Thermo ebook on eQTL - 24

also display defined splicing QTLs along the y-axis in
yellow (not shown). Finally, a diagram showing linkage disequilibrium between the different variants is
below the bar graphs (not shown).

Example 5: Visualizing the eQTLs in the
context of the genome
Finally, the GTEx portal can also provide a view of
eQTLs in a genomic context. This interface makes
use of some of the features in the IGV developed at
the Broad Institute.7 Clicking on "IGV eQTL Browser" will bring up a default view of the first chromosome's first 500,000 nucleotides. Immediately below
the drawing of the chromosome are light green boxes showing the location of SNPs that have been associated with GWAS (GWAS Catalog space). Clicking
on one of these boxes will bring up information on
the strongest SNP-risk allele, disease, P value, odds

Studies further examining the link between SNPs
and gene expression can be performed using the
appropriate TaqMan SNP Genotyping and Gene
Expression Assays. It is important to note that the
TaqMan SNP Genotyping Assays must be searched
and ordered using the rsID (rs190222032) and not
the GTEx ID (e.g., 11_73806478_G_A_b37), as displayed in the main view.

Figure 5. Visualization of eQTL data for a gene. The "GTEx Locus Browser" provides a large amount of information
about known eQTLs for a gene. SNPs that have a positive influence in the indicated tissue are shown in red; SNPs
with a negative influence are shown in blue. The intensity indicates the magnitude of the influence; the size of the
bar is a measure of the P value. An unmagnified view of the locus, including neighboring genes, is shown at the very
top. Note that that view is not to scale.

Thermo ebook on eQTL

Table of Contents for the Digital Edition of Thermo ebook on eQTL