Regional plot and genome browser view of 14q13.

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Regional plot and genome browser view of 14q13. Regional plot and genome browser view of 14q13. The chromosomal position (based on GRCh37) of SNPs on 14q13 against −log10P values for ER+ breast cancer is shown. The blue arrow denotes the signal rs73258644 and the red arrow denotes rs12883049, which is a better marker of the index signal. The purple circle denotes the index variant rs2236007. SNPs surrounding the index variant are colored to indicate the LD structure using pairwise r2 in reference to rs2236007 from the May 2012 EUR panel of 1000 Genomes. The plots were generated using LocusZoom (55). Genome browser views with epigenetic chromatin features in breast cells (MCF7, HCC1954, MDAMB231, HMEC) on 14q13 are generated using the UCSC genome browser (56). Below is a magnified view of rs12883049 with selected enhancer chromatin marks and DNA sequence of a response element. The gray shading indicates the location of the variant rs12883049. Ye Feng et al. Cancer Epidemiol Biomarkers Prev 2017;26:1016-1026 ©2017 by American Association for Cancer Research