Table 1 Genes significantly associated with estrogen receptor (ER)-positive breast cancer that have not been identified in previous TWAS of breast cancer
Loci | Gene Name | Min. 11 Tissue ACAT p-valuea | Min. Breast p-valueb | TWAS-significant Approachesc | Max. PIP (eQTL)d | Max. PIP (sQTL)e |
|---|---|---|---|---|---|---|
1p34.1-p33 | RAD54L | 5.24E-07 | NA | express | 0.56 | NA |
1p34.1-p33 | UQCRH | 1.48E-06 | 9.11E-01 | express | 0.06 | NA |
1p34.1-p33 | FAAH | 7.08E-09 | 3.39E-07 | express|splice | 1 | 0.39 |
1q21.1, L1 | FCGR1CP | 5.05E-11 | NA | splice | NA | 1 |
1q21.1, L2 | ITGA10 | 1.46E-06 | 1.91E-06 | splice | NA | 0.36 |
1q21.1, L2 | HJV | 9.75E-07 | 6.46E-01 | splice | NA | 0.3 |
1q22 | DPM3 | 2.51E-06 | 2.51E-06 | splice | NA | 0.02 |
1q22 | ARHGEF2 | 4.02E-07 | 2.10E-04 | express | 0.44 | NA |
3p14.1 | THOC7 | 5.21E-06 | 5.81E-07 | splice | NA | 0 |
3p24.1, L2 | TGFBR2 | 3.47E-09 | 1.14E-02 | express | 1 | NA |
3p26.1 | ITPR1 | 7.41E-11 | 3.17E-01 | splice | NA | 1 |
4q21.23 | HELQ | 1.16E-06 | 1.42E-06 | splice | NA | 0.93 |
4q34.1 | RP13-577H12.2 | 1.97E-12 | NA | splice | NA | 1 |
5q11.1 | PARP8 | 2.96E-06 | 1.08E-06 | express | 0 | NA |
5q14.3 | ARRDC3 | 3.39E-10 | 9.52E-11 | splice | NA | 1 |
5q33.3 | EBF1 | 1.61E-15 | NA | splice | NA | 1 |
6p22.1-p21.33 | TRIM31 | 1.43E-06 | 7.78E-02 | express | 0.94 | NA |
6p22.1-p22.2 | BTN3A1 | 1.93E-06 | 1.24E-06 | splice | NA | 0.87 |
6p22.1-p22.2 | ABT1 | 7.41E-07 | 7.70E-02 | splice | NA | 0.74 |
6p22.1-p22.2 | ZSCAN9 | 1.34E-06 | 9.36E-03 | splice | NA | 0.12 |
6p22.1-p22.2 | PGBD1 | 9.86E-07 | 4.75E-07 | splice | NA | 0.48 |
6p22.1-p22.2 | ZSCAN23 | 1.45E-07 | 8.88E-08 | splice | NA | 0.55 |
6p23 | SIRT5 | 5.03E-06 | 3.31E-06 | express | 0.76 | NA |
7q21.2 | ANKIB1 | 6.90E-07 | 7.75E-07 | splice | NA | 0.01 |
10p12.31-p12.2 | MLLT10 | 2.22E-16 | 1.98E-02 | splice | NA | 0.5 |
10p12.31-p12.2 | PIP4K2A | 4.38E-07 | 8.95E-07 | splice | NA | 1 |
10q21.2-q21.3 | EGR2 | 9.53E-08 | 9.53E-08 | splice | NA | 0.98 |
10q26.13 | ENSG00000273767 | 1.66E-06 | NA | splice | NA | 0.53 |
11p15.5, L2 | AC051649.12 | 2.22E-16 | NA | splice | NA | 0.07 |
11p15.5, L2 | H19 | 2.96E-09 | 1.63E-09 | splice | NA | 0 |
12q24.21 | RP11-116D17.3 | 1.06E-06 | 3.14E-01 | express | 0.95 | NA |
14q24.1 | RAD51B | 2.23E-07 | 8.64E-01 | splice | NA | 0.99 |
14q32.11-q32.12 | CCDC88C | 5.45E-10 | 8.72E-11 | splice | NA | 1 |
14q32.11-q32.12 | PPP4R3A | 4.79E-07 | 2.63E-02 | splice | NA | 0.95 |
15q22.33 | SMAD3 | 2.31E-06 | 4.07E-02 | splice | NA | 0.88 |
15q24.1 | SCAMP2 | 4.84E-07 | 3.59E-03 | splice | NA | 0.93 |
15q26.1 | VPS33B | 8.09E-11 | 6.34E-11 | splice | NA | 1 |
16q13 | AMFR | 2.85E-06 | 2.85E-06 | splice | NA | 0.72 |
17q11.2 | ATAD5 | 5.93E-07 | 6.22E-01 | splice | NA | 0.98 |
18q11.2, L2 | CHST9 | 6.74E-09 | NA | splice | NA | 1 |
19p13.13 | NACC1 | 4.72E-07 | 4.72E-07 | splice | NA | 0.51 |
19q13.31 | ZNF45 | 6.32E-12 | 6.69E-12 | splice | NA | 1 |
22q12.1-q12.2 | CTA-292E10.6 | 3.01E-09 | 8.71E-03 | splice | NA | 0.9 |