Hi Jirong, On the dbSNP page you provided, in the "Integrated Maps" section there is a column labeled "SNP to Chr" which contains "-" in the row labeled GRCh37.p5. This is the mapping we use for hg19, and the strand matches what we have in snp135.
If you are looking in the "Submitted records for this RefSNP Cluster" section, there is a column labeled "ss to rs Orientation/Strand". dbSNP clustered a bunch of submitted SNPs (ss's, that we don't store) into rs1000026. It chose ss1459614 as the representative ss because it had the longest flanking sequence, and used it as the basis of rs1000026 -- keeping the orientation of ss1459614 which is on the reverse strand of the reference genome. Then it reports all the ss's on the forward strand of the reference as "rev/B", because their orientation is the opposite of ss1459614. I hope this information is useful and answers your question. Please contact us again at [email protected] if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group On 4/25/2012 1:53 PM, Long, Jirong wrote: > > Thanks Luvina. > > The Alleles_dbSNP are based on the forward strand from dbSNP website, > eg, http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=1000026. > It is A/G on forward strand in dbSNP, but C/T on UCSC. Could you > please help to check? > > Thanks. > > Jirong > > *From:*Luvina Guruvadoo [mailto:[email protected]] > *Sent:* Wednesday, April 25, 2012 3:50 PM > *To:* Long, Jirong > *Cc:* [email protected] > *Subject:* Re: [Genome] inconsistent alleles between dbSNP and UCSC > > Hi Jirong, > > The allele information you provided is actually based on the reverse > strand, which is consistent with what we have here at UCSC. > > Please contact us again at [email protected] > <mailto:[email protected]> if you have any further questions. > > --- > Luvina Guruvadoo > UCSC Genome Bioinformatics Group > > On 4/24/2012 1:06 PM, Long, Jirong wrote: > > Dear Sir/Madam, > > We found the allele information (based on forward strand) for the attached > SNP list is inconsistent between dbSNP and UCSC. Could you please help to > check which is correct? Thanks. > > Jirong > > ******************************************** > Jirong Long, PhD, > Assistant Professor > Vanderbilt Epidemiology Center > Institute of Medicine& Public Health > Vanderbilt University Medical Center > Eighth Floor, Suite 800 > 2525 West End Avenue > Nashville, TN 37203-1738 > E-mail:[email protected] > <mailto:[email protected]><mailto:[email protected]> > Tel: 615-343-6741 > Fax:615-322-0502 > www.mc.vanderbilt.edu/epidemiology > <http://www.mc.vanderbilt.edu/epidemiology><https://email.mc.vanderbilt.edu/owa/redir.aspx?C=ed5e61c26c634aad9f4aef28b262a88d&URL=http%3a%2f%2fwww.mc.vanderbilt.edu%2fepidemiology> > > <https://email.mc.vanderbilt.edu/owa/redir.aspx?C=ed5e61c26c634aad9f4aef28b262a88d&URL=http%3a%2f%2fwww.mc.vanderbilt.edu%2fepidemiology> > > > > > > _______________________________________________ > Genome maillist [email protected] <mailto:[email protected]> > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
