Lead Snp and snp that was linked to gene are not matching

[akhilpampana]

Hello,

Thank you for the pipeline. It is really useful for me to run the analysis. I could able to generate results for eQTL colocalization. I got a few genes and variants showing expression and posterior probability. I was extracting effect estimates for the variants that are used in the analysis and found that there are differences in variants that are used for coloc. I see the lead SNP and variant that was reported in *_full_summary.txt are different. I tested with multiple gene regions and got the same results. Have you observed this before? If so how to deal with the results? I thought coloc works only if there are common variants among two datasets so thought of reaching out to you.

Thank you so much for your help and looking forward to hearing from you.

Regards
Akhil