Question: chromosomal locations of snps in humvar variant set
0
gravatar for arronslacey
3.8 years ago by
arronslacey260
United Kingdom
arronslacey260 wrote:

Hi - in the humsavar dataset there are variants given by protein position and amino acid change. http://www.uniprot.org/docs/humsavar

Is there a way to convert these to chromosome positions and nucleotide changes? thanks.

I should probably add for clarification that some snps listed to do not have an rsid. this is a particularly challenging case because i am not able to join to UCSC snp tracks via rsid (where chromosomal positions exist)

uniprot snp humvar variation • 1.1k views
ADD COMMENTlink modified 3.8 years ago by Elisabeth Gasteiger1.7k • written 3.8 years ago by arronslacey260
2
gravatar for Elisabeth Gasteiger
3.8 years ago by
Geneva
Elisabeth Gasteiger1.7k wrote:

This file (humsavar.txt) is complemented by files of amino acid altering variants imported from Ensembl Variation databases. Mapped sequence variants are supplied per species in a tab delimited text file.ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/variants/

In particular, the human file is homo_sapiens_variation.txt.gz: The variants listed are the Ensembl Variation databases' set of 1000 Genomes project (http://www.1000genomes.org/) and Catalogue of Somatic Mutations In Cancer (COSMIC) v71, imported directly from COSMIC and via Ensembl Variation, protein altering variants (SO:0001583). COSMIC v71 variants are the last freely available somatic variants from COSMIC before their licence change; therefore the accuracy of the information provided for a COSMIC variant should be verified with COSMIC. (Text from README file in that directory)

Please don't hesitate to contact the UniProt helpdesk in case of questions about these files.

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by Elisabeth Gasteiger1.7k

Thanks Elisabeth - very helpful! I had also looked into the Bisoconductor package VariantAnnotation that includes data objects such as polyPhen.Hsapiens.dbSNP131 - which maps most of the rsids to the humsavar dataset. it's obviously a bit out of date now so I much appreciate alternative data scourses that you mentioned.

ADD REPLYlink written 3.8 years ago by arronslacey260
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