You could perform a targeted motif discovery using the genomic positions of the GWAS markers. But you need to take into account that GWAS SNPs rarely are the causal genetic variant. I would thus recommend to you to take the estimated distance of linkage disequilibrium for the population you are analyzing as a threshold to define the size of the genomic windows to be employed for motif discovery.

you can assess the effect of SNPs associated with diseased ( and SNPs in LD) on TF motifs using the RSAT tool. In addition, you can cross these results with the catalog of TF ChIP-seq peaks ReMap.

Weblink for RSAT :http://rsat.sb-roscoff.fr/

Weblink for ReMap:https://remap.univ-amu.fr/