Are maps of regulatory regions available for hg38?

Question

[JJ]

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!

[WouterDeCoster]

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

Answer 1

[ATpoint]

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

[JJ]

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.

[microfuge]

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

[JJ]

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?

[Alex Reynolds]

UCSC liftOver: https://genome.ucsc.edu/cgi-bin/hgLiftOver