how to look at interaction between SNP and gene
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14 months ago
rheab1230 ▴ 140

Hello

I have a model file with genes containing model with snps. Like for this particular gene:

gene       rsid               varID ref_allele alt_allele 
ENSG00000181404.15 rs10814410  chr9_46587_C_T_b38          C T
ENSG00000181404.15  rs7857873 chr9_546432_G_C_b38          G C
ENSG00000181404.15 rs16924533 chr9_548464_A_C_b38          A C
ENSG00000181404.15  rs2804279 chr9_550782_A_G_b38          A G

So, according to this file: for this particular gene there are only 4 SNPs associated with gene. I want to see if there could be more SNPs associated with this gene at a long distance using the contact map downloaded from GEO datasets which gives interacting frequencies between two genomic region. Is there any software that can do this?

Thank you

SNP Gene Hi-C • 648 views
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14 months ago
Mark ★ 1.5k

I think you are talking about perform a GWAS?

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No, I want to look at interaction betwene snps and gene through hi-c matrix

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