Why some SNP's are not assigned to any gene?

Question

[farshad.madani]

Hi everyone,

I am doing polygenic risk analysis (PRS) ; As you may know PRS is done based on SNP's. On the other hand, I would like to do some visualizations at gene level. Thus, I used rsnps library (ncbi_snp_query command) to map SNP's on genes. I shared the image of the result which is a csv file. As you see, some SNP's are not assigned to a gene. I would like to know what the possible reasons are.

FYI: rsnps library extracts information from dbsnp belonged to NCBI.

Thanks in advance

[German.M.Demidov]

Genes (~exome) occupy <2% of human genome =)

[farshad.madani]

Does it mean I should get rid of rsIDs without gene assigned?

[German.M.Demidov]

No, why would you?

Answer 1

[GiantSilverSoy]

I have never used the tool but I think it is because those SNPs are in the intergenic regions.

Answer 2

[fznajar]

SNPs can occur in intergenic regions as well. they could be SNPs affecting regulatory sequences changing the expression of a regulon.