Question: How can I find the most studied SNP of a gene?
0
gravatar for lol
3.7 years ago by
lol20
Greece
lol20 wrote:

Hi,

How can I find the most studied SNP of a gene and diseases that the most studied SNP has been related to?

I search in dbSNP database but I can't find it.

What is the process?

snp database bioinformatics gene • 1.5k views
ADD COMMENTlink modified 3.7 years ago by rbagnall1.4k • written 3.7 years ago by lol20
1
gravatar for rbagnall
3.7 years ago by
rbagnall1.4k
Australia
rbagnall1.4k wrote:

It would be difficult to find the 'most studied SNP' and, moreover, this might not be the best way to phrase your question. For example, a SNP in gene X may be associated with height; a different SNP in gene X may be associated with ageing. The SNP associated with height may have been reported many years ago and so has lots of publications replicating the very weak association. The other SNP may have a very strong association with ageing, but may be a recent finding. Also, the two SNPs may be in complete linkage, so you are essentially looking at equivalent SNPs. Perhaps it would be better to explain what you are trying to do? 

Anyway, have a look at the following resources:

1. There is a catalogue of SNPs that are associated with traits shown at the GWAS catalogue http://www.ebi.ac.uk/gwas/ . Enter a gene symbol (e.g. BRCA1) and on the search results page, select 'associations' in the left column to show SNPs within the gene that are associated with different traits.

2. The HapMap project has been around for many years and the reported SNPs that 'tag' a haplotype block within a gene may be often studied simply because that are validated and often included in commercial 'genotyping arrays'. http://hapmap.ncbi.nlm.nih.gov/

 

 

ADD COMMENTlink written 3.7 years ago by rbagnall1.4k

I want to find the most studied SNP for BRCA1 gene and other diseases/phenotypes that the most studied SNP has been related to.

ADD REPLYlink written 3.7 years ago by lol20

I don't understand the meaning "the most studied".

How can I find it?

ADD REPLYlink written 3.7 years ago by lol20
1

If you don't understand it, why are you asking for it?

ADD REPLYlink written 3.7 years ago by Emily_Ensembl19k

Do you mean 'number of publications'?

If you go to the NCBI variation viewer tool http://www.ncbi.nlm.nih.gov/variation/view/ and search for BRCA1, then filter the search results for 'has publications' (bottom of left column). This shows rs8176323 has 2 publications, and clicking on the number 2 will take you to the pubmed entries, which will lead you to the phenotypes that this SNP has been related to. 

ADD REPLYlink written 3.7 years ago by rbagnall1.4k

An additional resource to find many SNP-specific results is to search (or download) results from GRASP. You can search by SNP rsID or genomic position/range: https://grasp.nhlbi.nih.gov/Search.aspx

ADD REPLYlink written 2.5 years ago by johnsonad20
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