I have an annotated set of SNPs and I would like to explore the difference in the binding affinity of the transcription factor (TF) if I have a SNP in my locus. As my SNPs are annotated (I know wether it is in an intron variant, downstream gene variant, missions variant, etc...) I might explore the binding affinity of those SNPs that are categorized as intron variant, downstream variant,upstream_gene_variant, non_coding_transcript_variant, 5_prime_UTR_variant and not take into consideration SNPs that are "missense variants". The reason why I want to do so is that transcription factor binding sites (TFBS) might be located before gene and after it.
What do you think about it? Can a TFBS be located in the exon of a gene? What are the locations of the TFBS regarding the exons,introns, 5' UTR etc?