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Welcome to the GenomeWeb Human Genome Databases Search for:

OMIM (Online Mendelian Inheritance in Man)
GDB (Genome DataBase)
GeneCards - integrated biomedical genetic information
OMIM gene map
The HuGeMap database
Human Genome Map Search (Pennsylvania University)
GenAtlas
Genome Navigator: Whitehead/MIT STS-based Map of the Human Genome
The Genome Channel
HGBASE - human genic bi-allelic sequences - SNPs
Single Nucleotide Polymorphisms in the Human Genome
dbSNP - A Database of Single Nucleotide Polymorphisms
Human SNP Database
Whitehead/MIT STS-Based Map of the Human Genome
Transcript Map of the Human Genome
Human Telomere Information
The Genetic Location Database (LDB)
The dysmorphic human and mouse homology database
BodyMap - Anatomical Expression Database of Human Genes
CEPH-Genethon integrated map
CEPH Genotype database
Cooperative Human Linkage Center (CHLC)
GeneMap '98 - The International RH Mapping Consortium Map
Radiation Hybrid Mapping data (RHdb)
dbEST Expressed Sequence Tag Database
UniGene - Unique Human Gene Sequence Collection
dbSTS Sequence Tagged Site Database
Whitehead Institute/MIT Genome Center
V BASE: A Directory of Human Immunoglobulin V Genes
Human CpG Island database
Human population genetics database (Genography)
Anthony Nolan Research Institute (ANRI)
GDB Nomenclature Committee
Atlas of Genetics and Cytogenetics in Oncology and Haematology

Detailed information on the above options

OMIM (Online Mendelian Inheritance in Man)
This database is a catalog of human genes and genetic disorders authored and edited by Dr. Victor A. McKusick and colleagues at NCBI, Bethesda, Maryland.

GDB (Genome DataBase)
GDB holds data on Human gene loci, polymorphisms, mutations, probes, genetic maps, GenBank, citations and contacts.

GeneCards - integrated biomedical genetic information
Although it will take some years until the human genome is totally sequenced, and still a much longer time to learn about the functions of the products of those genes, the complex organization and the vast amount of biomedical information already accessible often cause certain problems that are somehow connected to the phenomenon of "information overflow" and the often very time-consuming process of information retrieval or mining. Thus, many scientists feel that new approaches to organize scientific information are urgently needed.

GeneCards is a database that intends to address some of these problems by integrating biomedical information taken from several sources (GDB, MGD, OMIM, SWISS-PROT, HGMD, Doctor's Guide to the Internet), and by presenting them in a way facilitating a quick.

OMIM gene map
The OMIM gene map presents the cytogenetic map location of disease genes and other expressed genes described in OMIM.

You enter a position, say '17q11' and you get all the omim records in that regionn, even things that map to '17cen-q12'

The HuGeMap database
HuGeMap is a database that contains:

• the genetic maps from Genethon,
• the genetic maps from Cooperative Human Linkage Center,
• the physical maps from CEPH/Ginithon
• the physical maps from the Whitehead Institute-MIT

Human Genome Map Search (Pennsylvania University)
Human Genome Map Search retrieves GenBank entries that have been mapped to positions on human chromosomes and finds all the non-human homologs of those entries. The query uses map data from the Genome DataBase.

GenAtlas
Compiles the information relevant to the mapping efforts of the Human Genome Project.

GENATLAS/GEN is a repertory of three types of objects : genes, diseases, and markers.

Genome Navigator: Whitehead/MIT STS-based Map of the Human Genome
Genome Navigator is an attempt to provide a visual interactive gateway to major databases containing physical and genetic mapping information about the human genome.

Genomic maps of these organisms are displayed using DerBrowser, a Java applet, designed as a universal tool to display and navigate various types of maps. Among other features, it allows a user to query external databases about any map object.

The Genome Channel
This system is a prototype graphical browser for querying the annotated reference genome.

The Java interface relies on a number of underlying resources, analysis tools and data-retrieval agents to provide an up-to-date view of genomic sequences as well as computational and experimental annotation. Designed to be simple enough for a layperson, the channel also offers sophisticated capabilities for hypothesis testing.

HGBASE - human genic bi-allelic sequences - SNPs
HGBASE lists human intra-genic promoter to transcription end point DNA sequence polymorphisms. It has been constructed by The Department of Genetics and Pathology at Uppsala University and Interactiva Biotechnologie GmbH. HGBASE does not include gene mutations, but is a catalogue of intra-genic sequence variants found in normal individuals. Despite its name, HGBASE contains all types of gene based variation and is not limited to bi-allelic Single Nucleotide Polymorphisms SNP s. Functionally consequential polymorphisms e.g. promoter and non-silent codon changes and other polymorphisms e.g. intron sequence differences are included.

Search tools are provided to find data within HGBASE. Searches utilise a text string or a DNA sequence. Data submission is by a series of Web page data submission forms. All submitted data is made available to other public databases. The exponential growth in polymorphism discovery requires that scientists make every effort to submit their data to HGBASE to ensure it remains up to date. HGBASE does not claim any rights to publicly available or submitted data, instead this remains the property of the original submitter/discoverer. Deposition of data within HGBASE requires only the allelic DNA sequence, the allele frequencies, the host gene name, and the intra-genic domain. Additional information, such as assay conditions, can be supplied but this is optional.

Single Nucleotide Polymorphisms in the Human Genome
This website is designed to provide the human genetics community with access to single nucleotide polymorphism (SNPs) that have been developed as genetic markers on the human genome. The site is organized by chromosomes and cytogenetic location. Each SNP has PCR primer and conditions associated with it.

Currently, we only post the SNPs that we have helped to develop. After we have posted all of our SNPs, we'll be adding SNPs from the literature and from collaborators, and we will be happy to have others contribute to the database.

dbSNP - A Database of Single Nucleotide Polymorphisms
In collaboration with the National Human Genome Research Institute, The National Center for Biotechnology Information has established the dbSNP database to serve as a central repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms. Once discovered, these polymorphisms could be used by additional laboratories, using the sequence information around the polymorphism and the specific experimental conditions. (Note that dbSNP takes the looser 'variation' definition for SNPs, so there is no requirement or assumption about minimum allele frequency.) The data in dbSNP will be integrated with other NCBI genomic data. As with all NCBI projects, the data in dbSNP will be freely available to the scientific community and made available in a variety of forms.

Human SNP Database
This is the Whitehead/MIT SNP data.

Whitehead/MIT STS-Based Map of the Human Genome
This contains YAC screening data for several thousand STSs. For each STS, information is held on the following types of raw data (where available):

• Chromosomal assignments
• YAC library screening results
• Radiation hybrid panel screening results

• Doubly-linked YAC contigs
• Singly-linked YAC contigs
• Radiation hybrid maps
• Integrations between genetic, radiation hybrid, and YAC contig maps.

Transcript Map of the Human Genome
A small portion of each cDNA sequence is all that is needed to develop unique gene markers, known as sequence tagged sites or STSs, which can be detected in chromosomal DNA by assays based on the polymerase chain reaction (PCR). To construct a transcript map, cDNA sequences from a master catalog of human genes were distributed to mapping laboratories in North America, Europe, and Japan. These cDNAs were converted to STSs and their physical locations on chromosomes determined on one of two radiation hybrid (RH) panels or a yeast artificial chromosome (YAC) library containing human genomic DNA. This mapping data was integrated relative to the human genetic map and then cross-referenced to cytogenetic band maps of the chromosomes. (Further details are available in the accompanying article in the 25 October issue of SCIENCE).

The histograms reflect the distributions and densities of genes along the chromosomes. Because the individual genes (>16,000) are too numerous to represent, images have been chosen to illustrate the myriad aspects of human biology, pathology, and relationships with other organisms that can be revealed by analysis of genes and their protein products.

Human Telomere Information
This is a section of GenLink's Teldb giving literature citations and other information on human telomeric regions.

The Genetic Location Database (LDB)
Ldb is an analytical database for constructing fully integrated genetic and physical maps. The ldb program generates an integrated map (known as the summary map) from partial maps of physical, genetic, regional, somatic hybrid, mouse homology and cytogenetic data.

The summary maps and the data used to build up such maps are available from this site. The files for each chromosome are stored in the same directory which include the summary map, partial maps, lod files and the parameter files. As this server is experimental many of the chromosome directories are incomplete with the most complete map sets being chromosomes 1,9,21 and X.

The dysmorphic human and mouse homology database
This consists of three separate databases of human and mouse malformation syndromes together with a database of mouse/human syntenic regions. The mouse and human malformation databases are linked together through the chromosome synteny database. The purpose of the system is to allow retrieval of syndromes according to detailed phenotypic descriptions and to be able to carry out homology searches for the purpose of gene mapping. Thus the database can be used to search for human or mouse malformation syndromes in different ways:-

• By specifying specific malformations or clinical features, or chromosome locations.
• By Homology.
• By asking for human syndromes located at a chromosome region syntenic with a specific mouse chromosome region (and vice versa from human to mouse).

BodyMap - Anatomical Expression Database of Human Genes
BodyMap is a data bank of expression information of human genes, novel or known, in various tissues or cell types. It is created by random sequencing of clones in 3'-directed cDNA libraries. Since these clones were not amplified, redundancy of the same sequence reflects the quantitative aspect of gene expression in various tissues.

You can enter your sequence and it will be matched using fasta to the cDNA sequences in this database.

CEPH-Genethon integrated map
This page allows you to search the CEPH-Genethon mapping data used to build the first generation physical map of the human genome. It gives information on the CEPH YAC library and the QUICKMAP database with the infoclone program to get information about a STS or a YAC.

CEPH Genotype database
The Centre d'Etude du Polymorphisme Humain (CEPH) maintains a database of genotypes for all genetic markers that have been tested in the reference families for linkage mapping of the human chromosomes.

• browse data by chromosome, probe, D-number, Gene name and Heterozygote frequency
• output data for several markers on the same chromosome in CEPH, LINKAGE and CRIMAP formats.
• CEPH Collaborators can now submit data for new markers directly through Internet by using a browser supporting JAVA applets.

Cooperative Human Linkage Center (CHLC)
The goal of the Cooperative Human Linkage Center is to develop statistically rigorous, high heterozygosity genetic maps of the human genome that are greatly enriched for the presence of easy-to-use PCR-formatted microsatellite markers.

• Genetic maps showing the positions of genetic markers
  • Integrated Maps showing the position of genetic markers constructed using genotype data from the CEPH reference panel.
  • CHLC Marker Maps showing the positions of CHLC generated markers in various reference maps.
• Search by name for information on markers.
  • Search by name for information on markers, including map location primer and pcr conditions, and sequence templates.
  • Likely locations of current CHLC markers, in Version 2.0 Skeletal Maps
  • Tables of CHLC markers characterized by linkage analysis.
  • List of full information on markers generated by CHLC
    • In Current Linkage Map
    • Candidate Linkage Markers
    • Somatic Cell Hybrid Assigned
  • Prior versions of the CHLC generated markers.
  • Marshfield CA-repeat Markers
    • Table of initial typing data
    • Table of sequence data
    • Table of PCR Primers
• CHLC publications.
  • Science Maps and Data
  • Copies of the CHLC Newsletter
• CHLC project information.

GeneMap '98 - The International RH Mapping Consortium Map
This is the latest Radiation Hybrid Consortium Human map.

Radiation Hybrid Mapping data (RHdb)
Radiation hybrid maps are an indispensable alternative to genetic maps as they can include non-polymorphic markers and are also powerful enough to order unresolved genetic clusters of polymorphic STSs. An international collaborative project has been started which will produce a large number of these hybrids for the human genome. This in turn will allow the generation of a very precise STS map that will be indispensable in the study of multifactorial diseases.

RHdb, the radiation hybrid database is an archive of raw data with links to other related databases. The main data is stored in a relational database. Submissions to this database are made using a standard format. Various export formats will be supported, as well as different ways of accessing the data.

dbEST Expressed Sequence Tag Database
The dbEST Database holds many Human ESTs.

UniGene - Unique Human Gene Sequence Collection
This holds clusters of human EST sequences that represent the transcription products of distinct genes.

These sequences are being used for transcript mapping in collaboration with several genome mapping centers. Some of the clusters have already been localized to chromosomes, but more detailed mapping map information is not available at this time.

dbSTS Sequence Tagged Site Database
The dbSTS Database holds many Human STSs.

Whitehead Institute/MIT Genome Center

• Human YAC screening data for sequence tagged sites (STSs) screened on the CEPH mega-YAC library with over 1100 contigs assembled using double linkage between STSs.
• For each STS, they report addresses for the YACs found to contain the STS.
• Human, Rat and Mouse marker map data files.

V BASE: A Directory of Human Immunoglobulin V Genes
A directory of human immunoglobulin germline variable region sequences compiled from over a thousand published sequences (including those in the current releases of the Genbank and EMBL data libraries). There are seven directories: D, JH, JK, JL, VH, VK and VL. Each directory consists of a folder or file containing the germline sequences and a file containing the corresponding reference list.

Human CpG Island database
Look at the Human CpG Island database. This is a flat file containing a description of genes and their associated CpG islands.

Human population genetics database (Genography)
The Genography project comprises four parts:

• database (DNAbase)
  • object-oriented database for population genetic data
  • includes data from multiple species
  • includes data from individuals as well as population samples
  • includes cultural and linguistic data
  • data entry, editing, and selection via hybrid SQL/OQL subset
• analysis
  • a graphical front-end for data selection and data analysis programs
  • allows selection of subsets of data by area and marker
  • carries out interpolation, principal components analysis, wombling, removal of principal components, and tree-building
  • saves results and displays result datasets
  • allows full control over parameters of analysis and display
• simulation (Diaspora)
  • cellular automaton simulation of thousands of generations of human genetic and cultural evolution
  • diaspora is group movement: colonization, migration, and invasion
  • density and technology affect birth, death, survival, and diaspora rates
  • variable terrain with local carrying capacities
  • carrying capacity affected by technological development
  • genetic loci, with mutation and admixture dynamics
  • linguistic characters, with shift and creolization dynamics
  • cultural traits, with ogamy, diaspora, and technological development
• monitor
  • background monitoring and data-mining of Genography-database
  • controls access to data according to authorization
  • searches and logs errors and anomalies
  • attempts to detect and report patterns

Anthony Nolan Research Institute (ANRI)
The WHO Nomenclature and HLA Sequence alignments are available from this site, together with monthly updates.

GDB Nomenclature Committee

• Activities of the Nomenclature Committee
• Nomenclature mailing list
• Committee members
• Guidelines for choosing a gene symbol
• Submit a proposed gene symbol
• Browse approved gene symbols
• Gene Family Nomenclature
• Checking for existing symbols

Atlas of Genetics and Cytogenetics in Oncology and Haematology
The Atlas of Genetics and Cytogenetics in Oncology and Haematology is a cooperative process of reviewing and updating on somatic genetics, clinical entities in cancer, and on cancer-prone diseases; it is made for and by: cytogeneticists, molecular biologists, and geneticists in general, clinicians in oncology and in haematology, and pathologists.