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Table 1 SNPs selected for the study and their functional consequences.

From: SNP-SNP interactions in breast cancer susceptibility

SNPs Minor Allele (%) Interacting SNPs* Alteration Function Breast Cancer Association§ Selected Biological Processes¶
Higher Rank (Direct Functional Evidence)
XPD-[Lys751Gln] C: 32.3 Yes Missense Gln (C) allele has decreased DNA repair capacity [15-18] Yes [83] transcription-coupled nucleotide-excision repair, ATP-dependent DNA helicase activity
COMT-[Met108/158Val] G: 47.3 Yes Missense Met (A) allele has lower enzymatic activity [20,21] Yes [84] neurotransmitter catabolism, catecholamine metabolism
GSTP1-[Ile105Val] G: 31.2 Yes Missense Val (G) allele is associated with reduced enzymatic activity [22,23] Yes [85] Metabolism, glutathione transferase activity
MTHFR-[Ala222Val] T: 35.6 No Missense Val (T) allele is associated with reduced enzyme activity [19] Yes† [86] Folate metabolism, methylene-tetrahydrofolate reductase (NADPH) activity
CCND1-[Pro241Pro] A: 46.1 Yes Splice Variant (A) allele affects protein stability [24-27] Yes [87] G1/S transition of mitotic cell cycle
MMP1-[1G(-1607)2G] Ins: 49.7 No Regulatory (Ins) allele shows increased transcription [28,29] No collagen catabolism, interstitial collagenase activity
IL10-[G(-1082)A] G: 47.6 Yes Regulatory G allele is associated with increased expression [30-32] No cell-cell signaling, B-cell differentiation and proliferation, anti-apoptosis.
Medium Rank (Indirect Functional Evidence)
BARD1-[Pro24Ser] T: 37.5 Yes Missense Proline to serine change is a significant alteration No response to DNA damage, protein ubiquitination, regulation of apoptosis
IL13-[Arg130Gln] A : 18.3 No Missense Gln allele associated with increased IgE levels [41] No immune response, inflammatory response, signal transduction,
p27-[Val109Gly] G: 19.4 No Missense Possible function [33] No regulation of cyclin dependent protein kinase activity
GSTM3-[4595 (3bp ins/del)] Del: 16.8 No UTR creates recognition site for transcription factor YY1 [34] No Metabolism, glutathione transferase activity
TNFA-[G(-308)A] A: 17.6 No UTR increased transcriptional activity; also no functional change [35-38] No inflammatory response, signal transduction, regulation of transcription, apoptosis
CYP17-[C(518)T] C: 34.3 No Regulatory Associated with increased serum estradiol [39,40] Yes [4] C21-Steroid hormone metabolism,
Lower Rank (No Functional Evidence)
IL1A-[Ala114Ser] T : 27.4 No Missense no published functional evidence No MAPK signaling pathway, regulation of progression through cell cycle
GADD45-[C(IVS3+168)T] C: 31.2 No Intronic no published functional evidence No regulation of cyclin dependent protein kinase activity, DNA repair, apoptosis
PTEN-[(IVS4+109)ins/del5 Ins: 30.1 No Intronic no published functional evidence No negative regulation of cell cycle, protein tyrosine/serine/threonine phosphatase activity
ESR1-[Ser10Ser] C: 48.5 No Silent no published functional evidence No steroid hormone receptor activity, signal transduction, regulation of transcription
G-CSF-[Leu185Leu] G: 38 No Silent no published functional evidence No immune response, cell-cell signaling, positive regulation of cell proliferation
ESR1-[Pro325Pro] G: 24.1 No Silent no published functional evidence No steroid hormone receptor activity, signal transduction, regulation of transcription
  1. *No and Yes indicates whether the SNP has been shown to be "interacting" or "not interacting" with other SNPs in this study; § The studies that showed statistically significant overall SNP-disease risk associations were considered (Ncases > 250 and Ncontrols > 250).
  2. †Cases are women diagnosed with breast cancer before age 40; ¶ GeneCards [88]