I have performed GWAS and got some significant SNPs. How can I get candidates genes in the flanking regions of those SNPs and also their functional annotations (eg. KEGG).
You can use BEDOPS' closest-features tool. You only need to have the SNPs coordinates in .bed format and a .bed file with gene locations. BEDOPS will look for the closest genes upstream and downstream of your SNPs. The command will look something like this:
closest-features yourSNPs.bed yourAnnotation.bed
Then, you can obtain your functional annotations through different tools such as biomart.