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The input for Annotate peaks is a Peaks type data node. The Annotate regions task works the same way, but takes Region counts as the input. 

• Click a Peaks data node
• Click the Peak analysis section in the toolbox
• Click Annotate peaks
• Set the Genomic overlaps parameter

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Intergenic is regions that do not overlap and are not located within 1000bp of a transcript

Annotate peaks vs. Annotate regions

Annotate regions is almost identical to Annotate peaks. Annotate regions takes Region counts data as the input and outputs Annotated region counts. One important difference is that you cannot filter the Annotated region counts from the task report. 

It is important to run Annotate regions prior to performing differential analysis if you will want to filter regions by gene section in the differential analysis task report.