This User Guide has been designed to help you navigate through the full suite of options available in SNPnexus v5. Use the menu below to help you navigate this guide:
Before entering your data, you must select the appropriate Human Assembly Reference. SNPnexus supports both GRCh37 (hg19) and GRCh38 (hg38).
In SNPnexus, you can enter your variants manually or use the batch option to upload VCF or Text files to your query
keyboard_double_arrow_right Manual Variant Entry: Use the manual entry form to input specific coordinates (Chromosome, Position, Ref/Alt alleles) or a dbSNP rsID. Click Add to move these into your query list.
Important: All manually entered variants must be Validated before you can proceed to the next steps.
keyboard_double_arrow_rightBatch Queries: For large-scale analysis, you can drag and drop up to six files into the upload area. SNPnexus supports two primary formats:
#CHROM POS ID REF ALT QUAL FILTER INFO
1 72662224 . A T . . .
2 103886224 . CG C . . .
2 136322246 . T TAA . . .
chromosome 1 72662224 A T
chromosome 2 103886224 CG C
chromosome 2 136322246 T TAA
dbsnp rs4133590
Important: After adding files to the queue, you must click Upload, followed by Validate. The system will notify you if the format is correct or if errors were detected.
If your query exceeds the 150,000 variant limit, or if you wish to narrow your focus, you can apply pre-processing filters:
(*) If pasting a gene list, you must click Validate Filters to ensure they match our internal database.
Select the specific biological datasets you wish to query (e.g., Population Frequency, ClinVar, In-Silico scores). Once chosen, click Submit Query.
Note: The Submit button is only active if your query has been successfully validated.
This page provides a real-time view of your analysis progress, divided into three sections:
Query Information and Status: Displays the unique query Id, the number of samples and variants submitted, and a dedicated url for your results. It also tracks the progress of the annotation engine.
Valid Variants Table: Appears after pre-processing to show the variants being annotated
Plots: An ideogram plot of variant distribution across chromosomes, the top mutated genes, and a summary of variants types.
The Results Page is a dynamic interface designed to help you transition from thousands of raw data points to a shortlist of high-priority variants. Below is a short description of its sections:
Query Data and Export Options: This section displays the unique query ID, the precise date and time until which your data will be retained in our servers, and a bullet list showing every filter are currently applied to the view. You can also download a ZIP file containing individual tab-separated text files for every annotation and sample in your query; or alternatively, containing one VCF file per sample in the query with all the annotations integrated.
Dynamic Filtering Panel: This section is the "command center" for variant prioritization. The available filters appear based on the annotation categories you selected during the query submission. You can narrow variants based on functional consequence, population thresholds, known mutations, or if you uploaded multiple samples, you can find variants present in a subset of samples, or variants unique to each sample.
Visual Analytics: Cohort and Sample Plots: SNPnexus provides high-level cohort-wide and sample specific visualisations to help users spot patterns before exploring the raw data.
Interactive Results Tables: The bulk of the data is organised into searchable, sortable tables. Each table can be exported individually as VCF or Text file, respecting any active search or local filters.
View per Variant: Clicking the variant ID in the first column of any table opens a dedicated "deep-dive" page. This page presents the variant as a full report, instead of a row in a table, showing its presence across all samples and its complete annotation profile.
Below is a description of the key columns provided in your results:
Genomic Mapping:
Genomic Consequence:
Non-Synonymous Single Nucleotide Mutations:
Non-Coding Single Nucleotide Mutations:
Population Frequency - ALFA:
Population Frequency - 1000 Genomes:
Population Frequency - gnomAD:
Conserved Regions - Phast:
Conserved Regions - GERP++:
Biological Context - Reactome Pathways:
Biological Context - KEGG Pathways:
Biological Context - Genotype/Tissue Expression GTEx:
ClinVar:
Cosmic:
GWAS Catalog: