Best TWAS P=7.68e-18 · Best GWAS P=1.65e-15 conditioned to 0.115
# | 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 | Adrenal Gland | TPM2 | 0.29 | 0.22 | lasso | 5 | 0.25 | 1.8e-09 | 8.0 | -6.6 | 4.0e-11 | -0.96 | 0.00 | 1.00 | FALSE |
2 | GTEx | Artery Aorta | GBA2 | 0.15 | 0.10 | lasso | 6 | 0.07 | 9.8e-05 | -5.3 | 5.3 | 1.4e-07 | 0.17 | 0.67 | 0.07 | FALSE |
3 | GTEx | Artery Aorta | SPAG8 | 0.11 | 0.10 | lasso | 7 | 0.06 | 2.0e-04 | 6.5 | -6.8 | 1.1e-11 | -0.74 | 0.08 | 0.90 | FALSE |
4 | GTEx | Artery Tibial | NPR2 | 0.15 | 0.03 | enet | 17 | 0.13 | 3.6e-10 | 0.5 | 5.9 | 3.6e-09 | 0.65 | 0.02 | 0.98 | FALSE |
5 | GTEx | Brain Cerebellar Hemisphere | TPM2 | 0.56 | 0.55 | lasso | 3 | 0.56 | 2.7e-17 | 8.0 | -8.0 | 1.1e-15 | -1.00 | 0.00 | 1.00 | FALSE |
6 | GTEx | Brain Cerebellum | TPM2 | 0.63 | 0.43 | lasso | 4 | 0.53 | 4.0e-18 | 8.0 | -8.1 | 7.2e-16 | -0.98 | 0.00 | 1.00 | FALSE |
7 | GTEx | Brain Cerebellum | RMRP | 0.27 | 0.00 | enet | 15 | 0.02 | 7.9e-02 | 1.2 | 5.3 | 1.2e-07 | 0.25 | 0.06 | 0.10 | FALSE |
8 | GTEx | Brain Hippocampus | TMEM8B | 0.27 | 0.14 | enet | 15 | 0.14 | 4.4e-04 | 8.0 | -6.2 | 4.7e-10 | -0.81 | 0.02 | 0.86 | FALSE |
9 | GTEx | Brain Nucleus accumbens basal ganglia | TPM2 | 0.29 | 0.30 | lasso | 8 | 0.29 | 2.0e-08 | 8.0 | -7.3 | 2.9e-13 | -0.98 | 0.00 | 1.00 | FALSE |
10 | GTEx | Breast Mammary Tissue (Female) | OR13E1P | 0.06 | 0.05 | lasso | 2 | 0.01 | 1.4e-01 | 6.1 | -6.1 | 9.5e-10 | -0.59 | 0.05 | 0.12 | FALSE |
11 | GTEx | Cells EBV-transformed lymphocytes | ARHGEF39 | 0.28 | 0.00 | enet | 10 | 0.01 | 1.0e-01 | 4.4 | -5.8 | 7.3e-09 | -0.48 | 0.05 | 0.33 | FALSE |
12 | GTEx | Liver | NPR2 | 0.18 | 0.04 | lasso | 3 | 0.02 | 1.1e-01 | 6.7 | -6.7 | 1.9e-11 | -0.69 | 0.10 | 0.40 | FALSE |
13 | GTEx | Muscle Skeletal | GBA2 | 0.15 | 0.11 | lasso | 5 | 0.08 | 1.4e-08 | -5.2 | -5.1 | 2.7e-07 | -0.16 | 1.00 | 0.00 | FALSE |
14 | GTEx | Muscle Skeletal | TPM2 | 0.06 | 0.02 | lasso | 5 | 0.02 | 6.2e-03 | 7.9 | 8.6 | 7.7e-18 | 0.82 | 0.01 | 0.98 | TRUE |
15 | GTEx | Nerve Tibial | GBA2 | 0.11 | 0.11 | lasso | 1 | 0.09 | 3.4e-07 | -5.3 | 5.3 | 1.3e-07 | 0.19 | 0.98 | 0.01 | FALSE |
16 | GTEx | Pancreas | TPM2 | 0.11 | 0.15 | lasso | 2 | 0.14 | 1.8e-06 | 8.0 | -8.0 | 1.5e-15 | -1.00 | 0.00 | 0.99 | FALSE |
17 | GTEx | Thyroid | RP11-112J3.16 | 0.26 | 0.13 | lasso | 7 | 0.13 | 1.9e-10 | 6.4 | -5.1 | 2.9e-07 | -0.59 | 0.99 | 0.01 | FALSE |
18 | GTEx | Vagina | TMEM8B | 0.30 | 0.04 | enet | 31 | 0.04 | 4.5e-02 | 6.0 | -5.1 | 2.9e-07 | -0.43 | 0.06 | 0.10 | FALSE |
19 | GTEx | Whole Blood | GBA2 | 0.10 | 0.07 | lasso | 4 | 0.04 | 5.4e-05 | -5.2 | -5.6 | 1.7e-08 | -0.20 | 0.99 | 0.00 | FALSE |
20 | METSIM | Adipose | TPM2 | 0.12 | 0.13 | lasso | 5 | 0.14 | 1.1e-19 | 8.0 | -7.2 | 6.4e-13 | -0.99 | 0.00 | 1.00 | FALSE |
21 | NTR | Blood | RGP1 | 0.03 | 0.03 | lasso | 1 | 0.02 | 2.1e-08 | -5.3 | 5.3 | 1.3e-07 | 0.18 | 1.00 | 0.00 | FALSE |
22 | NTR | Blood | TPM2 | 0.04 | 0.04 | lasso | 4 | 0.04 | 2.3e-13 | 7.8 | -8.0 | 1.2e-15 | -0.98 | 0.00 | 1.00 | FALSE |
23 | ROSMAP | Brain Pre-frontal Cortex | TPM2 | 0.55 | 0.60 | enet | 21 | 0.61 | 1.1e-100 | 7.9 | -7.6 | 3.1e-14 | -0.99 | 0.00 | 1.00 | FALSE |
24 | ROSMAP | Brain Pre-frontal Cortex | RP11-112J3.16 | 0.11 | 0.12 | bslmm | 410 | 0.11 | 1.5e-13 | 6.4 | -5.9 | 4.0e-09 | -0.60 | 1.00 | 0.00 | FALSE |
25 | YFS | Blood | TPM2 | 0.46 | 0.50 | enet | 22 | 0.50 | 1.1e-194 | 8.0 | -7.8 | 5.5e-15 | -0.98 | 0.00 | 1.00 | FALSE |
26 | The Cancer Genome Atlas | Breast Invasive Carcinoma | C9orf128 | 0.14 | 0.15 | blup | 50 | 0.16 | 1.4e-32 | 6.2 | -6.1 | 1.3e-09 | -0.60 | 0.08 | 0.92 | FALSE |
27 | The Cancer Genome Atlas | Cervical Squamous Cell Carcinoma | GBA2 | 0.07 | 0.03 | blup | 44 | 0.03 | 1.1e-02 | -4.0 | -7.7 | 1.9e-14 | -0.63 | 0.03 | 0.26 | FALSE |
28 | The Cancer Genome Atlas | Colon Adenocarcinoma | C9orf128 | 0.07 | 0.03 | blup | 50 | 0.06 | 2.3e-04 | 6.1 | -5.5 | 3.5e-08 | -0.61 | 0.02 | 0.91 | FALSE |
29 | The Cancer Genome Atlas | Esophageal Carcinoma | GBA2 | 0.11 | 0.10 | lasso | 1 | 0.08 | 1.8e-03 | -5.2 | -5.2 | 1.7e-07 | -0.19 | 0.05 | 0.16 | FALSE |
30 | The Cancer Genome Atlas | Head and Neck Squamous Cell Carcinoma | GBA2 | 0.05 | 0.05 | blup | 44 | 0.05 | 3.7e-06 | -6.5 | -7.2 | 8.2e-13 | -0.44 | 0.87 | 0.09 | FALSE |
31 | The Cancer Genome Atlas | Kidney Renal Papillary Cell Carcinoma | GBA2 | 0.07 | 0.08 | lasso | 4 | 0.07 | 6.4e-05 | -5.3 | -5.3 | 1.3e-07 | -0.18 | 0.27 | 0.04 | FALSE |
32 | The Cancer Genome Atlas | Kidney Renal Papillary Cell Carcinoma | TPM2 | 0.11 | 0.08 | enet | 6 | 0.11 | 1.0e-06 | 7.8 | -7.1 | 1.2e-12 | -0.85 | 0.01 | 0.98 | FALSE |
33 | The Cancer Genome Atlas | Brain Lower Grade Glioma | TPM2 | 0.11 | 0.16 | lasso | 5 | 0.17 | 3.5e-19 | 7.8 | -6.7 | 2.1e-11 | -0.96 | 0.01 | 0.99 | FALSE |
34 | The Cancer Genome Atlas | Lung Adenocarcinoma | C9orf128 | 0.07 | 0.07 | lasso | 2 | 0.07 | 1.6e-08 | 6.2 | -5.8 | 6.7e-09 | -0.55 | 0.05 | 0.95 | FALSE |
35 | The Cancer Genome Atlas | Lung Squamous Cell Carcinoma | C9orf128 | 0.02 | 0.01 | blup | 50 | 0.01 | 2.3e-02 | 6.1 | -6.5 | 7.6e-11 | -0.60 | 0.04 | 0.77 | FALSE |
36 | The Cancer Genome Atlas | Prostate Adenocarcinoma | C9orf128 | 0.11 | 0.18 | lasso | 2 | 0.16 | 3.7e-16 | 6.1 | -6.1 | 1.3e-09 | -0.57 | 0.04 | 0.96 | FALSE |
37 | The Cancer Genome Atlas | Prostate Adenocarcinoma | TMEM8B | 0.04 | 0.02 | blup | 58 | 0.05 | 1.5e-05 | 6.4 | 6.0 | 1.7e-09 | 0.50 | 0.02 | 0.98 | FALSE |
38 | The Cancer Genome Atlas | Stomach Adenocarcinoma | C9orf128 | 0.04 | 0.06 | lasso | 2 | 0.05 | 2.8e-04 | 6.2 | -6.2 | 4.8e-10 | -0.70 | 0.02 | 0.80 | FALSE |
39 | The Cancer Genome Atlas | Stomach Adenocarcinoma | GBA2 | 0.04 | 0.03 | blup | 44 | 0.02 | 1.0e-02 | -5.3 | -7.2 | 9.0e-13 | -0.48 | 0.07 | 0.06 | FALSE |
40 | The Cancer Genome Atlas | Thyroid Carcinoma | C9orf128 | 0.12 | 0.19 | lasso | 1 | 0.20 | 8.5e-19 | 6.1 | -6.1 | 1.3e-09 | -0.57 | 0.12 | 0.88 | FALSE |
41 | The Cancer Genome Atlas | Uterine Corpus Endometrial Carcinoma | SPAG8 | 0.18 | 0.07 | blup | 47 | 0.09 | 1.7e-03 | 5.9 | -6.9 | 6.0e-12 | -0.54 | 0.02 | 0.25 | FALSE |