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
SNPs are not the best way to look for a phenotypic effect, outside Mendelian diseases. The overall effect of variants on gene(s) should be a better way of assessment, unfortunatelly, you do not come across such databases/sites as this require computing many omics data. There are two reasons for looking at genes instead just of variants: firstly, is the nature of SNPs - they can have many flavours e.g. protective, risk, or unknown, and their effect cannot be easily predicted in-silico; secondly, genes are the real effectors or acting agents in metabolic and biological pathways. Let's say you have two risk and one protective variants hitting one gene, what would be the overall effect on the functional activity of the gene? To overcome these problems, I use specific gene scoring matrix based on layers of omic data. Still, the phenotype is a guessing game, but more predictable compared to the current methods. The next step would be the application of AI to remap the scoring using actual phenotype data. As an interim solution, try GeneCards Suite of ap[plications, it should take you where you are heading.
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