Definition of the different DNA regions
We can take a look at the following picture (from wikipedia):



The regions are then:


intergenic: everything outside of the shown gene region
&lt;5 Kb downstream: outside of the transcribed region, but possibly part of the promoter or an enhancer (yellow boxes before coding region).
UTR 5′: in the transcribed region, but not part of the coding region, as shown in the picture (blue box before coding region).
intronic: In the Introns, as shown in the picture (grey boxes)
intragenic: These have to be mutations inside the coding region (red boxes), which is confusing since the authors specifically describe them as 'non-coding' mutations. If you read that as 'mutations that don't change the protein sequence', these could be silent mutations
UTR 3′: in the transcribed region, but not part of the coding region, as shown in the picture (blue box after coding region)
&lt;5 Kb upstream: outside of the transcribed region, but possibly part of an enhancer (yellow boxes after coding region)