how to look at interaction between SNP and gene

Question

[rheab1230]

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

Answer 1

[Mark]

I think you are talking about perform a GWAS?

[rheab1230]

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