Quick search

Users can quickly access the genetic and clinical data of VarCards by employing the tool of quick search at any web page. Our website can recognize a variety of key terms when they are typed in search box.

For quick search in the home page, users can identify your information of interest by entering one of the following:

quick-search

An example search result is shown below

quick-search

Advanced search

In our web interface, it also supports batch search. We give examples of a number of input formats available for querying VarCards. When you choose a format, click the “example” in blue and the example queue occur in box below. The formats are as follows:

advanced-search

More importantly, users can specify datasets and obtain various information including primary information, allele frequency and disease- and phenotype-related information in excel or csv format.

specify-datasets advanced-search-result

Annotate

If you want to obtain the primary information for thousands of mutations in a file, the annotation function will be a good choice to get specify annotate information by one uploading operation.

The process will be easy if you follow the steps below.

  1. Enter your e-mail address
  2. Upload your file
  3. Specify datasets of your interest and submit
  4. Result will be sent to your e-mail onece the annotation complete
annotate

Browse

To facilitate users to browse the data in VarCards, genes are indexed by alphabet. The table you get will display the gene symbol, numbers of different mutations (stopgain, stoploss, splicing, frameshift, nonframeshift, synonymous, nonsynonysmous), short description and Cytoband of the gene.

browse

To further explore the gene, you can click the correspongding gene and it will switch to the detailed information page. It will show two different level implications as follows:

Variant-level implication page

This page including a table in which each row represents a variant, showing genomic location, ref and alt sequence, gene symbol, effect, amino acids change, D:A algorithms, damaging score, extreme, gnomAD, respectively. To get more detailed information by clicking the button with "+", functional consequences of variant in silico predictive algorithms, allele frequency in different population and information in disease-related databases will be displayed. You can filter result by field including Effect, Extreme, Damaging score and gnomAD. Furthermore, if you want to further explore about the gene in gene-level, you can click the gene and it will be turn to the gene-level imolication page.

gene-variants.png

Gene-level implication page

This page integrates 7 gene-related sections that display decriptions of a gene’s basic information, function, phenotype and disease, expression, homology, variants in different populations and drug-gene interactions, respectively. And each section represents different biology information.

Basic information

This section integrates the basic information of corresponding gene that includes the official symbol, official full name, location, gene type, synonyms,qucik links from different databases, gene summary and genic intolerance.

gene-basic

Gene function

This section provides molecular function from UniProtKB, biology process ontologies visualized by the Gene Ontology Consortium, protein omain from InterPro, protein-protein interactions from InBio Map and pathway from NCBI BioSystems.

Gene function

Phenotype and disease

This section provides annotated information about gene function according to OMIM, ClinVar, denovo-db, MGI, HPO.

Phenotype and disease

Gene expression

This section contains expression images from GTEx and subcelluar location from The Human Protein Atlas.

Gene expression

Homology

This section contains a partial listing of orthologs in other species reported from HomoloGene.

gene homology

Variants in different populations

This section provides number of variants in different populations according to gnomAD.

gene-variant-distribution

Drug-gene interaction

This section provides the relationships between genes and drugs from DGIdb. It contains drug-gene interactions and gene druggability for precision medicine.

gene-drug-interaction

Download

We integrates all possibile single nucleotide variants (n=110,154,363) and cataloged all reported insertion and deletions (n=1,223,370) in coding regions or splicing site. Then we annotated them with repected to functional consequences from more that 60 genomic data source. Because the large file size , the file can be downloaded by chromosome for your convenience.

Download