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Figure 3 | Breast Cancer Research

Figure 3

From: Functional variants at the 21q22.3 locus involved in breast cancer progression identified by screening of genome-wide estrogen response elements

Figure 3

Schematic diagrams of the 21q22.3 block and the 21q22.3 region that binds estrogen receptor α. (A) Three single-nucleotide polymorphisms (SNPs) were found to be significantly associated with breast cancer progression, of which two (rs2839494 and rs1078272) were associated with estrogen response elements (EREs) and located at a region that binds estrogen receptor α (ERα). These two SNPs were used in the initial screening stage, and rs2251362 was used in the validation stage. Two additional SNPs, rs2839500 and rs2839501, were exonic SNPs detected by direct sequencing of the 21q22.3 block (see text for details). All five SNPs are located in the same 21q22.3 haplotype block. The linkage disequilibrium (LD) plot shows LD between the SNPs in 21q22.3 in Han Chinese women. The strength of the LD between SNPs, indicated by the color scheme, was measured using a combination of the statistic D' and the logarithm of odds (LOD) score (dark red shading, D' =1 and LOD score ≥2; light red shading, D' <1 and LOD score ≥2). (B) Top panel: The 21q22.3 block (yellow) and the 21q22.3 region to which ERα binds (gray). Middle panel: Enlarged view showing the half-ERE sites (thin gray bars), exons (red) and untranslated regions (blue) of TMPRSS3/TFF1, and the regions to which ERα and the ER coactivator Rad21 bind, detected by using the Encyclopedia of DNA Elements (ENCODE). Bottom panel: The 21q22.3 region to which ERα binds. The major and minor alleles of the three SNPs in this region are indicated. ChIP, Chromatin immunoprecipitation.

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