TABLE 3.
Conditional and joint analysis of gene region with multiple TWAS significant genes
| Marginal TWAS |
COJO |
||||
|---|---|---|---|---|---|
| Regiona | Gene (colocalized) | Z score | p Value | Z score | p Value |
| 2q33 | ALS2CR12 | 6.7 | 2.15E–11 | 4.6 | 3.70E–06 |
| CASP8 | −5.22 | 1.76E–07 | −2 | 5.00E–02 | |
| 5q14 | ATG10 | −6.37 | 1.85E–10 | −6.37 | 1.85E–10 |
| ATP6AP1L | −5.18 | 2.25E–07 | −0.85 | 0.4 | |
| 6q22 | RP11-73O6.3 | −6.92 | 4.46E–12 | 0.18 | 0.86 |
| L3MBTL3 | −7.46 | 8.45E–14 | −7.46 | 8.45E–14 | |
| 15q24 | ULK3 | −4.11 | 3.87E–05 | −4.1 | 3.90E–05 |
| MAN2C1 | −4.95 | 7.37E–07 | −5 | 7.40E–07 | |
| CTD-2323K18.1 | −4.95 | 7.49E–07 | −1.7 | 0.083 | |
| 17q21 | LRRC37A4P | 6.29 | 3.12E–10 | 0.25 | 0.8 |
| CRHR1-IT1 | −6.3 | 2.91E–10 | −6.3 | 2.91E–10 | |
| CRHR1 | −5.46 | 4.84E–08 | −0.28 | 0.78 | |
| KANSL1-AS1 | −6.28 | 3.37E–10 | −0.04 | 0.97 | |
| LRRC37A | −5.37 | 7.89E–08 | 1.83 | 0.07 | |
| LRRC37A2 | −5.12 | 3.07E–07 | 1.81 | 0.07 | |
| 19q13 | ZNF404 | 7.35 | 2.04E–13 | 3.5 | 0.001 |
| ZNF155 | 5.75 | 8.81E–09 | −2 | 0.042 | |
| RP11-15A1.7 | 6.81 | 9.67E–12 | 2.8 | 0.005 | |
Abbreviations: COJO, conditional and joint; TWAS, transcriptome-wide association studies.
a
Bolded genes remain significant in conditional analyses. Analysis was performed using GWAS summary statistics of ER+ subtypes. Our primary goal in these analyses is to establish whether any of the marginally significant TWAS genes remains significant after conditioning for the most significant gene in the region; sincesince all of the regions with multiple significant genes contain 2–3 significant genes, using a conditional p value threshold of .05 is a reasonable threshold for identifying independent signals.