[Genome] Haplotype data of HapMap - ENCODE regions

[Heather Trumbower]

Makoto:

You are indeed looking for HapMap data which is available from 
http://www.hapmap.org.

Specifically, genome-wide phasing data is available by going to
http://www.hapmap.org/ and clicking on 'Bulk Data Download' under
'Project Data'.

This takes you to http://www.hapmap.org/downloads/index.html.en.
You can then click on 'Phasing Data' under ('Bulk Data').

There are two directories there.  Phase II includes all of Phase I.
The documentation for the Phase II data is
http://www.hapmap.org/downloads/phasing/2006-07_phaseII/00README.txt.

You may also be interested in the 'ENCODE Project' link which is available 
from the main page in the 'Project Data' section.

As far as I know, the ENCODE re-sequencing data have not been phased 
separately.

The HapMap mailing list -- help at hapmap.org -- may be able to provide more 
information.

Heather Trumbower
UCSC Genome Bioinformatics Group


On Thu, 5 Apr 2007, Makoto Shimada wrote:

> To whom it may concern,
>
> I wonder if I could have public haplotype data around genic regions by
> re-sequencing of some human population containing several individuals.
> I guess that there are haplotype data of HapMap - ENCODE regions, which
> were re-sequenced in 48 unrelated individuals.
> Could you tell me where those are available?
>
> I know how to get genotype data in each SNP site from following site,
> http://www.hapmap.org/downloads/genotypes/  .
> However these are not done haplotype inference (phasing).
> I would like to have (phased) haplotype data.
>
> I attached archives relating this subject.
>
> With my best,
> Makoto
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Makoto Shimada, Ph.D.
> Integrated Database Team
> Japan Biological Information Research Center
>
> AIST Tokyo Waterfront Bio-IT Bldg 7F
> 2-42 Aomi, Koto-ku,
> Tokyo, Japan, 135-0064
> TEL: +81-3-3599-8537, FAX: +81-3-3599-8801
> E-mail: mashimad at jbirc.aist.go.jp
> http://www.jbirc.aist.go.jp/idt/index_e.html
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~