SNPnexus Web Annotation Tool

SNPnexus is a comprehensive web-based variant annotation tool designed to simplify the selection and prioritisation of both known and novel genomic alterations. The platform provides deep insights into genomic consequences, predicted deleteriousness, population prevalence, disease associations, and more. Once the annotation is complete, our intuitive results interface allows you to filter and prioritise variants based on a diverse range functional and clinical criteria.

For more information on how to get started, please refer to our User Guide and Example sections.

Important: SNPnexus is freely available for all usage, but please note that some integrated datasets require a license for commercial usage. Users are encouraged to consult our About section, or the original data sources for updated licensing details. SNPnexus is not responsible for the unauthorised or incorrect use of its datasets.

Commercial users: Service providers or organisations requiring larger queries, or interested in a customised version of SNPnexus, are encourage to contact us at info@snp-nexus.org

SNPnexus Version 5: New features at a glance:

Multi-File Upload: Submit up to 6 files (VCF or Text) simultaneously for comparative analysis.
Pre-Filtering: Focus your analysis by chromosomal position or specific gene lists before processing.
Maximum Variant Limit: The platform supports now up to 150k variants. This applies to the total count across all uploaded files after the optional pre-filters have been applied.

label_important Follow the flow chart below to ensure your analysis runs smoothly:

Researcher: Institution:

Institutional Email:

Click here if you want to be notified by email when your results are ready to browse

Click here if you want to join the SNPnexus users' community and be notified of any updates and news. You can opt-out at any time by sending an email to help@snp-nexus.org

Dataset Name:

Select the Human Genome Assembly Reference for your query (Default GRCh38):

Add your variants by genomic coordinates or by dbSNP. Warning: up to 150k variants after filtering.

Click here to fill the text area with an example.

Input by Genomic Coordinates

Input by dbSNP

rs#:

Or paste your query below in the format shown:

Drag and drop files here

Upload up to 6 tab-separated VCF or text files (.txt or .tsv).
You can also upload one .zip or .tar.gz archive containing up to 6 files.
Warning: total variants across all uploaded files must not exceed 150k after filtering.

Accepted file formats and examples

Important: Files must use tab-separated columns. Follow one of the templates below.

VCF format

Standard VCF with at least 8 columns:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO
1   72662224    .   A   T   .   .   .
2   103886224    .   CG   C   .   .   .
2   136322246    .   T   TAA   .   .   .

Tab-separated text (`.txt` or `.tsv`)

First column must be chromosome or dbsnp:

chromosome  1   72662224    A   T
chromosome  2   103886224   CG  C
chromosome  2   136322246   T   TAA
dbsnp   rs4133590

Next steps: 1) Click Upload file(s). 2) Click Validate file(s). 3) Continue if validation passes. If validation fails, fix the reported errors and re-upload.

Using these options, you can focus your query on only variants overlapping genes, a gene or specific set of genes, or a set of chromosomal regions. After setting your filters, you need to "validate the prefilters" before continue

Filter by gene(s)

Consider only variants overlapping (and in the up/down stream of) genes

Or select one or more genes from the list below (genes in your query): Or paste a comma-separated list of genes below:

Filter by coordinate(s)

Or paste a list of regions below:

Contact details

Input Query

VCF format

Tab-separated text (.txt or .tsv)

Filters before processing (Optional)

Annotations

Tab-separated text (`.txt` or `.tsv`)