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First off let's define some concepts. DNAse hypersensitive regions are DNA regions which are in an open chromatin conformation (i.e. euchromatin). This means that those regions are more active at the genomic level (i.e. higher gene expression, gene regulation and higher TF binding) and are less prone to form nucleosomes. Histone mark sites are DNA regions ...


Keep in mind that it is not individual histones that are binding, there are 8 histone proteins forming a compact nucleoside particle, and the particle has 146 bp of DNA tightly wrapped around it. Since the interaction between the histones and the DNA are not sequence-specific, it is unlikely that a single nucleotide polymorphism would have a measurable ...


I would link your data with the ENCODE dataset. This dataset provides locations of TFBS. It is also accessible via the UCSC genome browser. For the actual question TFBS are located pretty much everywhere, including exons (as described here), introns and of course intergenic regions (e.g. enhancers, silencers, control locus regions - here a reference).

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