Schema for RGD Rat QTL - Rat Quantitative Trait Locus from RGD Coarsely Mapped to Human
  Database: hg19    Primary Table: rgdRatQtl    Row Count: 5,804   Data last updated: 2010-12-12
Format description: Browser extensible data
fieldexampleSQL type info description
bin 1smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 870934int(10) unsigned range Start position in chromosome
chromEnd 14874065int(10) unsigned range End position in chromosome
name Vra3varchar(255) values Name of item

Connected Tables and Joining Fields
        hg19.rgdRatQtlLink.name (via rgdRatQtl.name)

Sample Rows
 
binchromchromStartchromEndname
1chr187093414874065Vra3
1chr187093430447467Strs2
1chr187093420267156Lanf1
1chr187093411907822Bp131
1chr187093430447467Apr2
1chr187093438165854Anxrr4
1chr1107183159012763Scl20
1chr1242087043424594Bp103
1chr1489611342321952Bp147
1chr1786384859012763Bp7

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

RGD Rat QTL (rgdRatQtl) Track Description
 

Description

This track shows Rat quantitative trait loci (QTLs) from the Rat Genome Database (RGD) that have been coarsely mapped by UCSC to the Human genome using stringently filtered cross-species alignments. A quantitative trait locus (QTL) is a polymorphic locus that contains alleles which differentially affect the expression of a continuously distributed phenotypic trait. Usually a QTL is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci.

For a comprehensive review of QTL mapping techniques in the rat, see Rapp, 2000.

To map the Rat QTLs to Human, UCSC's chained and netted blastz alignments of Rat to Human were filtered to retain only those with high chain scores (>=500,000). This removed many valid-but-short alignments and in general retained only very long chains (>10,000, usually >100,000 bp), so that only large regions could be mapped. This choice was made because QTLs in general are extremely large and approximate regions. After the alignment filtering, UCSC's liftOver program was used to map Rat regions to Human via the filtered alignments.

To get a sense of how many genomic rearrangments between Rat and Human are in the region of a particular Rat QTL, you may want to view the Human Nets track in the Rat Nov. 2004 (Baylor 3.4/rn4) genome browser. In the position/search box, enter the name of the Rat QTL of interest.

Credits

Thanks to the RGD for providing the Rat QTLs. RGD is funded by grant HL64541 entitled "Rat Genome Database", awarded to Dr. Howard J Jacob, Medical College of Wisconsin, from the National Heart Lung and Blood Institute (NHLBI) of the National Institutes of Health (NIH).

References

Rapp JP. Genetic analysis of inherited hypertension in the rat. Physiol Rev. 2000 Jan;80(1):135-72. PMID: 10617767