From a linkage study, we have identified a significant signal on a chromosomal region. Sequencing that region identified ~1000 significantly associated SNPs laying in intergenic-intron regions with none in exonic regions. Running these SNPs on various databases (e.g. ensembl's VEP) is not getting much results. Any suggestions on how to proceed next? I know a similar question was posted, but that was ~5 years ago so it is probably outdated by now.
You could look for eQTL databases, whether SNPs in that region have an effect on a gene further away. Could also be that an unannotated lncgene or miRNA is present there... SNPs can have an effect up to megabases from where they are situated, so it's hard to say what the functional role is. You could look around for ENCODE annotation or riboseq signals to tell you something about functional/transcribed elements. You could give CADD, fathmm or DANN a shot to make a prediction about pathogenicity of variations.