Question

Where to find information on LD ~ distance?

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6.5 years ago

moxu ▴ 510

We want to know how far away Linkage Disequilibrium (LD) can go between SNPs, but I have difficulty locating such information. I checked out SNPsnap from Broad Institute at https://data.broadinstitute.org/mpg/snpsnap/database_download.html, but it actually does not have such information.

Any help would be highly appreciated.

SNP genome • 1.5k views

ADD COMMENT • link 6.5 years ago by moxu ▴ 510

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Haploreg LD data based on 1000 Genomes Phase 1: http://archive.broadinstitute.org/mammals/haploreg/data/

ADD REPLY • link 6.5 years ago by zx8754 12k

score 2 · Accepted Answer · 2018-05-16

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6.5 years ago

Pierre Lindenbaum 164k

ftp://ftp.ncbi.nlm.nih.gov/hapmap/ld_data/latest

?

ADD COMMENT • link 6.5 years ago by Pierre Lindenbaum 164k

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That is it!

Thanks so much!

ADD REPLY • link 6.5 years ago by moxu ▴ 510

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One more question: it looks like the they limited the distance between SNPs to be under 200kb, while at 200kb, there are still tons of significant LDs as the data can tell. I am not sure why they cut it off at 200kb and do not look beyond 200kb?

ADD REPLY • link 6.5 years ago by moxu ▴ 510