Dataset

HapMap

Added By Infochimps
  1. Description

The International HapMap Project is a partnership of scientists and funding agencies from Canada, China, Japan, Nigeria, the United Kingdom and the United States to develop a public resource that will help researchers find genes associated with human disease and response to pharmaceuticals.

  1. Datasets

From

The following directories contain HapMap project related data, software, and documentation, that have been made publicly available. (See HapMap Data Access Policy for more information). More details about each dataset can be found in READMEs in the respective directories:

  • Bulk data
    • Genotypes: Individual genotype data submitted to the DCC to date.
    • LD Data: Linkage disequilibrium properties D’, LOD , R2 compiled from the genotype data to date
    • Phasing Data: Phasing data generated using the PHASE software, compiled from the genotype data to date.
    • Allocated SNPs: dbSNP reference SNP clusters that have been picked and prioritized for
      genotyping according to several criteria (see info on how SNPs were selected). The file 00README contains per-chromosome SNP counts and further details.
    • Frequencies: Allele & genotype frequencies compiled from genotyping data submitted to the DCC to date. These have also been submitted to dbSNP and should be available in the next dbSNP build.
    • Recombination rates and Hotspots: Recombination rates and hotspots compiled from the genotyping data.
    • SNP assays: Details about assays submitted to the DCC to date. PCR primers, extension probes etc., specific to each genotyping platform.
    • Perlegen amplicons: Details for mapping Perlegen amplicons to HapMap assayLSID. For primer sequences, see Perlegen’s Long Range PCR Amplicon data.
    • Raw data: Raw signal intensity data from HapMap genotypes. Currently includes data from Affymetrix GeneChip 100k and 500k Mapping Arrays.
    • Inferred genotypes: Genotypes inferred using the method of Burdick et al. Nat Genet 38:1002-4
    • .

  1. Openness: OPEN
  • License: see
  • Access: good
  • bulk: yes.
  • web: yes. [generic genome browser](http://www.hapmap.org/cgi-perl/gbrowse/gbrowse) and report generation using [HapMart](http://hapmart.hapmap.org/BioMart/martview)