Here are some useful resources for genomewide analysis studies and genetic epidemiology. It mainly focus on single nucleotide polymorphisms (SNP), copy number variations (CNV), and genes. Several links to existing databases were collected on the biostar.stackexchange.com QA website. They are listed in no particular order.

• dbSNP: the NCBI search engine for SNP on NCBI Reference Assembly
• HuGE Navigator: an integrated, searchable knowledge base of genetic associations and human genome epidemiology
• Human Variome Project: a website collecting curated human genetic variation effecting human disease
• OMIM: the Online Mendelian Inheritance in Man, from NCBI
• SNPedia: a wiki investigating human genetics
• A Catalog of Published GWAS: a complete list of GWAS attempting to assay at least 100,000 single nucleotide polymorphisms (SNPs) in the initial stage * NCBI ELink: can be used to map diseases from OMIM to dbSNP
• dbVar: a database of Genomic Structural Variation, from NCBI
• CNV CHOP: a database on all known CNV in the human genome, from the Children's Hospital of Philadelphia
• DGV: a curated catalogue of structural variation in the human genome
• BioGPS: the gene portal hub about gene annotation
• DECIPHER: features a database of submicroscopic chromosomal imbalance with clinical information about chromosomal microdeletions/duplications/insertions, translocations and inversions and displays this information on the human genome
• ECARUCA: a database which collects and provides cytogenetic and clinical information on rare chromosomal disorders, including microdeletions and microduplications
• KEGG DISEASE: the japanese database where diseases are viewed as perturbed states of the molecular system, and drugs as perturbants to the molecular system
• UCSC Genome Browser: includes reference sequence and working draft assemblies for a large collection of genomes, and an online query system -- see an example of how to fetch the UCSC server using mysql
• PolyPhen-2: a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein
• Ensembl Genome Browser: features genome databases for vertebrates and other eukaryotic species
• Distributed Annotated System: webservice to retrieve all genes/phenotypes associated to a specific SNP, hosted by the WTC
• BioMart: a query-oriented data management system to retrieve; MartView allows to map SNP IDs to gene/protein IDs, and from there to GO terms
• GenGen: a suite of free software tools to facilitate the analysis of high-throughput genomics data sets
• ALIGATOR: a program for testing for Gene Ontology categories over-represented on a list of significant SNPs from a GWA analysis
• Genevar: Genevar is a database and Java tool designed to integrate multiple datasets, and provides analysis and visualization of associations between sequence variation and gene expression in eQTL studies
• GRAIL: a tool to examine relationships between genes in different disease associated loci

Sam sep 25 01:33:46 CEST 2010