Thursday, October 31, 2013

v26 (1 of 3): SNP track

SNP information is a long-desired feature and we've finally got it on our browser. Credit goes to UCSC Genome Browser for making SNP information nicely curated and easily accessible.

In version 26 only the human hg19 genome has its SNP track (dbSNP release 137). We are working to add SNP tracks for all applicable genomes as well as enabling SNP custom tracks.

Click to see the SNP track.

Display hg19 SNP track

Go to the browser website and display human hg19 genome. Click "Tracks" > "Genomic annotation tracks", and find SNP track in "Variation" category:

Click the SNP track item to show the track on the browser:

By default the SNP track is shown in "full" mode, with the "rs..." name printed on the left of SNP location. SNPs are colored differently according to their classification:

  •       single nucleotide variation
  •       insertion/deletion
  •       heterozygous variation
  •       microsatellite
  •       text name but not sequence
  •       a cluster of multiple classes
  •       multiple nucleotide polymorphism
  •       insertion
  •       deletion
Click on a SNP to see details about it:

Erratum: rs78276647 should be on "forward" strand

You can use the "link" on the top-right of the tooltip to see original record of this SNP in dbSNP website.

Search for SNPs
To search for SNPs, you need to have SNP track displayed first.

Right click on SNP track and find the search box:

Enter SNP name in the box and press Enter to find the hit:

Click the hit to show it in browser. The hit SNP will be highlighted:

Get v26 source code here, or here.