This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Haplotype Block Database

Hi,

I'm trying to find a database of precomputed haplotype blocks (really interested in just the CEU population or cell line GM12878). However searching around doesn't seem to provide me with anything.

I obviously have access to the HapMap LD data and I am trying to associate haplotype blocks with a list of SNPs I have ( trying to see if there is anything interesting within then). Do most people download the hapmap data and then process it themselves using haploview / plink etc ? This seems a little wasteful. I had assumed that there would be a precomputed set of blocks somewhere to download and just use.

Thanks

hapmap haplotype database
• 7,797 views • link
updated by scottwilliamrobinson scottwilliamrobinson • written by Nathan Harmston • Nathan Harmston

3 answers

HapMap also has phased data, not only LD, check:

ftp://ftp.hapmap.org/hapmap/phasing/2009-02_phaseIII/HapMap3_r2/

• 0 views • link
written by tiagoantao tiagoantao

Perhaps try the SNAP Proxy Search tool (http://www.broadinstitute.org/mpg/snap/ldsearch.php)?

• 0 views • link
written by mrxcm3 mrxcm3

Try DistiLD, click the mutation tab, enter your 'rs' number then at the following page click submit. I think this is what you are after :)

• 0 views • link
written by scottwilliamrobinson scottwilliamrobinson

Log in to answer this question.

More posts like this