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shown, where red bars indicate the position of eQTLs
that have increased expression relative to the reference, and blue bars have decreased expression. The
size of the bar and the intensity of the color indicate
the significance and magnitude of the SNP.

Example 4: Visualizing all the eQTLs
associated with a gene
Sometimes it is useful to examine all known eQTLs
associated with a gene. The GTEx portal provides a
way to do this, using the "Locus Browser" section of
the portal. To use this feature, click on "Locus Browser" and enter the gene name in the query box. The
page returned is a display rich with visual information. The top of the page shows a mini genome
browser showing 1 Mb upstream and downstream
of the locus being queried. Clicking on a gene name
will change the query to that gene (Figure 5). Below that, a high-level representation of the gene is

In this view, the y-axis shows the different tissue
types for which eQTL information exists. Note that,
in this depiction, the distance between SNPs is not
measured to scale. Hovering the mouse over a bar
will bring up specific information, including the rsID,
tissue, and NES in that tissue. Clicking on a bar will
bring up a violin plot of the expression in different
genotypes in that tissue (not shown). This view will

A

B

Figure 4. Determining whether a SNP is an eQTL. (A) To determine whether the GTEx database contains data identifying a SNP as an eQTL for a gene in a tissue, enter the rsID, gene name, and tissue type in the GTEx eQTL calculator.
If a SNP has been identified as an eQTL for a tissue, the P value returned will be small. (B) If a SNP has not been shown
to be an eQTL for a tissue, the P value will reflect this. Note that a negative result does not mean that the SNP is not
an eQTL; it may act as an eQTL in tissues or conditions that are not present in the GTEx database.

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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
Thermo ebook on eQTL - 3
Thermo ebook on eQTL - 4
Thermo ebook on eQTL - 5
Thermo ebook on eQTL - 6
Thermo ebook on eQTL - 7
Thermo ebook on eQTL - 8
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