Need help annotating of non coding regions

[ghausiabegum]

Hi,

I used Annovar to annotate my SV calls. I need to find out if my SV overlaps with regulatory elements such as promoters, enhancers, and non-coding RNAs (lincRNAs, miRNAs, siRNAs), etc. The following headers are present in my txt file

['Chr', 'Start', 'End', 'Ref', 'Alt', 'Func.refGene', 'Gene.refGene', 'GeneDetail.refGene', 'ExonicFunc.refGene', 'AAChange.refGene', 'cytoBand', 'ExAC_ALL', 'ExAC_AFR', 'ExAC_AMR', 'ExAC_EAS', 'ExAC_FIN', 'ExAC_NFE', 'ExAC_OTH', 'ExAC_SAS', 'SIFT_score', 'SIFT_pred', 'Polyphen2_HDIV_score', 'Polyphen2_HDIV_pred', 'Polyphen2_HVAR_score', 'Polyphen2_HVAR_pred', 'LRT_score', 'LRT_pred', 'MutationTaster_score', 'MutationTaster_pred', 'MutationAssessor_score', 'MutationAssessor_pred', 'FATHMM_score', 'FATHMM_pred', 'PROVEAN_score', 'PROVEAN_pred', 'VEST3_score', 'CADD_raw', 'CADD_phred', 'DANN_score', 'fathmm-MKL_coding_score', 'fathmm-MKL_coding_pred', 'MetaSVM_score', 'MetaSVM_pred', 'MetaLR_score', 'MetaLR_pred', 'integrated_fitCons_score', 'integrated_confidence_value', 'GERP++_RS', 'phyloP7way_vertebrate', 'phyloP20way_mammalian', 'phastCons7way_vertebrate', 'phastCons20way_mammalian', 'SiPhy_29way_logOdds', 'avsnp147']

Can someone please help me proceed?

Thanks!