If you have the TF binding sites in UCSC BED format, you can use BEDOPS convert2bed to convert gene annotations to BED, bedops to make a file of gene promoters (say, a region 500 nt upstream of the gene TSS), and bedmap to associate binding sites with the promoters of genes.

Get some gene annotations and write them to a BED-formatted file:

$ wget -qO- ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_27/gencode.v27.basic.annotation.gff3.gz \
    | gunzip --stdout - \
    | awk '$3 == "gene"' \
    | convert2bed -i gff - \
    > genes.bed

Or replace this step with whatever annotation source you prefer, for your reference genome.

Make a file of promoter regions from the genes:

$ awk -v OFS="\t" '($6 == "+") { print $1, $2, ($2+1), $4; }' genes.bed | bedops --range -500:0 --everything - > promoters.for.bed
$ awk -v OFS="\t" '($6 == "-") { print $1, ($3 - 1), $3, $4; }' genes.bed | bedops --range 0:500 --everything - > promoters.rev.bed
$ bedops --everything promoters.for.bed promoters.rev.bed > promoters.bed

Sort your BED-formatted TF binding sites:

$ sort-bed tfbs.unsorted.bed > tfbs.bed

Map binding sites to gene promoters:

$ bedmap --echo --echo-map --delim '\t' promoters.bed tfbs.bed > answer.bed

Each line of the file answer.bed contains a promoter region, its associated gene ID, and any TF binding sites that overlap the gene's promoter.

Hi!

I actually have the regions on the genome where certain transcription factors bind, thanks!