Common haplotype search
Xuei, Xiaoling
Dear UCSC Genome Browser Support,
We are trying to search for common haplotype block information. This feature used to be easily accessible via HapMap.org (viewed as upside-down triangle plots). However, since 1000G era, HapMap.org has been shut down. I noticed that you have HapMap SNP info in your hg19 version of the browser. But I can’t seem to find its common LD block information. Do you have those info in your browser and how can I find it? If you don’t have the feature, may I ask where I can find the info?
Thanks very much for your help.
Ling
Xiaoling Xuei, Ph.D
Research professor and Technical director
The Center for Medical Genomics
Department of Medical & Molecular Genetics
Indiana University School of Medicine
980 W. Walnut St, Rm C418
Indianapolis, IN 46202
Phone: (317)278-5201
Email: xx...@iu.edu
Brian Lee
Dear Xiaoling,
Thank you for using the UCSC Genome Browser and your question about finding common LD block information in regards to our hg19 HapMap SNP track.
Before sharing about the resources at UCSC, please know that there are still hosted HapMap data at these NCBI locations:
https://ftp.ncbi.nlm.nih.gov/hapmap/
https://ftp.ncbi.nlm.nih.gov/hapmap/ld_data/
You may also be interested in these other Linkage Disequilibrium resources:
https://www.broadinstitute.org/medical-and-population-genetics/hapmap-3
http://www.ensembl.org/Homo_sapiens/Tools/LD?db=core
What the UCSC Genome Browser does currently have is a track that can display hg18 HapMap data, which at this point is quite old:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=hapmapLdPh
https://genome.ucsc.edu/s/brianlee/hapMap_18
This data has not been updated since 2008. We do have plans to create new LD tracks, and your interest has been noted in the work tickets, although there is no estimate of when these will be available.
For custom visualization we do have custom tracks for the .hic format: https://genome.ucsc.edu/goldenPath/help/hic.html
Thank you again for your inquiry and for using the UCSC Genome Browser. If you have any further public questions, please send new questions to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly accessible forum to help others find answers to similar questions. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu, which is a private internal list to our support team.
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Xuei, Xiaoling
Thanks very much Brian for the info. Greatly appreciated.
Ling
From:
Brian Lee <bria...@soe.ucsc.edu>
Date: Wednesday, June 22, 2022 at 5:52 PM
To: Xuei, Xiaoling <xx...@iu.edu>
Cc: gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
Subject: [External] Re: [genome] Common haplotype search
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