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Fig. 5 | Genome Biology

Fig. 5

From: Universal annotation of the human genome through integration of over a thousand epigenomic datasets

Fig. 5

Full-stack states’ relationship with human genetic variants. A Enrichments of full-stack states with duplication and deletion structural variants from [45]. Only states that are in the top ten most enriched states for either duplications or deletions are shown. Top five fold enrichments for each class of structural variants are colored in increasing darker shades of red for higher ranked enrichments. . The columns from left to right are the state label, percent of genome the state covers, the fold enrichment for deletions, and fold enrichment for duplications. B Emission probabilities corresponding to states in A. The coloring is the same as Fig. 2A. The figure highlights how states most associated with structural variants generally had higher emission of H3K9me3 compared to other chromatin marks. C Enrichments of full-stack states with top 1% prioritized bases in the non-coding genome by 14 variant prioritization scores previously analyzed [30]. Only states that are among the top five most enriched states by at least one score are shown. The top five enrichment values for each score are colored in increasing darker shades of red for higher ranked enrichment values. Enrichment values below one, corresponding to depletions, are colored in yellow. The columns from left to right are the state label, percent of the genome covered, the 14 score enrichments, and a detailed description of the state. D Log base 10 of ratios of states’ enrichment with GNOMAD variants [46] with the lowest MAFs (< 0.0001) vs. GNOMAD variants with the highest MAFs (0.4–0.5). States are ordered as in Fig. 2A. Top five states with the highest and lowest enrichment ratios are labeled to the right. E States most enriched with fine-mapped phenotypic variants against the background of common variants. Fine-mapped phenotypic variants were identified by either CAVIARBF [47] or FINEMAP [48] (“Methods”). F State enrichments with somatic mutations associated with four cancer types in the non-coding genome. Only states that are among the ten most enriched with variants from at least one cancer type are shown. States in the top five are colored according to their ranks. The top five enrichment values for each cancer type are colored in increasing darker shades of red for higher ranked enrichment values. The columns are the state label, the percent of the genome the state covers, and the fold enrichments of variants from breast, haematopietic and lymphoid, liver, and pancreas cancer types. G Emission probabilities corresponding to states in F, as subsetted from Fig. 2A. The coloring is the same as Fig. 2A. The figure highlights how states with the greatest enrichments for cancer-associated variants tend to have higher emission probabilities for H3K9me3 compared to other chromatin marks

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