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bioRxiv · 10.64898/2026.05.03.722523

SNPWay: streamlined SNP-to-function and pathway over-representation analysis

Queme, B.·Kakkar, A.·Muruganujan, A.·Thomas, P. D.·Gauderman, W. J.·Mi, H.
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Abstract

MotivationPost-GWAS interpretation frequently requires translating variant lists (e.g., lead SNPs, clumped loci, credible sets, or curated panels) into pathway and functional hypotheses. In practice, obtaining pathway and functional over-representation results from SNP inputs often requires stitching together multiple tools for variant annotation, regulatory annotation, gene identifier handling, and statistical testing. This integration burden can reduce reproducibility and restrict end-to-end analysis to groups with dedicated bioinformatics support. SummaryWe present SNPWay, a web server and R package that performs end-to-end SNP-to-function and pathway over-representation analysis in a single standardized workflow. SNPWay accepts rsIDs, VCF files, or hg19/GRCh37 genomic coordinates. It queries Annotation Query (AnnoQ) to obtain SNP-to-gene mappings from ANNOVAR, SnpEff, and VEP under both Ensembl and RefSeq gene models, and incorporates enhancer-gene links via PEREGRINE to augment mappings for noncoding variants. SNPWay aggregates mapped genes into a single, non-redundant, combined gene list and submits it to PANTHER for over-representation testing against the Homo sapiens reference list, returning over-represented pathways and functional categories (e.g., Gene Ontology) with direct links for interactive exploration in PANTHER. SNPWays modular architecture is designed for extensibility, enabling incorporation of additional analysis methods in future releases. A step-by-step walkthrough is provided in Supplementary Data. Availability and implementationWeb server: https://snpway.annoq.org/. R package and source code: https://github.com/USCbiostats/Annoq_Overrepr_Workflow. Documentation: https://snpway.annoq.org/about. Examples: The website contains Sample files for the input formats, also provided in Supplementary Data. SNPWay is free to use with no mandatory login. Contacthuaiyumi@usc.edu Supplementary informationSupplementary data are available at Bioinformatics online

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Queme, B., Kakkar, A., Muruganujan, A., Thomas, P. D., Gauderman, W. J., Mi, H.. 2026-05-06. SNPWay: streamlined SNP-to-function and pathway over-representation analysis. https://doi.org/10.64898/2026.05.03.722523

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