This ends up not being a bioinformatics question, but I'm guessing you don't know that (otherwise, you wouldn't have asked). Presuming that this is a transcription factor, you need to either over/under express the protein (better yet, do both to avoid ceiling/floor effects) and then do RNAseq. Your genes or interest are only those with peaks in their promoters, as any other DE genes are likely due to secondary effects.
Edit: Of course, if someone has already done the aforementioned experiment and released the dataset then just download and analyze it.
Edit2: You can also whittle down the candidate list by only looking at genes meaningfully expressed in your tissue of interest. If you 're lucky, perhaps that will limit the list to the size you're expecting (I'll not bother to question why you have a certain target number in mind).
" On average, 14.7% of genes bound by a factor were differentially expressed following the knockdown of that factor, suggesting that most interactions between TF and chromatin do not result in measurable changes in gene expression levels of putative target genes. "
To assign functional binding sites to their target genes, one may consider to use BETA developed in Shirely Liu's lab http://cistrome.org/BETA/. It integrates ChIP-seq data and gene expression data to infer the TF target genes.
You may be also interested in this paper:
Assessing Computational Methods for Transcription Factor Target Gene Identification Based on ChIP-seq Data