How to Annotating Human Genomic Variants for Disease Associations?

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3 months ago

octpus616 ▴ 100

Hello,

I am new to the analysis of human genomic mutations and have identified a series of gene loci of interest, including variant positions and types (eg: chr1 10001 A C). I am now looking to associate these data with published databases related to gene loci diseases or phenotypes (eg: GWAS). My aim is to annotate these loci as comprehensively as possible using these databases.

Could you please suggest some databases resources that I could use for this purpose? Are there any user-friendly tools that could assist me with this task?

Any guidance would be greatly appreciated. Thank you in advance.

R variant-annotation GWAS • 218 views

ADD COMMENT • link updated 3 months ago by Ram 43k • written 3 months ago by octpus616 ▴ 100

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If you have a small number then you could use Web interfaces (otherwise there are command line tools)

VEP - https://www.ensembl.org/vep
VEP Web version - http://www.ensembl.org/info/docs/tools/vep/online/index.html

ClinVar - https://www.ncbi.nlm.nih.gov/clinvar/

ADD REPLY • link 3 months ago by GenoMax 141k

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