 1.9e-10 | 1.66 | 5.3 | 9.8e-08 | -0.11 | 0.27 | 0.64 | FALSE |
66 | The Cancer Genome Atlas | Thyroid Carcinoma | CATSPER1 | 0.03 | 0.01 | blup | 41 | 0.02 | 3.4e-03 | -5.04 | 5.3 | 1.1e-07 | -0.02 | 0.01 | 0.73 | FALSE |