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Are maps of regulatory regions available for hg38?

Hi,

Does anyone know if there are maps (preferable as bed file) of (candidate) regulatory regions available for hg38? I found i-cisTarget but it's just for hg19.

Thanks!

sequence
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updated by ATpoint ATpoint • written by JJ JJ

You can get a lot of bed files from the UCSC table browser, including regulatory features.

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written by WouterDeCoster WouterDeCoster

1 answer

Check ReMap, a collection of transcription factor binding sites as well as the regulatory data from UCSC/ENCODE for hg38 (UCSC/ENCODE).

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written by ATpoint ATpoint

Thank you, I know about remap but that's basically a collection of TFBS peaks. I was looking for a bed file as provided by i-cis-target for hg38. They provide:

General Binding Preference models, CpG islands, proximal promoters, conserved non-coding sequences, ultra-conserved elements, regulatory elements from OregAnno, VistaEnhancers, predicted cis-regulatory modules and DNAseI Hypersensitive (DHS) uniform clustered peaks across 125 cell lines from ENCODE.

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written by JJ JJ

The i-cis-target website seems to last updated in 2015. Would a liftover or crossmap work to lift these coordinates to hg38 ?

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written by microfuge microfuge

Thanks - I figured this would be the only solutions if nothing else more updated is out there. What tool would you recommend for liftover of a bed file?

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written by JJ JJ

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