Haplotype Block Database
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10.0 years ago
Nathan Harmston ★ 1.1k

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 • 6.3k views
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10.0 years ago
tiagoantao ▴ 690

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

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

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10.0 years ago
mrxcm3 ▴ 60

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

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9.3 years ago

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 :)

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