The Traceability Matrix Report

It shows the links between the issues of whatever two saved filters on a matrix view. It allows to manage links (create, view and delete) from the matrix itself and it also supports pan & zoom with the mouse.
It is available from two locations:

1. The JIRA top menu Links > Matrix:

The link can be disabled by a JIRA Administrator from the Links Hierarchy installed modules:

1. The JIRA Project Reports > Other section:

Click on Select Filter.. link to bring up the Filter Picker dialog:

for the rows and the columns:

Click on any cell to bring up an interactive dialog showing the current links with the option of "Delete" any regular link as well as a dialog at the bottom for new link creation.
Each cell having linked issues have an arrow. The arrows must be read from the rows to columns direction:

Outward links:

Inward links:

Inward & outward:

The Links Filter menu at the top left allows to show and hide links on the matrix accordingly their link type:

The Matrix data can also been exported to Excel:

Since version 5.4.1, you can now mark rows and columns. This will help you easily identify links between particular issues, especially for large matrices.