In my understanding information regarding the gene expression come from mRNA (exon) and control or regulation of a gene can get from non-coding part of DNA (intron etc.). If it is true then I have a hypothesis that SNPs from mRNA (Exonic part) can provide the information related to a trait (through SNP-GWAS) and SNP form DNA (only Intronic or intergenic part) may can provide the information related to Repeat elements such as TE (small RNA species, lncRNAs and Cis-regulatory elements) and Tandem repeats (TR) (what we can get from it TR, I have no knowledge, please guide me). Waiting for the kind suggestions from experts here. Many thanks for your kind time!
Dear Shawn,
Many thanks for your reply and it really improved my knowledge regarding this area.