Genomic position to genomic feature

Question

[irfanwustl]

Hi, We have some Methylation samples and obtained some differentially methylated regions (DMR) from those samples. Now we are asking are those DMR makes biological sense. So we want to know if a DMR is in promoter, gene body, intron, exon, repeat regions, or low complexity regions. To test the promoter and gene body we have collected a database and checked whether a DMR falls in the gene body or promoter. But the problem is with intron, exon, repeat regions, or low complexity regions. Is there any database for those features where for a given genomic position (e.g. chr10:100006425), we can know where (intron, exon, repeat regions, or low complexity regions) it falls?

[bernatgel]

For genes (exons, introns, promoters, UTRs...) if you are using R and working on human or a fairly common model organism, you can use Bioconductor's TxDb objects. For example TxDb.Hsapiens.UCSC.hg38.knownGene for human or TxDb.Mmusculus.UCSC.mm10.knownGene/ for mouse.

You can find some documentation in their respective vignettes or here for a more general view, but you'd basically be using genes, exons, ... functions.