Thermo ebook on eQTL - 25

ratio, and PubMed ID for the study. Below the GWAS
Catalog space are intron/exon diagrams of genes
covered by the view.

bol or rsID, then eQTLs associated with the gene or
SNP are shown as red dots instead of gray dots.
As described in the other examples, studies further
examining the link between SNPs of interest and
expression of affected genes can be performed using the appropriate TaqMan SNP Genotyping Assays
and Gene Expression Assays. From this view, it is
easy to see the genes that may be of interest for further examination. rsIDs can be obtained by clicking
on the dot of interest. Again, the TaqMan SNP Genotyping Assays can only be searched and ordered
using the rsID (rs190222032), not the GTEx ID (e.g.,
11_73806478_G_A_b37).

A track showing eQTLs can be added by choosing
a tissue (or tissues) via "Click Here To Select Tissue
Tracks" at the top left of the viewer. The view can be refined by zooming in and out or by entering genomic
coordinates or specific gene names in the search box.
For example, entering "chr11:74,000,000 75,000,000"
in the search box brings up the region around the
XRRA1 locus (Figure 6). eQTLs that have been mapped
to the region are shown as gray dots giving a comprehensive view of the region. Clicking on any of the individual dots will bring up information about that eQTL.
Note that, in this region, there are data from only
eleven GWAS-mapping a SNP to POLD3 and CHRLD2
regions. If the search is done by entering a gene sym-

Case example-SERPINH1 and breast cancer
We illustrate how these tools might be employed
by making use of a hypothetical example. Brows-

Figure 6. View of eQTLs using the IGV browser interface. The location of eQTLs for particular tissues can also be visualized using the IGV interface. Tracks showing eQTLs for specific tissues are chosen by clicking on the "Click Here
to Select Tissue Tracks" button and selecting the desired tissue type. Shown here are eQTLs in blood and mammary
tissue that fall within the genomic coordinates entered (ch11:74,000,000-75,000,000). Clicking on a gray dot (or
red if a specific gene is entered in the query box) displays details about that SNP. In addition to gene structures that
map to this region (genes track), data from GWAS that fall into the same region are shown by light green bars on
the "GWAS Catalog" track.

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Thermo ebook on eQTL

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

Contents
Thermo ebook on eQTL - 1
Thermo ebook on eQTL - Contents
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