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I have identified a genomic region (CpG island) that is enriched for a characteristic of interest in the vast majority of my samples.

After viewing it in the UCSC genome browser, I have confirmed that it does not overlap any annotated gene promoters, gene bodies, or retrotransposons, but am convinced that it is functionally interacting with something long range.

Is there a publicly available visualization tool where I can input my genomic region and get a list of topologically associated domains from 3C or other chromatin-chromatin interaction data?

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    $\begingroup$ What assembly is your genomic region of interest in? $\endgroup$
    – juniper-
    Sep 18, 2017 at 0:32
  • $\begingroup$ The assembly I used was hg19/GRCh37 $\endgroup$
    – Ben D.
    Sep 26, 2017 at 18:00

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I would also recommend two very recent Hi-C visualization frameworks (with some public data available in both): HiGlass and JuiceBox.

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If you have more than a dozen or even hundreds of regions that you want to compare you could check a companion tool of HiGlass called HiPiler. HiPiler lets you arrange, cluster, and pile up to thousands of genomic regions. Take a look at this 5min video introduction to see if the tool could help you to answer your questions.

Disclaimer: I am the creator of HiPiler.

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Depending on the genome you want, you may be able to use the chorogeneome navigator, which is from some of my colleagues. This uses a number of public HiC datasets and allows you to view interactions.

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