I'm trying to add rsID information to pQTL summary statistics and then use those rsIDs to match the variants with data from another study. Initially, I didn't know that there are 'SNP RSID maps' folder in 'Metadata', so I added rsIDs by running Ensembl-VEP, using the 'Existing_Variation' column from the output. Later, I found the 'SNP RSID maps' folder and compared rsids, but the rsIDs did not match the ones I had obtained from Ensembl-VEP, even for variants with the same chromosome, position, reference allele, and alternative allele (Around 1/10 of all variants did not match). The data from the other study I want to match already has a rsID column, and sometimes all three datasets ( Ensembl-VEP, result, RSID from this database, and the other study's) have non-matching rsIDs. I checked that I'm using GRCh38 position in all steps. When I search individual variants on dbSNP the results do not match rsids from 'SNP RSID maps' folder but match the results of Ensembl-VEP annotation. I would like to insert examples but it seems like I'm unable to insert images to this post so I'm inserting the URL link to my biostars post instead: https://www.biostars.org/p/9592078/ Could anyone help me find out what's wrong? Thank you.