OMIM contains general information about associations between genotype (gene variants) and phenotype (mendelian disorders). As you may have noticed, it does not contain any GWAS data itself, only references to studies related to a specific phenotype or genotype.

There is a number of resources that may be useful for you. HGMD (Human Genome Mutation Database, http://www.hgmd.cf.ac.uk/ac/index.php) is a commercial analogue of OMIM, but it provides free access for academic purposes. As OMIM, it summarizes studies having been published and have broader coverage for human genome mutations.

Another resource of such kind is GAD (Genetic Association Database, http://geneticassociationdb.nih.gov). It also provides genetic association data on hereditary disorders. GAD was retired in last year and is not updated anymore, however, it still may be useful.

Also there are two NIH resources directly related to GWAS:

• NCBI dbGaP (databases of genotypes and phenotypes): http://www.ncbi.nlm.nih.gov/gap,
• NIH GWAS Catalog: http://www.genome.gov/gwastudies/.

OMIM contains general information about associations between genotype (gene variants) and phenotype (mendelian disorders). As you may have noticed, it does not contain any GWAS data itself, only references to studies related to a specific phenotype or genotype.

There is a number of resources that may be useful for you. HGMD (Human Genome Mutation Database, http://www.hgmd.cf.ac.uk/ac/index.php) is a commercial analogue of OMIM, but it provides free access for academic purposes. As OMIM, it summarizes studies having been published and have broader coverage for human genome mutations.

Another resource of such kind is GAD (Genetic Association Database, http://geneticassociationdb.nih.gov). It also provides genetic association data on hereditary disorders. GAD was retired in last year and is not updated anymore, however, it still may be useful.

Also there are two NIH resources directly related to GWAS:

• NCBI dbGaP (databases of genotypes and phenotypes): http://www.ncbi.nlm.nih.gov/gap,
• NIH GWAS Catalog: http://www.genome.gov/gwastudies/.

Hi Kyungtaek Lim,

PhenomicDB is a comprehensive phenotype-genotype database

dbGap is another comprehensive database

and PheGenl is another comprehensive database

Check the following weblinks below:

http://www.nature.com/ejhg/journal/v22/n1/full/ejhg201396a.html

http://www.ncbi.nlm.nih.gov/gap

http://www.phenomicdb.de/

Kind regards

Olugbenga

Thank you for the helpful comments.

Best,

Kyungtaek Lim

Try http://genome.ucsc.edu/ is a very comprensive database although complex

The best suggestion would be ' The Phenomizer' in Human Phenotype Ontology website. In this try to go for a tabular column module, so that you can get the list of Genes involved in the phenotype that you focus for.

Good luck and Here you go with!

http://compbio.charite.de/phenomizer/

http://www.human-phenotype-ontology.org/

Dear Michel and Srinivasan

Thanks for your suggestions. I will check out those web-servers.

Best,

Kyungtaek

Have you tried the EGA European Genome-Phenome Archive available at CRG and EBI?

https://ega.crg.eu/

You are welcome.

Kind regards

Olugbenga

For genome-wide association data we provide the GWAS Central database: http://www.gwascentral.org/

Here you can search for GWAS results on physical location, or via phenotype (HPO and MeSH ontologies are both supported).

For other variation data, there is an extensive network of locus-specific and disease-specfic databases. Most of these can be searched via the variation discovery tool Cafe Variome: http://www.cafevariome.org/discover.

Dear Eva

Thanks. EGA seems very comprehensive. They have a strict policy in data access.

and Dear Adam

Thank you for the info. I'm impressed by GWAS central's RESTFUL-like service.

Best,

Kyungtaek

As far as I know, only dbGAP and EGA provide genotype data and/or raw data, but it is not open access. You need to apply it first, which may take several months. If you only want to check the final results, I think GWAS Catalog is good enough. 

In addition to recently posted DataBases I use GWAS Integrator:

http://hugenavigator.net/HuGENavigator/gWAHitStartPage.do

Thanks everyone for helpful answers.

The monarch initiative (http://monarchinitiative.org) integrates gene/genotype, phenotype / disease sources across human and several dozen other species. We import a subset of the GWAS data above a certain level of significance. All of the data is programmatically accessible via a BioLink API instance here. http://api.monarchinitiative.org/api/