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](http://biostar.stackexchange.com)
QA website. They are listed in no particular order.


* [dbSNP](http://www.ncbi.nlm.nih.gov/projects/SNP/): the NCBI search
  engine for SNP on NCBI Reference Assembly
* [HuGE Navigator](http://www.hugenavigator.net/): an integrated,
  searchable knowledge base of genetic associations and human genome epidemiology
* [Human Variome Project](http://www.humanvariomeproject.org/): a
  website collecting curated human genetic variation effecting human
  disease 
* [OMIM](http://www.ncbi.nlm.nih.gov/sites/entrez?db=omim): the Online
  Mendelian Inheritance in Man, from NCBI
* [SNPedia](http://www.snpedia.com/index.php/SNPedia): a wiki
  investigating human genetics 
* [A Catalog of Published GWAS](http://www.genome.gov/26525384): a
  complete list of GWAS attempting to assay at least 100,000 single
  nucleotide polymorphisms (SNPs) in the initial stage 
*
  [NCBI ELink](http://www.ncbi.nlm.nih.gov/corehtml/query/static/elink_help.html): can be used to map diseases from OMIM to dbSNP
* [dbVar](http://www.ncbi.nlm.nih.gov/dbvar/): a database of Genomic
  Structural Variation, from NCBI
* [CNV CHOP](http://cnv.chop.edu/): a database on all known CNV in the
  human genome, from the Children's Hospital of Philadelphia
* [DGV](http://projects.tcag.ca/variation/): a  curated catalogue of
  structural variation in the human genome
* [BioGPS](http://biogps.gnf.org/): the gene portal hub about gene
  annotation 
* [DECIPHER](http://decipher.sanger.ac.uk/): 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](http://agserver01.azn.nl:8080/ecaruca/ecaruca.jsp): a
  database which collects and provides cytogenetic and clinical
  information on rare chromosomal disorders, including microdeletions
  and microduplications
* [KEGG DISEASE](http://www.genome.jp/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](http://genome.ucsc.edu/): includes reference
  sequence and working draft assemblies for a large collection of
  genomes, and an online query system -- see an
  [example](http://biostar.stackexchange.com/questions/1289/disease-associated-snps/1322#1322)
  of how to fetch the UCSC server using `mysql` 
* [PolyPhen-2](http://genetics.bwh.harvard.edu/pph2/): a tool which
  predicts possible impact of an amino acid substitution on the
  structure and function of a human protein
* [Ensembl Genome Browser](http://www.ensembl.org/index.html):
  features genome databases for vertebrates and other eukaryotic
  species 
* [Distributed Annotated System](http://www.biodas.org/wiki/Main_Page):
  webservice to retrieve all genes/phenotypes associated to a specific
  SNP, hosted by the WTC
* [BioMart](http://www.biomart.org/): a query-oriented data management
  system to retrieve;
  [MartView](http://www.biomart.org/biomart/martview/) allows to map
  SNP IDs to gene/protein IDs, and from there to GO terms
* [GenGen](http://www.openbioinformatics.org/gengen/): a suite of free
  software tools to facilitate the analysis of high-throughput
  genomics data sets
* [ALIGATOR](http://x004.psycm.uwcm.ac.uk/~peter/): a program for
  testing for Gene Ontology categories over-represented on a list of
  significant SNPs from a GWA analysis
* [Genevar](http://www.sanger.ac.uk/resources/software/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](http://www.broadinstitute.org/mpg/grail/): a tool to examine
  relationships between genes in different disease associated loci 
  
----------------------------
Sam sep 25 01:33:46 CEST 2010