Question: Where to find information on LD ~ distance?
0
gravatar for moushengxu
6 days ago by
moushengxu300
moushengxu300 wrote:

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 • 79 views
ADD COMMENTlink written 6 days ago by moushengxu300

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

ADD REPLYlink written 6 days ago by zx87544.3k
2
gravatar for Pierre Lindenbaum
6 days ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum107k wrote:

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

?

ADD COMMENTlink written 6 days ago by Pierre Lindenbaum107k

That is it!

Thanks so much!

ADD REPLYlink written 6 days ago by moushengxu300

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 REPLYlink written 6 days ago by moushengxu300
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