The Variant Browser is divided into 4 different sections:

• Filter panel (red): Contains the list of available parameters to filter the list of variants in the main panel
• Active filters (green): List of applied filters
• Main panel (blue): Table containing the list of variants and extra information about them
• Variant detail (yellow): Contains specific and extended information about the variant selected in the main panel

Filter panel

The list of variants in the main panel can be thoroughly filtered by any of the parameters listed below. Some sections appear collapsed by default, to expand them, just click on the title.

• Studies: users can filter the list of variants by its existence or absence in one or more published studies. To do so, select the studies to use and the desired option from the dropdown menu: Only in to include variants that appear only in all the selected studies but not in the unselected ones, In to include variants that appear in any of the selected studies but not in the unselected ones, At least in to include variants that appear in any of the selected studies and can also be present in the unselected ones, and, Not in to exclude all the variants that appear in any of the selected projects.
• Position: restrict the list of variants to a specified genomic region (specified by chr:start-end), gene (in HGNC symbol) or SNP (use the rsID).
• Type: Limit the search to just one or few types of variant: SNV (Single Nucleotide Variant), MNV (Multi-nucleotide Variant), CNV (Copy Number Variant), SV (Structural Variant) or INDEL (Insertion or deletion).
• Population Frequency: restrict the list of variants to those which have a MAF (Minor Allele Frequency) higher/lower/equal to a defined value in the 1000 genomes project, ExAc and/or ESP 6500. To do so, expand the "+" sign next to the desired project, select from the dropdown menu the comparison operator and specify the value (between 0 and 1) in the text box. MAF filtering can be applied to all of the samples in the specified project (ALL) or to one/few specific populations within the selected project.
• Protein Substitution Score: users can also filter by the annotated protein substitution scores such as SIFT and PolyPhen. Filtering can be done using their prediction keywords from the dropdown list or using an specified score. For the latter, just select "Score..." in the list of options, chose the comparison operator and specify a value (between 0 and 1) in the text box. Bear in mind that a score close to 0 in SIFT is considered deleterious while a score close to 0 in PolyPhen is considered benign.
• Conservation: filter by conservation scores using PhiloP, PhastCons and/or Gerp.
• Consequence Type: restrict the list of variants to those annotated with a particular consequence type.
• Gene Ontology: limit the list of variants only to the ones in a gene annotated with the specified Gene Ontology term(s).
• Human Phenotype Ontology: limit the list of variants only to the ones in a gene annotated with the specified Human Phenotype Ontology term(s).
• CADD: filter the search using CADD score. Users can chose to filter by the "raw" score or the "scaled" score. Please, see CADD's website to find information about the two options: http://cadd.gs.washington.edu/info

After one or more filters have been set, just click on the Search button at the top of the panel to apply them.

Active filters

Every time a filter is applied, this panel refreshes and includes a button with the filter. Users can easily remove individual filters just by clicking on the buttons in the panel. To remove all the active filters click on "Clear" at the left hand side of the panel.

Main panel

The main panel contains a table with the list of variants from a specified project/study. This list can be modified by any of the parameters in the filter panel. The table shows one row per variant and several columns containing general information about each variant:

• Variant: the variant coded as chr:position ref/alt
• SNP Id: if the variant is included in dbSNP, this field will show the rsID, otherwise, it will be empty
• Genes

Variant detail

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