how to look at interacting SNP for a gene using Hic contact map

Question

[rheab1230]

Hello everyone, I have one HiC contact map file corresponding to a particular cells( brain frontal cortex). I want to looking at how many snps are located within 40kb distance from this gene and are interacting with it and include those selected snps in my study.

Like suppose: I select a gene : cry1: for this particular gene I want to look at distance 40kb from the gene length upstream and downstream and select snps that are interacting with this gene based on the contact map

I have a contact map in form of bed file(40kb) for hg38 for brain frontal cortex that looks like this:

rf1     rt1     rf2     rt2     inf
79359   99359   79359   99359   0
79359   99359   99359   139359  0
79359   99359   139359  219359  709.12853856921
79359   99359   179359  2e+05   668.390446056238

Its basically means that 79359-99359 is interacting with 139359 to 219359 region in hg38 and have interacting freq of 709.128

Is there any tool that can develop a interacting contact map like this:

Answer 1

[james.hawley]

For the part of your question about finding all the SNPs in a given region, you can use standard tools like bedtools for performing genomic region intersections. If you have mutation calls from some sample(s) of interest, you can use those locations and find which ones are close enough to CRY1. Or, if you don't have specific sample mutations, you can start with a database of disease-associated SNPs, like dbSNP.

Similarly, it sounds like if you have Hi-C loop calls from some sample(s) of interest, so you can intersect the endpoints of those loops with your SNPs and CRY1. If you want to compare your results with other published data, you might be able to find some relevant Hi-C contact matrix from ENCODE or 4DNucleom.

For the second part of your question, where you want to visualize those loops and SNPs, you might be able to use the UCSC Genome Browser or WashU's 3D Genome Browser. If you're using private data that can't be uploaded to a server, then you might want to use software like HiGlass or Gosling. Each of these tools has documentation for adding and displaying different data types, like BED files, loops, and more.