Hi Kyle, The flanking sequences are submitted to dbSNP by individual scientists who observe SNPs in their sequencing projects, and the sequence sizes probably depend on the sequencing technology used. dbSNP collects the submitted SNP data, maps the flanking sequences to the reference genome, and uses the mappings to cluster the submitted SNPs into reference SNPs (the rs* IDs that we display). For each reference SNP, they choose a representative submitted SNP, and I believe those are the flanking sequences that they publish and we download for display.
On the details page for an rs* reference SNP, you can click through to dbSNP's report page (click the "dbSNP: rs12014875" link just below title). There you can see all submitted SNPs that have been clustered into that reference SNP, and their flanking sequences. More info about dbSNP's methods can be found at http://www.ncbi.nlm.nih.gov/SNP/ . Hope that helps, Angie ----- "Kyle Tretina" <[email protected]> wrote: > From: "Kyle Tretina" <[email protected]> > To: [email protected], "Pattle Pun" <[email protected]> > Sent: Tuesday, December 29, 2009 12:27:48 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] SNP Sequences question > > To whom it may concern, > > When I enter in an rs number that corresponds to a SNP in your database, > what determines how much sequence upstream and downstream is pulled from the > genome? For example rs34668160 yields 300bp upstream and 300bp downstream of > the SNP, while rs12014875 yields 500bp upstream and 500bp downstream. > What determines this? > > > > > Kyle Tretina > Wheaton College > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
