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