Opposite REF and ALT alleles

Question

[a.papadam]

Hi,

I recently did a gwas and found that snp xxx has A1 B A2 C with B to be the reference allele and a negative effect.

Then I looked eqtls and found that lower expression of the gene the snp is in is associated with the alt allele. However the alt allele is the reference allele on my data.

So my question is, my protective allele from the GWAS is associated with lower expression or higher expression

[Ram]

alt allele is reference allele on my data

They're all just alleles - the reference genome is not an absolute standard (if one even exists given how diverse humans are), it's just a genome we've all agreed to use. Ref allele is the allele on this agreed upon ref genome. It is not the one that's "supposed to be" the "normal" allele at that locus. Just think of alleles associated with phenotypes, don't worry if it's called REF or ALT elsewhere.