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. 2022 Oct 7;13:5827. doi: 10.1038/s41467-022-33427-1

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© This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2022

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Fig. 6 — Proportion of unique eQTLs (variant / eGene pairs) and unique eQTLs involving genes associated with eye disease (A) overlapping each chromatin compartment or (B) share the same observed (n = 1) or random TAD (n = 100; see methods). Boxplots represent the median and interquartile range (IQR); whiskers mark 1.5x the IQR; data beyond 1.5x the IQR are plotted as individual points.; *** indicates p < 0.001 by two-sided t-test between observed and random TADs. C Schematic of eQTL annotation depending on the variant position relative to TSS. D Number of unique eQTLs and unique eQTLs involving genes associated with eye disease overlapping with a loop that are not in contact with any TSS (eQTL only), in contact with any TSS excluding the eGene TSS (non-eGene pieQTL), or in contact with the TSS of their eGene (eGene pieQTL). E Number of unique eQTLs (variants / eGene pairs) and unique eQTLs involving eye disease genes with the variant overlapping a CRE or SE with plain colors indicating the variant position relative to the eGene TSS and stripes indicating variants overlapping their eGene. F Total H3K27Ac coverage around variants (±100 bp) of each unique eQTLs (variants / eGene pairs) and unique eQTLs involving genes associated eye disease, overlapping a CRE or SE (n = 1677 eQTLs overlapping a distal CRE, n = 744 eQTLs overlapping a promoter CRE, n = 12 glaucoma eQTLs overlapping a distal CRE, n = 5 glaucoma eQTLs overlapping a promoter CRE, n = 44 retinal disease eQTLs overlapping a distal CRE, n = 16 retinal disease eQTLs overlapping a promoter CRE, n = 2 AMD eQTLs overlapping a distal CRE; n = 763 eQTLs overlapping a distal SE, n = 121 eQTLs overlapping a promoter SE, n = 3 glaucoma eQTLs overlapping a distal SE, n = 2 glaucoma eQTLs overlapping a promoter SE, n = 34 retinal disease eQTLs overlapping a distal SE, n = 8 retinal disease eQTLs overlapping a promoter SE, n = 2 AMD eQTLs overlapping a distal SE). Boxplots represent the median and interquartile range (IQR); whiskers mark 1.5x the IQR; data beyond 1.5x the IQR are plotted as individual points. G Examples of promoters and pieQTLs associated to retinopathies (PRPH2 locus), glaucoma (MYO7A locus, top panels), AMD (ABCA1 locus, bottom left panel) and at PCK2 locus (bottom right panel). Tracks represent the chromatin loops, eQTLs variants, SEs, CREs, H3K27Ac coverage, TADs and genes.