You need to be super careful with this sort of analysis:

Long genes are more likely to have GWAS hits in them than short genes. Long genes (and highly expressed genes) are more likely to be differentially expressed than short genes.

Thus the overlap is much more likely to be significant than you'd expect, and the usual Fisher's/hypergeometric statistics for enrichment don't apply.

Several genesets/pathways are also enriched for long/highly expressed genes. For example, genes important to neurons are longer than other genes on average, thus if your set of DE/GWAS genes is longer than average, and neural genes are longer than average, then there is more likely to be a "chance" overlap between them than would be suggested by normal pathway enrichment statistics.

You could try Partek Pathway (http://www.partek.com/partek-pathway/). You can start with a list of genes and perform an enrichment test against the KEGG database. You can visualize pathway diagrams and annotate them with additional information.