How Does Dbsnp Decide If A Snp Is "Associated" With A Gene?

Question

[Snpdude]

Hi,

In dbSNP I can get a list of all SNPs "associated" with a gene by following these instructions: http://www.ncbi.nlm.nih.gov/books/NBK44466/#Search.how_do_i_get_a_table_report_of_al

I'm wondering though, what exact criteria dbSNP uses to decide if a SNP is "associated" with a gene? I.e. +/- X bps from the gene etc? I can't find this information anywhere that I've looked on the net!

Cheers in advance!

Answer 1

[Damian Kao]

In the instruction's [?]example page[?] displaying all human MAPK Snps, SNPs associated with a gene means SNPs that are in the mRNA sequence of the gene.

In the SNP list page, you can choose "in gene region" or "cSNP". If you choose "in gene region" you'll get SNPs that are 2kbp up stream and 0.5kpb down stream according to [?] this[?]

If you choose cSNP, you'll get SNPs in just the mRNA.

Further down the page of the instructions page you linked has a section for: How do I obtain a list of all the known variants (SNPs, indels, etc.) within a gene, and within the 10 kb immediately 5′ and immediately 3′ of the same gene?

[Damian Kao]

You have in gene region selected right now. If you select cSNP instead of in gene region, you'll get only SNPs within the mRNA. In gene region apparently means 2kbp upstream and 0.5 kbp downstream according to http://www.ncbi.nlm.nih.gov/books/NBK44455/#Build.your_documentation_states_that_a_s

[Snpdude]

It seems that SNPs "3' near gene" and "5' near gene" are also returned. Not sure how "near gene" is defined though, or even if it is the same distance for 3' and 5' ends?

[Damian Kao]

I don't see any of the nearby SNPs displayed on that example page. Which ones do you see that are the nearby SNPs?

[Snpdude]

Sorry, the gene "drosha".

[Damian Kao]

Can you link me the page that you are looking at

[Paul]

http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?chooseRs=all&locusId=29102&mrna=NM_001100412.1&ctg=NT_006576.16&prot=NP_001093882.1&orien=forward&refresh=refresh

Here we go! Thanks again!

[Snpdude]

Excellent that's exactly what I was looking for thatnks!