Click the links below to review example queries
If you have a favorite
SNP or
gene and want to determine if it is associated with any H2P2 phenotypes, on the
Phenotypic Associations page:
- Specify phenotype, SNP, gene, and/or position
- Default: All phenotypes. If you want to look only at the association of your SNP/gene with a particular phenotype,
select it from the Phenotype pull-down list.
- Enter SNP ID (rs2869462),
gene name (ART3),
or both (rs2869462 and ART3).
- Filter
- Default
SNP Sub-types
: All. To focus on more functionally relevant SNPs, select exonic or eQTL or other
categories.
- Default
–log10(p) lower bound
: 3. This will return SNP-phenotype associations that have
p < 10-3 and can be made more or less stringent. Note that the common threshold for genome-wide
significance is p < 5x10-8 (–log10(p) > 7.3). True associations can still be found
with less stringent p-value thresholds but false positives will also become more common.
- Default
Results to return
: 1000 (though for the sample SNP query, above, only two are returned).
- Review
- Click
Query and Review.
If instead you would like a CSV file of the associations, click Query and Save.
- Using the example SNP, from above, two associations will be returned. The entry with the lowest p-value is the
association of rs2869462 with Chlamydia-infected levels of CXCL10 (also known as IP-10) (IP10_Chlamydia;
p = 2x10-9). The output can be sorted by clicking on any of the column headings.
- Click on a row to see a plot of phenotypic response X genotype for LCLs in the selected phenotype and SNP. The default
is to plot all populations combined, but individual populations can be selected to generate a paneled plot. n
(LCLs in sample) and median response are given for each population and genotype. The
log-2 transform
option transforms response values to their log2 values. This is particularly useful for cytokine level
phenotypes.
- Click the
Results: Individual LCL Data
tab to see individual LCL IDs, genotypes, and phenotype values.
Click the Download
button to download a CSV file with this information for further analysis.
- Click
Results: SNP Details
or Query/Filter
tabs to examine other associations or change query parameters.
If you have a favorite
cellular phenotype and want to determine which SNPs are associated with it, on the
Phenotypic Associations page:
- Select the cellular phenotype you are interested in
(IP10_Chlamydia).
- Leave the SNP and gene entries blank. Filter based on –log10(p) lower bound
(8) and/or based on functional
categories (eQTL) as described
in step 2, above
(IP10_Chlamydia,
–log10(p) > 8, and eQTL).
- Review as in step 3, above.
To review summary plots for
individual cellular phenotypes, on the
GWAS Summary page:
- Select the cellular phenotype you are interested in
(IP10_Chlamydia).
- Select either Manhattan or QQ plot.
If you would like access to the complete dataset, please click here:
Bulk Data Download
Happy querying! Feel free to email with any questions or interesting results.