Is there a reference one can point me to which speaks about the different ways one can map SNP--> Genes for pathway analysis?
There seems to be many ways one can map SNP to genes: 500kb upstream and downstream of gene; 100kb upstream and downstream of gene; 20kb upstream and downstream of gene; 5kb upstream and downstream of gene; within gene; functional SNP (nonsynonymous, stop gained/lost, frame shift, essential splice site, regulatory region) . I found this on the i-Gsea4Gwas website but it doesn't say anything about use cases. One tends to get different answers in terms of top pathways with different mapping schemes. And I'm guessing that the rationale for choosing one of the scheme might also differ depending on the type of data one is using (say..just observed SNPs vs. 1000G imputed SNPS etc.).