When moving from BCOR to .txt files, what does the column called "correlation" mean?

The "correlation" column is the same as R^2. Idstore (which generates the result) does not return which alleles are linked so you cannot determine that from the output in the file.

The value reported is in-sample (i.e. using the cases and controls that were used in the association analysis). The value in Idstore is actually just pure correlation, hence negative values will appear.

The imputed data we provided as VCFs is phased, so you could extract the variant of interest carriers and those 5 variants to see what the haplotypes are.