Help exploring unknown region

Question

[gpng]

Hi! I am currently doing a project that involves calling copy number variants, and then running a GWAS with several quantitative traits.

I've found a particular deletion that seems to be associated with neutrophil levels, but a check on ensembl shows there are no genes in the region - only lncRNA, CTCF binding sites, and "open chromatin". I've checked gwas catalog/gtex too but found nothing.

Anybody has ideas on how to further explore the function of this region? Perhaps any tools or databases to see if the region interacts with distal sites? Or any way to predict the function of the lncRNA/CTCF binding sites?

Thanks in advance!

[Amitm]

Hi, Some suggestions. you might have checked already - 1) On UCSC Genome Browser, turn on the ENCODE region regulatory and expression level tracks. Though from cell line, there is a range of cell lines and stem cells and different histone marks & concurrent expression levels. 2) Recently, FANTOM had its pub. about comprehensive identification of lncRNAs. You can check your region at their dedicated genome browser here.

[Amitm]

Jean-Karim's answer below reminded me of this browser where you can explore effect of chromatin interaction 3D genome browser especially relevant in topologically associate domains (TADs)/ CTCF binding sites

[Emily]

lncRNAs are genes!!!

Answer 1

[Jean-Karim Heriche]

CTCF binding is involved in chromatin structure. In particular, CTCF binding sites define topologically-associated domains, see for example this review. If the deleted region removes CTCF sites then it likely changes the structure of the chromatin in this region with most likely consequences on gene expression as explained in this other review (see figure 2 for examples).

Answer 2

[Emily]

You could look at the SNPs in the region (particularly within the CTCF binding site) and see if any of them are eQTLs, then explore the genes that are affected by them. Click on the SNPs in the region and go to Genes and Regulation.