International HapMap Project   Home | About the Project | Data | Publications | Tutorial

Guidelines for the Responsible Use and Publication of HapMap data is available here.

Browse data graphically

Downloads

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. Phase 3 data is available in PLINK format and HapMap format.
• 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.
• 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.
• 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, 500k and GenomeWide 6.0 (hapmap3 samples only) Mapping Arrays.
• Inferred genotypes: Genotypes inferred using the method of Burdick et al. Nat Genet 38:1002-4.
• Mitochondrial and chrY haplogroups: Classification of phase I HapMap samples into mtDNA and chrY haplogroups. The distribution shown in Table 4 of the HapMap phase I paper (Nat Genet 38:1002-4) corresponds to unrelated parents in each one of the populations analyzed.


• Software
• Generic Genome Browser : Complete set of Gbrowse configuration files, GFF files, plugins and more to enable local installation of Genome Browser, with HapMap genotypes and allele frequency data.


• Documentation
• Protocols: Information on assay design, genotyping and other protocols used in the project.
• Samples/individuals: Information on the samples used in the project and the individuals from which they were drawn. Click here for an all inclusive Table. Also see About the project: Which Populations are Being Sampled. Click here for a summary table of samples genotyped during the phase 3 of the project.
• XML docs: Documentation on the XML format used in the project.

ENCODE regions

Ten ENCODE regions are being studied by HapMap centers. The work includes genotyping all dbSNP SNPs in each region, as well as resequencing in several samples and genotyping additional SNPs found.These regions were chosen by the Analysis Group and they include a range of chromosomes, recombination rates, gene density, and values of non-transcribed conservation with mouse. For more information about the ENCODE Project see HapMap ENCODE Page, special genotype data dumps are available here.

Release notes

HapMap data release #27, February 2009, on NCBI B36 assembly, dbSNP b126 --

This release contains genotypes and frequencies for non-redundant SNP assays from phases I+II 
and III of the HapMap project. For SNPs genotyped in both phases of the project, phase III SNP 
assays were preferentially selected, as they included all HapMap samples to date. 

Note for genotypes files: For SNPs with no data in phase III (ie, only included in phase I+II), 
"NN" was used as place holder.

Additional information may be found in the README document:
http://ftp.hapmap.org/genotypes/2009-02_phaseII+III/00README.txt 

SNP assays excluded from this data merging due to mapping or other inconsistencies are described in:
http://ftp.hapmap.org/genotypes/2009-02_phaseII+III/excluded/

Genotyped non-redundant QC+ SNPs:

    	    ASW	      CEU	CHB	  CHD	    GIH	      JPT	LWK	  MEX	    MKK	      TSI	YRI
 chr1	125,164	  314,024   317,029   103,706	111,741	  317,064   122,489   113,046	123,157	  112,832   313,089
 chr2	126,472	  329,831   330,327   105,178	113,345	  330,336   124,129   113,995	124,679	  114,423   323,672
 chr3	104,858	  259,412   259,203    87,824	 94,383	  259,234   102,919    94,614	103,429	   95,327   255,305
 chr4	 94,828	  248,215   248,219    79,033	 85,351	  248,212    93,104    84,253	 93,829	   86,343   243,525
 chr5	 95,689	  250,737   251,038    81,155	 87,120	  251,068    93,834    86,644	 94,545	   87,645   246,468
 chr6	 99,332	  272,260   275,906    85,080	 90,708	  275,745    96,847    90,521	 97,455	   92,312   270,243
 chr7	 82,175	  216,504   217,044    70,020	 75,158	  217,030    80,666    74,875	 81,168	   75,898   212,991
 chr8	 82,406	  215,909   218,713    68,789	 74,807	  218,728    80,795    74,056	 81,305	   75,166   215,260
 chr9	 69,344	  183,866   185,100    59,262	 63,740	  185,112    67,500    63,040	 68,067	   64,017   182,668
chr10	 79,805	  211,711   213,854    67,592	 72,893	  213,855    77,929    73,680	 78,508	   73,287   210,285
chr11	 76,819	  206,952   207,904    64,479	 69,181	  207,943    75,040    69,045	 75,554	   69,851   202,434
chr12	 74,290	  195,155   195,796    62,783	 67,738	  195,814    72,400    67,875	 72,875	   67,478   193,705
chr13	 57,082	  157,463   159,498    47,806	 51,852	  159,479    56,138    51,151	 56,677	   52,346   156,923
chr14	 49,241	  124,726   125,271    41,557	 44,698	  125,270    48,274    44,830	 48,553	   45,153   122,651
chr15	 45,561	  108,464   108,827    38,648	 41,086	  108,836    44,792    40,940	 44,854	   41,300   106,474
chr16	 48,073	  111,845   111,600    39,489	 42,710	  111,611    47,213    43,122	 47,204	   43,081   109,668
chr17	 40,775	   92,358    91,994    33,630	 36,357	   92,030    39,988    36,920	 39,983	   36,980    90,774
chr18	 44,892	  120,207   120,958    37,267	 40,082	  120,938    44,090    40,385	 44,294	   40,511   118,999
chr19	 27,754	   59,607    59,352    23,528	 25,035	   59,350    27,495    25,771	 27,154	   25,310    58,688
chr20	 38,747	  121,069   121,014    32,237	 34,992	  121,007    38,016    35,679	 38,227	   35,327   119,071
chr21	 21,186	   50,983    52,359    18,143	 19,391	   52,363    20,802    19,265	 20,964	   19,620    51,153
chr22	 21,785	   55,941    57,474    18,183	 19,752	   57,496    21,162    19,692	 21,246	   19,943    56,748
 chrX	 54,720	  122,601   122,933    40,409	 45,322	  122,979    53,704    46,475	 53,486	   45,376   122,642
 chrY	    384	      722	716	  354	    376	      716	367	  357	    348	      335	710
 chrM	     71	      212	207	   44	     59	      207	 71	   34	     77	       60	210

-----------------------------------------------------------------------------------------------------------------------
Total 1,561,453	4,030,774 4,052,336 1,306,196 1,407,877	4,052,423 1,529,764 1,410,265 1,537,638	1,419,921 3,984,356

-----------------------------------------------------------------------------------------------------------------------

help@hapmap.org

About

The HapMap Data Coordination Center (DCC) coordinates and manages project data flow, data storage, data release and presentation to the community. This includes managing the genotype database and this website. The DCC is operated by Lincoln Stein's group at Cold Spring Harbor Laboratory.

Last updated : index.html.en,v 1.19 2007/04/12 20:18:09 tellorui Exp