Functional enrichments of putative transcriptional target genes have been utilized to understand the functions of transcription factors and cascades in a cell. To investigate their features, transcriptional target genes were predicted using open chromatin regions of human immune and ES cells, as well as known transcription factor binding sequences. Gene Ontology annotations showed four times larger numbers of functional enrichments in putative transcriptional target genes than gene expression information alone in the cell types. More than two times larger numbers of functional enrichments in putative target genes was observed using forward-reverse orientation of CTCF-binding sites than without them. These analyses would be useful to find genomic features involved in chromatin interaction and improve the prediction of transcriptional target genes.