Looking for a data base of functional SNPs.

Question

[Pol]

Hi,

I’m looking for a data base of functional SNPs.

I’ve found F-SNP, which is very interesting for me, but it’s very old and I would like to obtain information for more SNPs.

I’ve read about other databases as Fast-SNP, but they aren’t working nowadays.

Do you know any other database of functional SNPs working nowadays? Or an easy way to obtain functional SNPs for a given gen?

I would like not only protein coding SNPs, the output of F-SNP is perfect for me and I’m looking for something similar. I’m interesting in SNPs affecting splicing sites, TF binding sites, phosphorylation sites…..

I’ve seen this post:

Tools For Predicting Functional Effects Of Snps?

but it’s 2.5 years old and perhaps there is something new.

Thank you very much.

Answer 1

[Carlos Borroto]

Take a look at dbNSFP.

dbNSFP is a database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome. Its current version is based on the Gencode release 22 / Ensembl version 79 and includes a total of 82,832,027 nsSNVs and ssSNVs (splicing-site SNVs). It compiles prediction scores from 14 prediction algorithms (SIFT, Polyphen2, LRT, MutationTaster, MutationAssessor, FATHMM, VEST3, CADD, MetaLR, MetaSVM, PROVEAN, DANN, fathmm-MKL, fitCons), 6 conservation scores (PhyloP x 2, phastCons x 2, GERP++ and SiPhy) and other related information including allele frequencies observed in the 1000 Genomes Project phase 3 data, UK10K cohorts data, ExAC consortium data and the NHLBI Exome Sequencing Project ESP6500 data, various gene IDs from different databases, functional descriptions of genes, gene expression and gene interaction information, etc.

[Pol]

Thanks for your answer. This db is quite interesting, but only covers SNP within the gene and I am also interested in upstream and downstream SNPs for a given gene.

[Carlos Borroto]

I see. I don't know of a database. I believe CADD is one of the few tools that tries to predict SNP effect outside of gene regions. You might want to take a look there.