SNPedia Track Settings
 
SNPedia   (All Phenotype and Literature tracks)

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 SNPedia with text  SNPedia pages with manually typed text   Data format 
Source data version: Downloaded April 15, 2017
Assembly: Human Dec. 2013 (GRCh38/hg38)

Description

SNPedia is a wiki investigating human genetics with information about the effects of variations in DNA, citing peer-reviewed scientific publications.

SNPedia all: SNPedia all SNPs (including empty pages)

The track "SNPedia all" shows all SNPs that exist as a page in SNPedia.com. As SNPedia's user collaboration grows, more detail will be added to SNPedia.com pages. For now, most of the pages are auto-generated by bots and have empty pages. According to Mike Carioso (SNPedia.com founder), SNPedia entries are mostly ClinVar entries marked as pathogenic with at least 4 stars as defined by the ClinVar review status.

SNPedia with text: SNPedia pages with manually typed text

The track "SNPedia with text" is a subset of the "SNPedia all" track. This track displays only SNPedia entries with a text page that was created manually by a user who typed in some text (approximately 5,000 entries). In the browser, click on the "configure" button and select "next/previous item navigation" to show clickable arrows in the browser which will jump to the next or previous item.

Clicks on the features show the text from the SNPedia.com page and a link to the original page.

Display Conventions and Configuration

Genomic locations of SNPedia entries are labeled with the dbSNP ID.

In the track "SNPedia all SNPs", the features are colored based on the SNPedia microarray annotation: grey for SNPs that are on no microarray, dark blue for Affymetrix, dark purple for Illumina and black for features on both arrays.

Methods

The mappings displayed in this track were used as provided in the SNPedia GFF file. For the "SNPedia with text" track, all SNPedia pages were downloaded and their content checked with a script that tries to remove pages that were auto-generated and not created manually by a user.

Credits

Thanks to Mike Cariaso for help with the GFF download and Max Haeussler at UCSC for building this track.

References

Cariaso Michael; Lennon Greg. SNPedia: a wiki supporting personal genome annotation, interpretation and analysis. Nucleic acids research. 2012 40Database issue:D1308-12. PMID: 22140107; PMC: PMC3245045