Table 1.
Results of the PWAS of smoking initiation.
| Gene | Chr | Banner | ROSMAP | Validated | Coloc (PP > .8) | Conditionally independent | Overlap with TWAS eQTL | Overlap with TWAS sQTL | TWAS FOCUS (PIP > .5) | Novele | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PWAS Z | PWAS pa | PWAS Z | PWAS pb | |||||||||
| NT5C2 | 10 | 7.29 | 3.17E-13 | 7.55 | 4.42E-14 | Yes | Yes | Yes | Yes | No | ||
| ARPC1B | 7 | 5.94 | 2.83E-09 | No | No | |||||||
| HEBP1c | 12 | −5.71 | 1.14E-08 | -0.68 | 4.94E-01 | No | No | No | No | |||
| GMPPB | 3 | 5.62 | 1.89E-08 | 5.01 | 5.39E-07 | Yes | Yes | Yes | Yes | |||
| NQO1 | 16 | −5.32 | 1.05E-07 | -5.16 | 2.42E-07 | Yes | Yes | Yes | Yes | No | ||
| SRR | 17 | −5.04 | 4.73E-07 | -5.36 | 8.45E-08 | Yes | Yes | Yes | Yes | Yes | Yes | |
| RHOT2 | 16 | 4.94 | 7.74E-07 | 5.64 | 1.71E-08 | Yes | Yesd | Yes | No | |||
| ACTR1B | 2 | −4.92 | 8.68E-07 | -4.8 | 1.61E-06 | Yes | Yes | Yes | No | |||
| BTN3A3c | 6 | −4.91 | 8.93E-07 | -3.25 | 1.16E-03 | No | No | No | Yes | |||
| WIPI2c | 7 | 4.22 | 2.43E-05 | -2.89 | 0.00375 | No | No | No | No | |||
| BTN2A1 | 6 | −4.21 | 2.59E-05 | 4.55 | 5.44E-06 | Yes | No | No | No | |||
| GFM1 | 3 | −4.18 | 2.95E-05 | No | ||||||||
| MAP1LC3A | 20 | −4.1 | 4.13E-05 | No | ||||||||
| C10orf32 | 10 | -6.91 | 4.77E-12 | Yes | Yes | Yes | No | Yes | ||||
| TYW5 | 2 | 5.24 | 1.57E-07 | Yes | Yes | Yes | No | |||||
| MCTP1 | 5 | -4.86 | 1.19E-06 | No | Yes | Yes | No | |||||
| PLD1 | 3 | -4.67 | 3.05E-06 | No | ||||||||
| RFT1 | 3 | 4.66 | 3.19E-06 | Yes | ||||||||
| NAT6 | 3 | 4.64 | 3.54E-06 | No | Yes | Yes | No | |||||
| AAGAB | 15 | 4.28 | 1.83E-05 | No | ||||||||
| PRKCDc | 3 | 2.06 | 3.94E-02 | 4.25 | 2.10E-05 | No | Yes | No | No |
Chr Chromosome, PWAS proteome-wide association study, pQTL protein quantitative trait loci, eQTL expression quantitative trait loci, sQTL splicing quantitative trait loci, ROSMAP Religious Orders Study and Rush Memory and Aging Project.
aBonferroni correction p-value for Banner proteome-wide significant (PWS) genes was set at 4.36E-5.
bBonferroni correction p-value for ROSMAP PWS genes was set at 3.39E-5.
cGenes that were PWS one human brain reference dataset and nominally significant (p < 0.05) in other brain proteome reference.
dGenes colocalized in one human brain reference dataset.
eGenes are novel compared with GWAS if > 1 MB away from a lead GWAS variant (R2 < 0.1).