Skip to main content
. Author manuscript; available in PMC: 2012 Jan 1.
Published in final edited form as: Breast Cancer Res Treat. 2010 May 23;125(1):207–214. doi: 10.1007/s10549-010-0947-3

Table 1.

Gene and SNP information for all SNPs with a Meff adjusted p-value (PMeff) less than 0.05 in a single SNP unconditional logistic regression analysis adjusted for matching factors (age, PMH use) and population structure. The outcome, breast cancer, was considered generally and with respect to estrogen receptor (ER) and progesterone receptor (PR) subtypes. (M: Total number of SNPs investigated within a gene. Meff: Effective number of tests given the linkage disequilibrium pattern within a gene. OR: Odds Ratio comparing heterozygous carriers of the minor allele to non-carriers.)

Gene Name Path M Meff rs number OR Raw P PMeff SNP Type
Breast Cancer vs. No Breast Cancer
RPA3 NER 65 42 rs17136898 1.34 0.0011 0.046 intronic
MSH3 MMR 46 20 rs6151838 0.73 0.0024 0.048 intronic
ER+ Breast Cancer vs. No Breast Cancer
LIG1 BER 30 22 rs274860 1.82 0.0003 0.006 intronic
LIG1 BER 30 22 rs2304136 1.63 0.0006 0.013 intronic
ER− Breast Cancer vs. No Breast Cancer
RPA3 NER 65 42 rs13237260 1.60 0.0002 0.007 intergenic
RPA3 NER 65 42 rs17136898 1.73 0.0002 0.010 intronic
RPA3 NER 65 42 rs10952069 1.57 0.0005 0.019 intergenic
POLE POL 18 10 rs5745066 2.44 0.0027 0.027 missense
APEX1 BER 25 21 rs2275008 1.46 0.0016 0.033 intronic
PR+ Breast Cancer vs. No Breast Cancer
FANCF FAN 3 3 rs12805507 0.76 0.0029 0.009 intergenic
FANCF FAN 3 3 rs408199 0.77 0.0029 0.009 intergenic
LIG1 BER 30 22 rs274860 1.80 0.0006 0.013 intronic
RPA3 NER 65 42 rs17136898 0.34 0.0009 0.038 intronic
LIG1 BER 30 22 rs2304136 1.40 0.0020 0.045 intronic
PMS1 MMR 12 10 rs5743030 0.61 0.0047 0.047 intronic
PR− Breast Cancer vs. No Breast Cancer
XRCC4 NH 34 23 rs10080123 0.71 0.0005 0.012 intronic
XRCC4 NH 34 23 rs1193693 0.72 0.0005 0.012 intronic
XRCC4 NH 34 23 rs1017794 0.72 0.0006 0.014 intronic
DCLRE1C NH 15 12 rs12572872 1.38 0.0016 0.020 intronic
XRCC4 NH 34 23 rs10040363 0.73 0.0009 0.021 intronic
XRCC4 NH 34 23 rs1011981 0.72 0.0011 0.026 intronic
XRCC4 NH 34 23 rs10042854 0.73 0.0013 0.029 intronic
XRCC4 NH 34 23 rs4591730 0.73 0.0013 0.031 intronic
XRCC4 NH 34 23 rs11949301 0.73 0.0016 0.038 intronic