GWAS data integration

Question

[ishtiaque.hossain]

Hello,

Is there a recommended workflow to cross-reference a list of genomic regions (say a bed file of H3K27Ac ChIP-seq peaks) against GWAS SNPs?

The output I am hoping for is basically, to assess all the genomic co-ordinates in my bed file and see which ones overlap a SNP, and whether that SNP is also a GWAS hit.

Thank you.

Answer 1

[Sam]

What you are looking for is call co-localization. One of the program is COLOC