Tuesday, March 29, 2016

New graphics and table summarize variant associations at a glance

Our variant information pages now contain two new sections that make it easy to see quickly whether a variant is associated with type 2 diabetes or related traits, and just how significant those associations are.

At the top of the Variant page for one particular variant, the section titled “Is (variant name) associated with disease?” opens to show the associations of that variant with T2D in all datasets that are currently available via the Portal (view an example). Click the link “expand associations for all traits” to see significant associations with other T2D-related traits.

Each box represents an association between this variant and a trait as detected in one data set, and the color of the box indicates the significance of the association. Dark green shows genome-wide significance (p-value < 5 x 10e-8); medium green shows locus-wide significance (p-value < 5 x 10e-4); and light green denotes nominal significance (p-value < 0.05). Associations that do not meet the threshold for significance are shown in a white box.


These new graphics make it easy to see quickly that the variant rs13266634 is strongly linked to T2D, fasting glucose levels, and proinsulin levels.

Just below this section, the “Association statistics across traits” table gives complete details about the associations between the variant and multiple traits. The same shades of green show the most significant associations.


In this table with more details about the associations of this variant, the consistent color scheme highlights significance levels.

Information shown in this table for the variant-trait associations may include p-value, direction of effect, odds ratio, minor allele frequency, and effect size. The table can be sorted by trait name. Where a variant-trait association was detected in more than one study, the most significant result is shown; plus signs allow you to expand the table and view results from additional studies. Some datasets can also be expanded to show associations in different ancestries or cohorts.

We’re still developing these new features, and your feedback could help us make them even better. Please explore them and let us know what you think!

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