Obtaining information about SNPs

This question was a while back on BioStar, ways to get information about a list of SNPs. It got me to thinking, what are the various ways to obtain a file of information about a list of SNPs  (I’m assuming no programming skills, web or other simple query)? The obvious way for me is the UCSC Table Browser. Our tutorial (free) has an exercise that does just that. The question, for a given gene find data about all the SNPs annotated for that region, is simply answered.

What other ways are there? Turns out there are quite a few, I’ve started to list them here. All these I’ve used “clock” in human as my query and pulled a list of information about the SNPS in that region. In no particular order:

UCSC Table Browser (many species): See (tutorial - free)
Genome Variation Server (GVS, human only): click “gene name” > select populations & parameters > select “display SNP summary” > add or remove columns of data needed.  (tutorial – subscription)
Ensembl BioMart (many species):  choose Database  (Ensembl Variation) > choose dataset (homo sapiens dbSNP 132) > choose filter (chromosome and start/end base pair) > choose attributes (name, strand, etc). (tutorial- subscription)
Varietas (human):  choose genes > type in gene name > click search (a video tip from the blog)
F-SNP (human):  click search > choose “query by gene” > type in “clock” > submit (a video tip from the blog)
dbSNP  of course (many species): choose SNP database > choose limits (chromosome & location) > click search (tutorial – subscription)
SNPVar (various): in the comments below, Glenn details how to obtain a list using this NCBI feature. More here about gettings SNPs in a gene at NCBI.

Which one you choose will depend on what you want  (species? data?) or what format you need. My favorite is still the Table Browser, but that’s a personal preference.

Do you have databases or tools to pull down a list of SNPs  and data in a gene? Please mention them in comments below. For our purposes for this list, let’s stick with web-interfaces or simple queries. They could be specialized by species, or by type (disease-related?) or by other specialization such as related by pathway. I’ll put them here in this list.

For sql query or programming interface, you might want to explore the link to Biostar above, there are a lot of answers there too for that!


2 thoughts on “Obtaining information about SNPs

  1. Glenn Hammonds

    Use the SNPVAR link from the ncbi GENE entry. Offers a choice of showing All snps over an interval, just those that map to a Refseq gene, or those that are clinically associated. All data is downloadable as text, in compressed form. If you know the NCBI gene id number, you can navigate directly to the relevant page without searching. For example, EGFR is gene 1956, so the SNPVAR page is http://www.ncbi.nlm.nih.gov/sites/varvu?gene=1956 . In addition NCBI compiled information on how to work with SNPs at NCBI, available here – http://www.ncbi.nlm.nih.gov/books/NBK3848/

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