Analysis Modules

From this page, you can access tools for interactive, custom analysis of the summary results and individual-level data in the Knowledge Portal. Both this page and the tools offered here are under continuous development, so check back often for updates.

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Custom Association Analysis

Custom association analysis, powered by the Genetic Association Interactive Tool (GAIT) software, allows you to filter samples and specify other parameters before running real-time association analysis. Enter a variant ID to perform single-variant analysis, or a gene name to perform a gene burden test. In order to protect patient privacy, visualization or analysis of data from fewer than 100 individuals is not supported.

Interactive Manhattan Plot

View genetic associations across the genome for all datasets and phenotypes in the Knowledge Portal.

LD (linkage disequilibrium) clumping may be performed for most datasets. Clumping reduces redundancy in genome-wide association plots by grouping variants into sets according to their LD relationships and displaying only the most significantly associated variant in each set.

Variant Finder

This versatile tool lets you specify multiple search criteria to find genetic variants whose associations meet those criteria.

Genetic Risk Score

The Genetic Risk Score (GRS) tool takes a defined set of T2D risk-associated variants and allows you to calculate the p-value for association of this set with different phenotypes, potentially revealing genetic relationships between phenotypes.