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 Webkit (v537.36).
  ↓ Use this button to view raw data from HAD database.
HAD database close input window
Type in genomic region, SNP(s) or gene name to search the database for.
 Examples
chr1:800000..900000
BRCA2 rs12534 rs12534, rs11827218
     I want more input space

  ↓ Use this button view SNP genotype images constructed from HAD data.
AAF Visualizer close input window
Type in genomic position(s), SNP(s) or gene name(s) to locate in visualizer image.
 Examples
chr1:800000..900000
chr1:36540000, chr3:19950000
BRCA2 rs12534 rs23432, rs34332
  I want more input space
Dataset:
HGDP Stoneking Hapmap2 Hapmap3

  ↓ Use this button to view ancestral nucleotides from the entire genome.
Ancestral Genome Visualizer close input window
Type in genomic region or gene name to generate its image in visualizer.
 Examples
chr1:800000..900000 BRCA2 PAN3
 
Use genomic sequences of:
Macaque Orangutan Chimp




Changelog

May 30, 2011

HAD database version changed to 1.0. Bug fixes in HAD database, AAF Visualizer and Ancestral Genome Visualizer. Ensembl gene track added to Ancestral Genome Visualizer.

August 25, 2010

Added new dataset (from Herraes et al.) to the AAF Visualizer.
It's based on the HGDP dataset with additional SNPs genotyped with Affymetrix 500K platform (marked with brown lines in the visualizer).

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

Added a list of genomic regions from various articles to be directly viewed in AAF Visualizer.

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 ().


Fetching SNPs from HAD database...