Question

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

0

Entering edit mode

3.3 years ago

farshad.madani • 0

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 • 1.6k views

ADD COMMENT • link updated 3.3 years ago by German.M.Demidov ★ 2.9k • written 3.3 years ago by farshad.madani • 0

2

Entering edit mode

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

ADD REPLY • link 3.3 years ago by German.M.Demidov ★ 2.9k

0

Entering edit mode

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

ADD REPLY • link 3.3 years ago by farshad.madani • 0

1

Entering edit mode

No, why would you?

ADD REPLY • link 3.3 years ago by German.M.Demidov ★ 2.9k

score 2 · Answer 1 · 2021-09-16

2

Entering edit mode

3.3 years ago

GiantSilverSoy ▴ 130

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

ADD COMMENT • link 3.3 years ago by GiantSilverSoy ▴ 130

score 0 · Answer 2 · 2021-09-19

0

Entering edit mode

3.3 years ago

fznajar • 0

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

ADD COMMENT • link 3.3 years ago by fznajar • 0