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

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

enter image description here

annotation gene SNP • 512 views
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1
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Genes (~exome) occupy <2% of human genome =)

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

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No, why would you?

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4 weeks ago

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

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29 days ago
fznajar • 0

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

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