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A cis-trans plot shows eQTLs with a certain LOD score on the X-axis for genes on the Y-axis.

Blue dots indicate peaks with a positive LOD score, red dots indicate peaks with a negative LOD score.

By clicking on an eQTL, the eQTL profile of the corresponding gene is shown in the panel on the right.

On the diagonal are the so called "cis eQTLs" that map to the gene's own location.

Below the cis-trans plot is a histogram of the number of eQTL peaks per marker. Clicking on a bar brings up the eQTL profiles for all genes with an eQTL at that location.

You can use the search box at the top to search for a specific AGI ID in the plot.