Table 2.

Characteristics of SNPs statistically significantly (20% FDR) interacting with RT in the case-only analysis

SNPLocusChrPosition*AllelesBreast cancer after HL cases, N = 327First primary breast cancer cases, N = 4671Statistical interaction with chest RT on breast cancer riskWeight RT-interaction-PRS
MAFN calledMAFN calledIOR95% CIPLog IOR
rs10505506 PVT1 129114473 G/C 0.407 327 0.306 4670 1.6 1.3-1.8 3.1E-08 0.44 
rs12086369 1p31.1 79644149 G/A 0.073 324 0.035 4667 2.1 1.5-2.8 9.4E-08 0.74 
rs9461776 HLA 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 70935424 G/A 0.041 327 0.020 4669 2.2 1.4-3.4 6.8E-06 0.79 
rs3815871 PVT1 129077760 G/C 0.437 327 0.341 4671 1.5 1.3-1.8 8.5E-06 0.40 
SNPLocusChrPosition*AllelesBreast cancer after HL cases, N = 327First primary breast cancer cases, N = 4671Statistical interaction with chest RT on breast cancer riskWeight RT-interaction-PRS
MAFN calledMAFN calledIOR95% CIPLog IOR
rs10505506 PVT1 129114473 G/C 0.407 327 0.306 4670 1.6 1.3-1.8 3.1E-08 0.44 
rs12086369 1p31.1 79644149 G/A 0.073 324 0.035 4667 2.1 1.5-2.8 9.4E-08 0.74 
rs9461776 HLA 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 70935424 G/A 0.041 327 0.020 4669 2.2 1.4-3.4 6.8E-06 0.79 
rs3815871 PVT1 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).