Dear Jinying, Although the SNP did not have a public name at the time of publication, dbSNP does have a record mapped to the equivalent location in more recent builds. To find the coordinate in the latest human assembly (GRCh37), you can use the Convert link in the Genome Browser's top blue bar. First visit the published coordinate in NCBI 34 by clicking the Genomes link and selecting "July 2003 (NCBI34/hg16" from the assembly menu (assuming the genome menu is set to "Human"). Then paste this into the "position or search term" input:
chr12:94896055-94896055 and click submit. Then click the "Convert" link in the blue bar at the top. Select "Feb. 2009 (GRCh37/hg19)" and click submit. One location is shown; click on that. In the SNPs (131) track, you can see the item rs61937881. Click on the item to see more information about it, including a link to dbSNP's report page. As for computing linkage disequilibrium, I don't think there is enough information to do this properly for rs61937881/SG12S16. Computing LD can be done by the program HaploView (http://www.broadinstitute.org/haploview/haploview), but it requires full genotypes in a large enough number of samples to be statistically significant. In the "Mar. 2006 (NCBI36/hg18)" assembly, we do have an LD track computed using phased genotypes from HapMap. Back on the Convert page, select "Mar. 2006 (NCBI36/hg18)" instead of the latest, and then click into the analogous location in NCBI36 (chr12:94,917,718-94,917,718). You can see rs61937881 in the SNPs (130) track (131 is not available for NCBI36). In the Variation and Repeats section of track controls below the image, find the HapMap LD Phased track, change its viewing mode to "full", and click submit. Nothing appears for this 1-base region, but try zooming out to view a larger region, or simply paste chr12:94,917,718-94,925,384 into the position/search input for a region that has rs61937881 on the left and rs2660880 on the right. Fortunately rs2660880 is a HapMap SNP, so we have some information about LD between rs2660880 and other nearby HapMap SNPs. The HapMap LD Phased track shows mountain plots of LD computed on HapMap SNP genotypes of many samples from 3 main population groups: CEPH (CEU),an Chinese from Beijing plus Japanese from Tokyo (CHB+JPT), and Yoruba (YRI). Click on the gray bar at the far left edge of the graphical image to view more details about the track data and display options. rs61937881 falls between the two HapMap SNPs rs17025016 and rs11108372. Paste chr12:94,917,626-94,925,384 into the position/search input to view the region between rs17025016 and rs2660880. The peak of the graph shows LD between rs17025016 and rs2660880, and below and to the right of that is a diamond showing LD between rs11108372 and rs2660880. Can those be used as a proxy for the LD between rs61937881 and other SNPs? Honestly, I don't know enough statistics and genetics to answer that. I offer this only as the information that is available using our browser and database. As more human genomes are sequenced, e.g. by the 1000 Genomes Project, I expect that LD can be calculated with much higher granularity. I hope that we will have better information within another year or two. Hope that helps and best wishes for your research, Angie > Subject: A question on SNP search > From: "Zhao, Jinying (HSC)" <[email protected]> > Date: Tue, 31 Aug 2010 08:05:12 -0500 > To: "[email protected]" <[email protected]> > > Dear UCSC Technical Support Team: > > I would like to find some information around a SNP that was genotyped > by decode company. The SNP (called SG12S16) does not have a public > name. The basepair position on chromosome 12 for this SNPs in the > human genome assembly build 34 (NCBI)) is 94896055. My questions are: > > 1. How to find other nearby SNPs that are in close linkage > disequilibrium with this SNP? > > 2. What is the distance of this SNP with rs2660880? > > Best wishes and thank you very much for your support! > > Jinying > > ===================================== > Jinying Zhao, MD, PhD > Associate Professor > Department of Biostatistics and Epidemiology > The University of Oklahoma Health Science Center > 801 NE 13th Street, Room 301 > Oklahoma City, OK 73104 > Tel: 405-271-2229 > Fax: 405-271-2068 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
