Human Genome build 36.3
dbSNP build 130
 
 
UCSC Genome Browser
 
 CGR Applications
 Genewindow
 
 Collaboration
 dbGAP
 454 Life Sciences
 NimbleGen
 ABCC

Region Search

There are several ways to search for a region:

  • On the left sidebar, enter a query string in the search field. After typing a string, you can either hit the Enter key or click the link "Search" to submit the query. The query string can be in one of the following formats:
    1. chromosome position. The format is chr[chromosome]:[start position] (chr8:128573000)
    2. contig position. The format is [accession]:[start position] (NT_008046:41624697)
    3. dbSNP ID (rs1800460)
    4. CGF ID (CGFID_300)
    5. HUGO ID (BRCA1)
    6. SNP500Cancer ID (BRCA1-02)
  • On the region page, click the left/right arrow to move back/forward 1000bp from the current search region.

Region View

The region page shows a Gene View and a Sequence View. A Gene View can display a full or partial gene image. In most cases, a full gene region is different from the region of Sequence View that is about 2000 bp long. The sequence region is represented as yellow shadow on Gene View. Polymorphisms are shown on Sequence View and Gene View if it contains partial gene image.

  • Length:
    1. One sequence view displays about 2000bp.
    2. One gene view displays about 2000bp or a full gene region.
  • Shape:
    1. A polymorphism is represented as a rectangle.
    2. A gene is represented as a line. Its direction is indicated by an arrow.
    3. MRNA is represented as a line in different width. The thick sections of the lines are for exons and the thin ones are for introns.
  • Color(polymorphism):
    1. Red only contains dbSNP data.
    2. Green only contains CGF data.
    3. Dark green contains both dbSNP and CGF data.
    4. The target polymorphism is bordered in purple
  • Color(sequence):
    1. Yellow represents CGF sequenced regions.
    2. Gray represents all other regions.
  • Color(MRNA)
    1. Red represents coding regions.
    2. Blue represents untranslated regions.
  • Clicking:
    1. Click a polymorphism to see detailed information on a popup window
    2. Click a HUGO ID to connect to the Entrez Gene website
    3. Click a gene to switch the full/partial image mode
  • Mousing over:
    1. Move the curser over nucleotide to see its genomic position
    2. Move the curser over polymorphism to see its ID
    3. Move the curser over MRNA to see the transcript ID and protein ID

UCSC Genome Browser

We generated a customer track (CGF SNP) of the UCSC genome browser. The customer track includes the polymorphisms in our sequenced region. To view the data on the UCSC genome browser, click the link "UCSC" on the left sidebar.

 
 
Disclaimer