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Integrative Modeling of eQTLs and Cis-Regulatory Elements Suggests Mechanisms Underlying Cell Type Specificity of eQTLs

Figure 4

eQTL SNPs are depleted within repressive chromatin contexts.

(A–I) CAP_LCL eQTL SNP () overlap with predicted cis-regulatory elements. (A–C) eQTL SNP overlap with chromHMM predicted heterochromatin, (D–F) eQTL SNP overlap with chromHMM predicted repressive chromatin, (G–I) eQTL SNP-TSS pairs with an intervening CTCF binding site. In each panel, SNPs are grouped into 25 equally spaced bins within the 50 kb upstream and downstream of the TSS and TES, and 10 bins between the TSS and TES. Each bin is plotted along the x-axis. Bold lines depict bin percentage, ribbons depict confidence interval. Each column of panels depicts a distinct SNP set contrast. (A,D,G) Observed eQTL SNPs (blue) and randomly drawn cis-linked SNPs at expressed genes(red). (B,E,H) eQTL SNPs that replicate in Stranger_LCL () (green) and SNPs that fail to replicate (purple). (C,F,I) CAP_LCL eQTL SNP overlap with CREs derived from the LCL line GM12878 (orange) and HepG2 cells (brown).

Figure 4

doi: https://doi.org/10.1371/journal.pgen.1003649.g004