Ah OK, thanks Brook. I get it now. Can you change the initial display so it shows the coordinate without adding on the flanking bases, e.g. when I search for it I get this, maybe it could just show the actual base?
E.g. change Simple Nucleotide Polymorphisms (dbSNP 135) rs76417519 at chr1:117142391-117142891 <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr1:117142391-117142891&hgsid=273423697&snp135=pack&hgFind.matches=rs76417519,> to Simple Nucleotide Polymorphisms (dbSNP 135) rs76417519 at chr1:117142641 <http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr1:117142391-117142891&hgsid=273423697&snp135=pack&hgFind.matches=rs76417519,> On Fri, May 25, 2012 at 5:25 PM, Brooke Rhead <[email protected]> wrote: > Hi Archie, > > When you paste rs76417519 into the position/search box on the Genome > Browser, the link you get is a result that says: > > rs76417519 at chr1:117142391-117142891 > > This is position chr1:117,142,641, with 500 extra bases that provide > "padding" on each side of the SNP. The SNP itself is still in the same > location. (We add the padding to avoid suddenly zooming people in to a > single base pair.) > > If you have further questions, please contact us again at > [email protected]. > > -- > Brooke Rhead > UCSC Genome Bioinformatics Group > > > > On 5/25/12 11:31 AM, Archie Russell wrote: > >> Hi >> >> I'm looking into rs76417519 >> >> I downloaded a file a while back with positions on hg19 >> and it says this SNP is at chr1:117,142,640-117,142,641 >> >> But when I look it up now at the browser I see it as >> position chr1:117,142,391 >> >> Any ideas why this is the case? Were the SNP positions >> updated? >> >> Thanks >> Archie >> >> >> >> The line from the file I downloaded some time ago: >> >> 1478 chr1 117142640 117142641 rs76417519 0 + G G A/G genomic single >> by-cluster,by-frequency 0.005297 0.051189 missense exact 1 8 >> BCM-HGSC-SUB,BL,BUSHMAN,**ENSEMBL,ILLUMINA,MPI_MOLGEN,**NHLBI-ESP,PJP, 2 >> A,G, >> 12.000000,4507.000000, 0.002655,0.997345, >> ______________________________**_________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/**mailman/listinfo/genome<https://lists.soe.ucsc.edu/mailman/listinfo/genome> >> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
