Characteristics of SNPs statistically significantly (20% FDR) interacting with RT in the case-only analysis
| SNP . | Locus . | Chr . | Position* . | Alleles . | Breast cancer after HL cases, N = 327 . | First primary breast cancer cases, N = 4671 . | Statistical interaction with chest RT on breast cancer risk† . | Weight RT-interaction-PRS . | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MAF . | N called . | MAF . | N called . | IOR . | 95% CI . | P‡ . | Log IOR . | |||||
| rs10505506 | PVT1 | 8 | 129114473 | G/C | 0.407 | 327 | 0.306 | 4670 | 1.6 | 1.3-1.8 | 3.1E-08 | 0.44 |
| rs12086369 | 1p31.1 | 1 | 79644149 | G/A | 0.073 | 324 | 0.035 | 4667 | 2.1 | 1.5-2.8 | 9.4E-08 | 0.74 |
| rs9461776 | HLA | 6 | 32683713 | A/G | 0.133 | 327 | 0.079 | 4671 | 1.8 | 1.4-2.3 | 1.1E-07 | 0.59 |
| MitoA7769G | MT | 7769 | A/G | 0.052 | 325 | 0.020 | 4653 | 2.1 | 1.5-3.0 | 2.8E-06 | 0.76 | |
| rs1017639 | CPT1A | 11 | 68355110 | A/C | 0.073 | 327 | 0.043 | 4669 | 1.9 | 1.4-2.6 | 2.8E-06 | 0.63 |
| MitoT9900C | MT | 9900 | A/G | 0.028 | 325 | 0.011 | 4669 | 2.0 | 1.3-3.2 | 3.7E-06 | 0.71 | |
| MitoA13781G | MT | 13781 | A/G | 0.036 | 306 | 0.011 | 4592 | 2.2 | 1.5-3.3 | 4.3E-06 | 0.80 | |
| rs2296008 | COL19A1 | 6 | 70935424 | G/A | 0.041 | 327 | 0.020 | 4669 | 2.2 | 1.4-3.4 | 6.8E-06 | 0.79 |
| rs3815871 | PVT1 | 8 | 129077760 | G/C | 0.437 | 327 | 0.341 | 4671 | 1.5 | 1.3-1.8 | 8.5E-06 | 0.40 |
| SNP . | Locus . | Chr . | Position* . | Alleles . | Breast cancer after HL cases, N = 327 . | First primary breast cancer cases, N = 4671 . | Statistical interaction with chest RT on breast cancer risk† . | Weight RT-interaction-PRS . | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MAF . | N called . | MAF . | N called . | IOR . | 95% CI . | P‡ . | Log IOR . | |||||
| rs10505506 | PVT1 | 8 | 129114473 | G/C | 0.407 | 327 | 0.306 | 4670 | 1.6 | 1.3-1.8 | 3.1E-08 | 0.44 |
| rs12086369 | 1p31.1 | 1 | 79644149 | G/A | 0.073 | 324 | 0.035 | 4667 | 2.1 | 1.5-2.8 | 9.4E-08 | 0.74 |
| rs9461776 | HLA | 6 | 32683713 | A/G | 0.133 | 327 | 0.079 | 4671 | 1.8 | 1.4-2.3 | 1.1E-07 | 0.59 |
| MitoA7769G | MT | 7769 | A/G | 0.052 | 325 | 0.020 | 4653 | 2.1 | 1.5-3.0 | 2.8E-06 | 0.76 | |
| rs1017639 | CPT1A | 11 | 68355110 | A/C | 0.073 | 327 | 0.043 | 4669 | 1.9 | 1.4-2.6 | 2.8E-06 | 0.63 |
| MitoT9900C | MT | 9900 | A/G | 0.028 | 325 | 0.011 | 4669 | 2.0 | 1.3-3.2 | 3.7E-06 | 0.71 | |
| MitoA13781G | MT | 13781 | A/G | 0.036 | 306 | 0.011 | 4592 | 2.2 | 1.5-3.3 | 4.3E-06 | 0.80 | |
| rs2296008 | COL19A1 | 6 | 70935424 | G/A | 0.041 | 327 | 0.020 | 4669 | 2.2 | 1.4-3.4 | 6.8E-06 | 0.79 |
| rs3815871 | PVT1 | 8 | 129077760 | G/C | 0.437 | 327 | 0.341 | 4671 | 1.5 | 1.3-1.8 | 8.5E-06 | 0.40 |
Chr, chromosome; CI, confidence interval; FDR, false discovery rate; IOR, interaction odds ratio; MAF, minor allele frequency; MT, mitochondrial DNA.
Positions are based on NCBI36/hg18.
Logistic regression analysis per SNP to test the log additive effect per allele (per-allele IOR) with adjustment for age at and year of breast cancer diagnosis, country, and ethnicity.
All listed SNPs were significant at a 20% FDR. Top 3 SNPs were statistically significant at the Bonferroni threshold (P < 2.6E-07).