Question: How To Get Info On "Clinically Associated Snps"
3
gravatar for Wayne
6.6 years ago by
Wayne1000
United States
Wayne1000 wrote:

Hello all,

I have a collection of SNPs that are labeled in UCSC as "clinically Associated" I have tried searching for them in OMIM/OMIA and clicked around on everything I can think of to find information about what this clinical association might be. Does anyone know where this information is stored, and if there is perhaps a downloadable database where I can find more information.

One example is this SNP rs59176601. Cant find anything on it, even though it is "Flagged as Clinically associated"

Thanks!!

dbsnp disease snp cancer • 1.9k views
ADD COMMENTlink modified 6.6 years ago by Philipp Bayer6.1k • written 6.6 years ago by Wayne1000
1

When I searched for rs59176601 - I found that it has not been implicated in association studies in dbGaP. It is however a variant that results in a frameshift in MAFA. It seems that the annotation 'Clinically associated' might be rather broad - this is perhaps something to keep in mind when mining for information on your set of SNPs.

ADD REPLYlink written 6.6 years ago by Darren J. Fitzpatrick1.1k
2
gravatar for Genotepes
6.6 years ago by
Genotepes940
Nantes (France)
Genotepes940 wrote:

Maybe this means that theyr are associated in GWAs context (although I have no clue of why it is "clinical" as there are a lot of traits). Have a look at the updated list at NHGRI URL.

http://www.genome.gov/gwastudies/#download

and try your SNP on the browser.

You may alos download the whole catalog at the "To download the full catalog: " tag

Christian

ADD COMMENTlink written 6.6 years ago by Genotepes940
2
gravatar for Darren J. Fitzpatrick
6.6 years ago by
Ireland/ United Kingdom
Darren J. Fitzpatrick1.1k wrote:

If those SNPs have an association with some trait above a certain p-value threshold - you will likely find the association in dbGaP. If you search under SNPs (rs ids) in the Phenotype-Genotype Integrator, it ewill return whether your SNPs have been reported as associations, the studies, the traits and also if your SNPs have been reported as eQTLs.

ADD COMMENTlink written 6.6 years ago by Darren J. Fitzpatrick1.1k
0
gravatar for Philipp Bayer
6.6 years ago by
Philipp Bayer6.1k
Australia/Perth/UWA
Philipp Bayer6.1k wrote:

Hi,

if you enter your SNP's name into openSNP.org's search you might get some interesting results - genome.gov, SNPedia, PLOS, Mendeley and Personal Genome project-annotations are summarised for SNPs of DTC-companies.

There is no information stored about your rs59176601-SNP, I guess that one isn't included in any 23andme/deCODEme/FamiltyTreeDNA-assay, as only these are listed.

Manually checking out some of the prior sources reveals:

In fact, not even pubmed has anything: https://www.ncbi.nlm.nih.gov/pubmed?term=rs59176601 Are you sure you spelled the SNP right?

Disclaimer: I'm a co-founder of openSNP

ADD COMMENTlink written 6.6 years ago by Philipp Bayer6.1k
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