TABLE 1.
Genes significantly associated with the overall breast cancer, estrogen receptor positive and negative subtypes, and estrogen receptor status, as identified by TWAS
| Cytoband | Gene | Chromosome: Position (start–end) | Number of SNPs | Heritability | Cross validation r2 | TWAS p values |
|||
|---|---|---|---|---|---|---|---|---|---|
| Overall vs. controls | ER+ vs. controls | ER− vs. controls | ER+ vs. ER− | ||||||
| p11.2 | HIST2H2BA | 1: 120906028–120915073 | 77 | 0.10 | 0.04 | 3.1E–30 | 2.0E–32 | 3.6E–01 | 1.4E–07 |
| q21.1 | NUDT17 | 1: 145586804–145589439 | 110 | 0.07 | 0.03 | 1.7E–09 | 8.8E–10 | 2.4E–01 | 3.3E–03 |
| q33.1 | ALS2CR12 | 2: 202152994–202222121 | 363 | 0.35 | 0.03 | 2.2E–11 | 8.4E–07 | 2.5E–06 | 8.8E–01 |
| CASP8 | 2: 202098166–202152434 | 371 | 0.32 | 0.15 | 1.8E–07 | 8.2E–06 | 2.9E–04 | 7.6E–01 | |
| q25.31 | LINC00886 | 3: 1156465135–156534851 | 452 | 0.17 | 0.04 | 4.7E–05 | 1.9E–04 | 3.2E–03 | 7.3E–01 |
| p16.3 | MAEA | 4: 1283639–1333925 | 374 | 0.42 | 0.23 | 3.9E–05 | 1.6E–04 | 2.3E–01 | 2.3E–01 |
| q14.2 | ATG10 | 5: 81267844–81551958 | 520 | 0.44 | 0.26 | 1.9E–10 | 2.4E–10 | 2.7E–01 | 2.4E–02 |
| ATP6AP1L | 5: 81575281–81682796 | 467 | 0.62 | 0.51 | 2.3E–07 | 3.3E–06 | 2.9E–02 | 2.3E–01 | |
| q14.1 | RP11–250B2.5 | 6: 81176675–81178797 | 402 | 0.12 | 0.08 | 6.9E–07 | 7.3E–03 | 5.9E–03 | 8.2E–01 |
| q22.33 | RP11–73O6.3 | 6: 130454555–1130465515 | 557 | 0.33 | 0.11 | 4.5E–12 | 1.2E–06 | 5.2E–09 | 5.5E–02 |
| L3MBTL3 | 6: 130334844–130462594 | 609 | 0.31 | 0.23 | 8.5E–14 | 3.6E–08 | 1.8E–10 | 1.4E–01 | |
| p15.1 | GDI2 | 10: 5807186–5884095 | 727 | 0.29 | 0.01 | 4.8E–07 | 3.1E–07 | 4.0E–01 | 2.1E–01 |
| p15.5 | MRPL23-AS1 | 11: 2004467–2011150 | 449 | 0.34 | 0.09 | 7.4E–06 | 1.4E–04 | 2.9E–01 | 2.2E–01 |
| q13.2 | RP11–554A11.9 | 11: 68923378–68927220 | 428 | 0.23 | 0.08 | 1.5E–06 | 4.9E–04 | 7.1E–03 | 6.9E–01 |
| q15 | NUP107 | 12: 69082742–69136785 | 538 | 0.27 | 0.05 | 6.1E–06 | 8.2E–07 | 4.3E–01 | 1.0E–01 |
| q24.3 | ULK3 | 15: 75128457–75135538 | 286 | 0.19 | 0.15 | 3.9E–05 | 2.1E–05 | 2.8E–02 | 5.2E–01 |
| MAN2C1 | 15: 75648133–75659986 | 226 | 0.37 | 0.34 | 7.4E–07 | 1.7E–04 | 1.8E–03 | 6.3E–01 | |
| CTD-2323K18.1 | 15: 75819491–75893546 | 226 | 0.36 | 0.19 | 7.5E–07 | 3.9E–04 | 2.3E–03 | 3.1E–01 | |
| q21.31 | HSD17B1P1 | 17: 40698782–40700724 | 245 | 0.09 | 0.07 | 1.4E–06 | 1.8E–03 | 6.4E–03 | 3.9E–01 |
| q21.32 | LRRC37A4P | 17: 43578685–43623042 | 149 | 0.34 | 0.35 | 3.1E–10 | 1.4E–06 | 2.2E–02 | 8.0E–01 |
| CRHR1-IT1 | 17: 43697694–43725582 | 87 | 0.35 | 0.41 | 2.9E–10 | 1.8E–06 | 2.7E–02 | 8.2E–01 | |
| CRHR1 | 17: 43699267–43913194 | 86 | 0.09 | 0.18 | 4.8E–08 | 1.8E–05 | 2.5E–02 | 7.6E–01 | |
| KANSL1-AS1 | 17: 44270942–44274089 | 27 | 0.27 | 0.43 | 3.4E–10 | 1.4E–06 | 2.5E–02 | 7.6E–01 | |
| LRRC37A | 17: 44370099–44415160 | 75 | 0.27 | 0.20 | 7.9E–08 | 2.5E–05 | 9.7E–02 | 4.5E–01 | |
| LRRC37A2 | 17: 44588877–44630815 | 130 | 0.37 | 0.18 | 3.1E–07 | 8.5E–05 | 8.4E–02 | 5.8E–01 | |
| q22 | STXBP4 | 17: 53062975–53241646 | 609 | 0.20 | 0.01 | 1.4E–25 | 1.6E–25 | 3.3E–02 | 1.5E–06 |
| q13.2 | ZNF404 | 19: 44376515–44388203 | 445 | 0.31 | 0.06 | 2.0E–13 | 5.1E–12 | 1.7E–08 | 6.9E–01 |
| ZNF155 | 19: 44472014–44502477 | 486 | 0.39 | 0.11 | 8.8E–09 | 1.0E–07 | 2.0E–05 | 3.3E–01 | |
| RP11–15A1.7 | 19: 44501048–44506988 | 477 | 0.29 | 0.14 | 9.7E–12 | 7.3E–10 | 5.1E–07 | 5.5E–01 | |
| q11.23 | CPNE1 | 20: 34213953–34220170 | 299 | 0.25 | 0.20 | 5.3E–05 | 3.3E–04 | 1.4E–01 | 4.9E–01 |
Note: Significant associations after Bonferroni adjustment (p < .05/901) are in bold.
Abbreviations: ER, estrogen receptor; SNP, single nucleotide polymorphisms; TWAS, transcriptome-wide association studies.