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. 2018 Dec;28(12):1812–1825. doi: 10.1101/gr.240390.118

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© 2018 Ye et al.; Published by Cold Spring Harbor Laboratory Press

This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.

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Figure 2. — Properties of local eQTLs and isoQTLs. (A) Frequency (y-axis) of the location of leading SNPs for local eQTLs and isoQTLs (permutation FDR < 0.05) with respect to meta gene structure (x-axis). Genes are normalized to five exonic regions (E1–E4 indicate exons 1 through 4; E* indicates exon 5 to the last exon) and four intronic regions (introns 1, 2, 3, and from intron 4 to the last intron). Upstream and downstream sequences are divided into 100-kb windows. (B) Log₂ fold enrichment (x-axis) of leading SNPs for local eQTLs and isoQTLs (permutation FDR < 0.05) for genomic annotations. eQTL enrichments are calculated using a background set of SNPs matched for distance to TSS and allele frequency. IsoQTL enrichments are calculated with respect to a background set of eQTLs matched for distance to TSS and allele frequency. Multiple testing significance is indicated. (*) P < 0.05; (**) P < 0.01; (***) P < 0.001.