Hi Mary, Yep, looks like yet another case of discrepancy between Entrez web interface and raw downloadable dbSNP data. Description of the protocol used by UCSC maintainers to create snp131 table clearly indicates that it originates from the dbSNP raw data.
Best, Ivan On Monday, June 14, 2010 06:29:18 pm Mary Goldman wrote: > Hi Ivan, > > Similar to our previous response, we obtain almost all of our > information from dbSNP (in this case from > ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/database/organism_data/b131 > _SNPContigLoc_37_1.bcp.gz, as is indicated on our details page for this > track). In this file you will find the 7 genomic locations of rs62635282. > > Again, feel free to contact dbSNP at snp-admin at ncbi.nlm.nih.gov if > you have any further questions about this SNP. > > Best, > Mary > --------------------- > Mary Goldman > UCSC Bioinformatics Group > > On 6/11/10 10:49 PM, Ivan Adzhubey wrote: > > Hi, > > > > I was wondering how some SNPs ended up being mapped to multiple different > > locations, e.g.: > > > > snp131 > > > > rs62635282 at chr1:11948-12448 > > rs62635282 at chr15:102518722-102519222 > > rs62635282 at chr16:61629-62129 > > rs62635282 at chr2:114358568-114359068 > > rs62635282 at chr9:12061-12561 > > rs62635282 at chrX:155257274-155257774 > > rs62635282 at chrY:59360280-59360780 > > > > snp130 > > > > rs62635282 at chr1:11948-12448 > > rs62635282 at chr15:102518722-102519222 > > rs62635282 at chr16:61629-62129 > > rs62635282 at chr2:114358568-114359068 > > rs62635282 at chr9:12061-12561 > > rs62635282 at chrX:155257274-155257774 > > > > dbSNP web interface only lists 4 mappings for this particular SNP (chr1, > > chr9, chr15, and chr16). I would appreciate any hints on why such > > discrepancies may have arisen. > > > > Thanks in advance! > > > > Best, > > Ivan > > > > > > > > _______________________________________________ > > Genome maillist - [email protected] > > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
