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Figure 3. Identifying eQTLs associated with a gene. Entering a gene name in the Browse "By gene ID" field on the
landing page returns a list of SNPs that are eQTLs in the database. eQTLs for XRRA1 are shown in this example. For
more details on navigating the other links on the page, see the text or the GTEx tutorial. To find the TaqMan Assays
for these SNPs, simply enter the rsID number into the TaqMan query form (thermofisher.com/taqman).
entering "rs9787897, RPS26, Whole_Blood" returns
data, meaning that there is information for the SNP,
but the P value is 0.98, and the NES score is very low
(Figure 4B). Thus, rs9787897 is not a significant eQTL
for RPS26 in blood. If the SNP is not in the database,
the page will clearly state this. Note that, in order
to make these types of queries, the tissue name entered in the box must match exactly to the text in
the database, as outlined in "allowable tissue names."
Once a positive association is made, studies can be
extended by analyzing more samples using TaqMan
SNP Genotyping and Gene Expression Assays.

Example 3: Making specific
association queries
The GTEx portal allows queries for specific SNP,
gene, and tissue associations to be addressed. To
make these queries, click on the "eQTL Calculator"
link in the QTL section of the portal. The resulting
page will have a box that will allow you to enter an
rsID, gene name/symbol, and tissue type. For example, entering "rs9787897, XRRA1, Whole_Blood" will
confirm that the SNP is indeed an eQTL for XRRA1
in whole blood with a P value of 1.5 x 10-218, a very
significant result (Figure 4A). On the other hand,

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http://www.thermofisher.com/taqman

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
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