How To Get Info On "Clinically Associated Snps"

Question

[Wayne]

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!!

[Darren J. Fitzpatrick]

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.

Answer 1

[Genotepes]

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

Answer 2

[Darren J. Fitzpatrick]

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.

Answer 3

[Philipp Bayer]

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:

• SNPedia has nothing ( http://www.snpedia.com/index.php?title=Special%3ASearch&profile=default&search=rs59176601&fulltext=Search )
• Mendeley has nothing ( http://www.mendeley.com/research-papers/search/?query=rs59176601 )

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