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SNPs selected for the study and their functional consequences. |
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| SNPs |
Minor Allele (%) |
Interacting SNPs* |
Alteration |
Function |
Breast Cancer Association§ |
Selected Biological Processes¶ |
|
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| Higher Rank (Direct Functional Evidence) |
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| 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. |
|
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| Medium Rank (Indirect Functional Evidence) |
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|
|
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| 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, |
|
|
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| Lower Rank (No Functional Evidence) |
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|
|
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| 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 |
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*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). †Cases are women diagnosed with breast cancer before age 40; ¶ GeneCards [88] | ||||||
Onay et al. BMC Cancer 2006 6:114 doi:10.1186/1471-2407-6-114 |
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