Table 1.
Single Nucleotide Polymorphisms Evaluated for Replication, Including Functional Information, in the Shanghai Breast Cancer Study, 1996–2005
| Gene | Variant | Alleles (Major/Minor) | Minor Allele Frequencya | Functional Informationb | SBCS Publication (First Author, Year, Reference No.) | Previous Denotation (If Applicable) |
| AHR | rs2066853 | G/A | 0.36 | Nonsynonymous, exon 10, codon 554, Lys→Arg | Long, 2006 (12) | Lys554Arg |
| ATM | rs1003623 | C/T | 0.39 | Intron 24; possible intronic enhancer | Ye, 2007 (13) | |
| AURKA (STK15) | rs2273535 | A/T | 0.34 | Nonsynonymous, exon 5, codon 31, Phe→Ile | Dai, 2004 (19) | Phe31Ile |
| BRCA1 | rs11655505 | C/T | 0.38 | Promoter; T allele shown to enhance promoter activity | Chan, 2009 (20) | −2,265C > T |
| CCND1 | rs9344 | A/G | 0.44 | Splice site, exon 4; G allele results in alternative transcript | Shu, 2005 (14) | A870G |
| ESR1 | rs2234693 | T/C | 0.26 | Intron 1; may influence transcriptional regulation | Cai, 2003 (15) | PvuII |
| ESR2 | rs1256054 | G/C | 0.03 | Exon 7 (synonymous); may influence splicing regulation | Zheng, 2003 (21) | C(33,390)G |
| GSTP1 | rs1695 | A/G | 0.18 | Nonsynonymous, exon 5, codon 105, Ile→Val | Egan, 2004 (16) | Ile105Val |
| IGF1R | rs2593053 | G/A | 0.26 | Intron 20; may influence transcriptional regulation | Unpublished data | |
| IGFALS | rs3764349 | G/A | 0.19 | Promoter | Unpublished data | |
| IGFALS | rs35587190 | C/T | 0.16 | Promoter | Unpublished data | |
| IGFBP3 | rs2854744 | A/C | 0.23 | Intron 1; may influence splicing | Ren, 2004 (22) | A-202C |
| C allele associated with lower circulating levels of insulin-like growth factor-binding protein 3 | ||||||
| SHBG | rs6259 | G/A | 0.18 | Nonsynonymous, exon 8, codon 356, Asp→Asn | Cui, 2005 (18) | Asp327Asn |
| A allele associated with higher postmenopausal circulating SHBG levels | ||||||
| STS | rs727519 | G/C | 0.31 | Promoter; may influence transcriptional regulation | Unpublished data | |
| STS | rs1131289 | G/A | 0.36 | Exon 10, 3′-UTR | Unpublished data | |
| SULT1E1 | rs4149525 | T/C | 0.29 | Promoter | Unpublished data | |
| TGFB1 | rs1800469 | T/C | 0.48 | Promoter; may influence transcriptional regulation | Shin, 2005 (17) | C-509T |
| VEGFA | rs3025039 | C/T | 0.19 | Exon 8, 3′-UTR | Kataoka, 2006 (23) | T936C |
Abbreviations: Arg, arginine; Asn, asparagine; Asp, aspartic acid; Ile, isoleucine; Lys, lysine; Phe, phenylalanine; Pro, proline; PvuII, Proteus vulgaris II [restriction enzyme]; SBCS, Shanghai Breast Cancer Study; SHBG, sex hormone-binding globulin; UTR, untranslated region; Val, valine.
a
Frequency of the minor allele among controls in stage 1 of the SBCS.
b
Functional information compiled from the literature, as well as from the dbSNP, Ensemble, FASTSNP, and F SNP Web sites.