Currently, I am looking for databases, which associate SNPs and phenotypes (like eye colour or breast cancer risk). These should get updated regularly with regards to recent GWAS etc. Ideally, these databases are manually curated.
In addition, it would be advantageous if it is listed how a SNP affects the phenotype (like contributing to blue or brown eyes or increasing or decreasing the cancer risk) or at least saying if a SNP is advantageous for not getting a certain disease or not.
Many thanks for your help in advance!
You can also check out GWAS Central at http://www.gwascentral.org
You can try David:
https://david.ncifcrf.gov/,
which annotates using functional analysis. Alternatively, download the dataset from:
http://diseases.jensenlab.org/Search
And run your SNPs against it - this site directly links genotype to phenotype. It also provides the ranking.
Dear Tobias,
The following web servers may help you regarding your question.
http://www.mutationtaster.org/
https://mutalyzer.nl/description-extractor
http://genetics.bwh.harvard.edu/pph2/
http://sift.jcvi.org/
http://agvgd.hci.utah.edu/
http://snpeffect.switchlab.org/
http://mutpred.mutdb.org/
http://mutationassessor.org/r3/
http://www.pantherdb.org/
Best of luck,
Abbas
For clinically relevant genomic variants + disease phenotypes, see ClinVar: https://www.clinicalgenome.org/data-sharing/clinvar/
You may also try Variowatch
http://genepipe.ncgm.sinica.edu.tw/variowatch
https://www.ebi.ac.uk/gwas/
The GWAS Catalog is a quality controlled, manually curated, literature-derived collection of all published genome-wide association studies assaying at least 100,000 SNPs and all SNP-trait associations with p-values < 1.0 x 10-5 (Hindorff et al., 2009).
Each study is assigned a trait description that best represents the phenotype under investigation. This is known as the reported trait as it is taken from the study publication. All reported traits are mapped to terms from the Experimental Factor Ontology resulting in one or more mapped traits. https://www.ebi.ac.uk/gwas/docs
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