I have a large set of data of nearly 200 individuals who were sequenced by NGS after a GWAS was performed to identify top variants. I have fine-mapped this region (including filtering steps) using GATK, samtools, bwa etc. and currently working with VCF files of nearly 6000 variants. I have removed all multi-allelic variants manually and used VCFtools to filter for minor allele frequencies. I currently need to prioritize these variants in order to perform subsequent genotyping using TaqMan because there are currently way too many. I would also like to mention that all the individuals that were sequenced had the phenotype of interest; therefore, no comparisons can be made. Do you have any suggestions for filtering out these variants (all of which are in a noncoding region) for regulatory influence or any other parameter?