the Reference Variant Store

The Reference Variant Store holds information on more than 520 million genetic variants using various methods of annotation. Sources for variants in RVS are re-sequencing projects such as the 1000 Genomes, ESP6500, UK10K, TCGA, Scripps Wellderly; clinical annotation databases such as ClinVar and HGMD; and hypothetical, amino-acid changing single-point mutations from dbNSFP. We provide annotations on low level effects, phenotypes and diseases, population frequencies, and predictive functional impact scores.

Available queries

Our query interface is available via the "Queries" menu. Entry points are searches by specific coordinate, dbSNP, or gene; or a comparison of cohorts based on populations in RVS. The first four queries are also wrapped in our REST API.

Query by dbSNP: enter dbSNP IDs (rs-numbers) to search RVS for matching variants.
Query by coordinates: enter specific chromosomal locations with alternate alleles to search RVS for genetic variants; or enter chromosomal regions to search RVS for all variants falling into those regions.
Query by gene: enter one or more genes and, optionally, genetic variants to search RVS.
Query by phenotype: enter a phenotype or disease name, and optionally a gene to search.
Query by cohorts: choose two cohorts from the available datasets and find the differences in allele frequencies with respect to selected genes.


  • 2015-08-20: literature citations of variants are available via our API and will soon be displayed in the regular output as well; sources: literature mining with SETH, dbSNP, OMIM, ClinVar, SwissVar, and others.
  • 2015-07-28: a RESTful web service to RVS allows accessing data in a batch mode; see API from the menu.
  • 2015-07-07: updated to Biodalliance 0.13; tracks shown include genes, ClinVar, HGMD, ENCODE, conservation, repeats, NA12878.
  • 2015-06-01: added "query by phenotype/disease"
  • 2015-04-24: population frequencies from ExAC release 0.3 (African, Native American, East Asian, European, Finnish, Latino, South Asian)