Figure 1.

Genetic Mapping and Chromatin State of the 5q11.2 Locus

(A) Manhattan plot of overall breast cancer risk in Europeans at the 5q11.2 locus. SNPs are plotted on the basis of their chromosomal position on the x axis and p values (log₁₀ values) for association. The span of the iCHAVs in terms of chromosomal location and p value is displayed with shading, and candidate causal variants from the iCHAV are colored black. The lead SNPs from each iCHAV, the original GWAS tag SNP (rs889312), and the three genes present in the region are shown. The dotted line intersects the y axis at p = 10⁻⁸ and indicates conventional genome-wide significance.

(B) The chromatin state of the 5q11.2 locus in human mammary epithelial cells is shown with ENCODE ChIP-seq data from H3K4me3, H3K4me2, H3k4me1, and DNaseI studies accessed from the UCSC Genome Browser. Transcription factor (TF) binding from ENCODE ChIP-seq studies of 161 TFs in 91 cell lines is also displayed.