Human Allele Database
HAD database contains data from following sources:
1. dbSNP - Human SNP data (dbSNP) NB! There is 2,35 million of SNP-s with same location but different rs ID;
2. Vista - genome alignments between primates (Human, Chimpanzee, Orangutang, Rhesus Macaque and Marmoset, Vista);
3. Neanderthal alleles from sequence fragments of Neanderthal sequencing project (Nature 2006);
4. Hapmap2 - Phase II genotypes (4 populations, 270 individuals, HapMap);
5. Hapmap3 - Phase III genotypes (11 populations, 1302 individuals, HapMap);
6. HGDP - genotypes of 51 human populations from all over the world (1043 individuals).
HAD database version 1.0 contains diverse information about 13,56 million SNPs (mapped once in human genome),
including 12,91 million of Chimpanzee alleles, 4,08 million HapMap II consensus alleles, 1,61 million HapMap III consensus alleles and 0,66 million HGDP consensus alleles.
Database contains SNP allele frequencies for every population genotyped in HapMap2, HapMap3 and HGDP projects.
In the web interface, user can either insert a list of human SNP id-s or choose a chromosome region. All data sources contain number of data fields.
User can choose records with nucleotide or allele frequencies data.
Note: Safari, Chrome or Firerfox (>v3.5) browser recommended. Internet Explorer is slower and may cause errors. You are currently using unknown browser (v...).
↓ Use this button to view raw data from HAD database.
↓ Use this button view SNP genotype images constructed from HAD data.
↓ Use this button to view ancestral nucleotides from the entire genome.
May 30, 2011
August 25, 2010
May 20, 2010
iHS (Integrated Haplotype Score; B. F. Voight, et al. 2006) values are now visualized in AAF Visualizer for HapMap2 populations.
Gene queries were switched to a local database for faster response times.
Draggable navigation controls box added to the AAF Visualizer for easier image navigation.
May 14, 2010
Additions to the AAF Visualizer. Now ancestral allele frequency can be seen for each single individual in any of the HGDP population samples. Just click the arrow next to the population size number to view additional image rows.
Draft sequence of the neanderthal genome (Richard E. Green et al., Science 2010) added to the Ancestral Genome Visualizer.
April 29, 2010
Ancestral Genome Visualizer is now fully functional. Added genomic sequence viewer.
April 23, 2010
There are now 4 sets of images for the HGDP dataset in AAF Visualizer, where ancestral allele frequency values are based on 1) six or 2) all individuals for every population (weighted for the population size). Both image sets are available in color or grayscale.
Also added Ensembl gene track in AAF Visualizer.
February 12, 2010
February 4, 2010
User can now simultaneously view multiple genomic regions over different chromosomes in AAF Visualizer. It can be accessed via view HAD images button above, when submitting multiple genomic positions from different chromosomes.
November 10, 2009
AAF Visualizer module added. Rebuild of the web page user interface.
May 18, 2009
Version 0.4 of Human Allele Database is available. HapMap v.2, Neanderthal (Nature 2006) allele and HAD ancestral allele has beed added.
October 8, 2008
Version 0.3 of Human Allele Database is available. Webpage is moved to bioinfo.ut.ee/HAD. Column selection has beed added.
September 17, 2008
Version 0.2 of Human Allele Database is available. New database has been created with HapMap, Vista and HGDB information.
August 5, 2008
Version 0.1 of Human Allele Database is available. This is a SNP database which stores the allele information for resequenced individuals, populations and closely related species.
Please send all questions and comments to Maido Remm (). The HAD visualization tools are built and maintained by Andres Veidenberg () and Tarmo Puurand ().