Assuming you are working with human sequences, identify the genomic co-ordinates of the -3000 to -6000bp upstream regions for genes of your interest and give it as input in bed format to UCSC table browser, once done extract it as fasta.  For more help in downloading from UCSC browser have a look at this links "http://fasta.bioch.virginia.edu/cshl/stubbs/meme-ex/meme.html" and "http://genome.ucsc.edu/FAQ/FAQdownloads.html#download32"

Or if you have the genome on your system, generate a bed file for the co-ordinates of your interest and you can use "fastaFromBed" option in BEDtools.

you can write a line command to do so:

e.g. your TSS is in the file TSS.bed which means three coloumns separated by tab containing :

Chr start end 

you just do

awk '{print $1,$2-6000,$2-3000}' OFS="\t" TSS.bed > enhancer.bed

#### now extract sequence , I hope you have genome_sequence and bedtools, if not ######please have it, they would help a lot for long term

fastaFromBed -fi genome_sequence.fa -bed enhancer.bed -fo enhancer.fa

enhancer.fa is your enhancer sequence upstream of TSS.

Thank you for your answer. I will ultilize the BED tools.

After isolating your enhancer sequence you need to test their activities.  In this case, I suggest that you can use the pJan25 vectors series for promoter testing. See attached article.  I hope this answer may help you. 

Article The pJan25 vector series: An enhancement of the Gateway-comp...