Schema for SNPedia - SNPedia
  Database: hg38    Primary Table: snpediaAll Data last updated: 2017-09-18
Big Bed File Download: /gbdb/hg38/bbi/snpediaAll.bb
Item Count: 107,172
Format description: bed9 with the Snpedia array and shortened notes
fieldexampledescription
chromchr1Reference sequence chromosome or scaffold
chromStart166348576Start position in chromosome
chromEnd166348577End position in chromosome
namers7523538Name of item
score0Score from 0-1000
strand.+ or -
thickStart166348576Start of where display should be thick (start codon)
thickEnd166348577End of where display should be thick (stop codon)
reserved0,0,0Used as itemRgb as of 2004-11-22
arraybothJust in dbSNP, Affymetrix, Illumina or on both arrays
noteSNPedia note

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEndreservedarraynote
chr1166348576166348577rs75235380.1663485761663485770,0,0both
chr1167077217167077218rs730288930.167077217167077218200,200,200snp[GWAS:QRS duration in tripanosoma cruzi seropositivity]
chr1167187262167187263rs98036590.1671872621671872630,0,0both[PharmGKB:Non-Curated GWAS results: Population-based genome-wide association studies reveal six loci...
chr1167312756167312757rs109186820.167312756167312757100,0,255affy
chr1167312909167312910rs21467270.167312909167312910200,200,200snp
chr1167401913167401914rs37674340.1674019131674019140,0,0both
chr1167439352167439355rs1939227410.167439352167439355200,200,200snp
chr1167439353167439355rs1939227390.167439353167439355200,200,200snp
chr1167439353167439354rs1939227400.167439353167439354200,200,200snp
chr1167439354167439355rs743152900.167439354167439355200,200,200snp[OMIM:?]

SNPedia (snpedia) Track Description
 

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