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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 and 500k 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 #24, October 2008, on NCBI B36 assembly, dbSNP b126 --

This release contains genotypes and frequencies from phases I+II of the HapMap project. 
Allele flips for over 40,000 SNPs have been corrected, and over 1,600 chrX SNPs which 
were inadvertently dropped during the ncbi_b35 -> b36 migration, were added back. 

For a list of SNPs with allele flips corrected, see 
http://ftp.hapmap.org/genotypes/2008-10_phaseI+II/allele_flips_r23a.txt

ChrX SNPs added back in this data release are listed by population panel in
http://ftp.hapmap.org/genotypes/2008-10_phaseI+II/chrX_added_back/

For additional information, please see the accompanying README document:
http://ftp.hapmap.org/genotypes/2008-10_phaseI+II/00README.txt


Genotyped SNPs (all QC+ SNP assays):

		CEU	JPT+CHB	YRI
chr1	nr-set	307,691	311,854	305,929
	QC+	379,506	260,621	376,965
chr2	nr-set	326,231	327,180	318,602
	QC+	426,859	424,975	414,218
chr3	nr-set	255,391	255,618	250,155
	QC+	318,915	316,662	310,203
chr4	nr-set	244,849	245,102	238,922
	QC+	300,279	297,978	290,898
chr5	nr-set	247,632	248,154	242,186
	QC+	305,479	305,234	297,753
chr6	nr-set	268,348	272,814	265,955
	QC+	331,958	336,210	328,528
chr7	nr-set	213,023	213,891	208,708
	QC+	266,683	263,442	257,664
chr8	nr-set	213,095	216,811	212,014
	QC+	265,094	267,622	262,075
chr9	nr-set	181,445	183,433	180,147
	QC+	226,324	227,313	223,471
chr10	nr-set	209,342	211,862	204,146
	QC+	258,207	260,597	256,150
chr11	nr-set	204,228	205,538	195,110
	QC+	249,446	250,502	241,634
chr12	nr-set	191,979	193,071	187,294
	QC+	238,713	237,374	234,775
chr13	nr-set	155,905	158,406	152,674
	QC+	189,784	192,325	188,017
chr14	nr-set	123,071	123,764	118,518
	QC+	152,823	153,121	148,619
chr15	nr-set	106,814	107,363	102,431
	QC+	133,787	133,933	129,902
chr16	nr-set	109,692	109,734	104,530
	QC+	136,362	135,992	132,181
chr17	nr-set	89,701	89,576	85,541
	QC+	113,052	112,582	109,703
chr18	nr-set	119,118	120,025	115,768
	QC+	148,442	148,229	145,067
chr19	nr-set	56,607	56,687	53,766
	QC+	72,005	71,829	69,650
chr20	nr-set	119,921	119,989	115,921
	QC+	144,461	143,623	140,243
chr21	nr-set	50,165	51,900	49,154
	QC+	63,893	65,475	63,078
chr22	nr-set	54,786	56,716	54,840
	QC+	68,148	69,964	68,946
chrX	nr-set	119,738	120,641	118,953
	QC+	145,870	146,956	144,261
chrY	nr-set	672	667	668
	QC+	676	672	670
chrMT	nr-set	212	207	211
	QC+	303	299	301

---------------------------------------------------------	
Total	nr-set	3,969,656	4,001,003	3,882,143
	QC+	4,937,069	4,823,530	4,834,972

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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.

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