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

Figure 2

Cell type specific eQTL replication frequencies.

(A, B, C) eQTL replication frequency (y-axis) as a function of discovery significance (x-axis: ). SNPs were grouped into 30 equally spaced bins by BF. (D, E, F) eQTL replication frequency (y-axis; thresholded at ) as a function of SNP position () (x-axis). Cis-eQTL SNPs within 250 kb of the TSS were grouped into equally spaced bins. (A, D) Replication frequencies for CAP_LCL eQTLs in Stranger_LCLs (blue) and Merck_liver (red). (B, E) Replication frequencies for UChicago_liver eQTLs in Merck_liver (blue) and Stranger_LCL (red). (C, F) Replication frequencies for Myers_brain eQTLs in Harvard_cerebellum (blue) and Stranger_LCL (red). In all panels, bold lines depict percentage of SNP-gene pairs with per bin, and ribbons depict confidence interval.

Figure 2