text: user5023: 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). 
  
  user678: 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. 
  
original_text: 5023: <p>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). </p>
   678: <p>You can use <a href="https://bedops.readthedocs.io/en/latest/content/reference/set-operations/closest-features.html" rel="nofollow noreferrer">BEDOPS' closest-features</a> 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: </p>
  
  <pre><code>closest-features yourSNPs.bed yourAnnotation.bed
  </code></pre>
  
  <p>Then, you can obtain your functional annotations through different tools such as biomart. </p>
  