I have a set of ChIP-seq data, and I would like to find out wheather transcription factor KLF1 binds both upstream (i.e. in the promoter) and downstream of the transcription start site (TSS). For this analysis I have been used the RefSeq annotation and define the upstream and downstream regions of interest to be the 1000 nucleotides upstream and downstream of the TSS, respectively. Furthermore I have been using first Get Flanks tool and then INNERJOIN tool and find that 103 places that overlap with my peaks. But how do I find out which of these 103 bounds upstream and downstream, respectively?