I have been using the annotatePeak function in ChIPseeker to annotate my ChIP-seq peaks. It works out just fine, but I am puzzled on what is considered as 'distal intergenic'. I saw from another posted inquiry that 'intergenic' refers to regions that do not overlap genes. However, annotatePeak is giving me intergenic regions with assigned genes to them (among more expected intergenic regions that do not associate with a particular gene), for example:
Txdb used was TxDb.Mmusculus.UCSC.mm10.ensGene. TSS range was +/- 3000 bp (assigned as promoter/downstream, which worked fine).
Why would regions like this be assigned to any genes? Are these known enhancer/silencer regions, and if they are, from which database was this derived from? I tried looking through UCSC but there does not seem to be no information on defined enhancer/silencer regions. The ChIPseeker manual does not address this, and it has been giving me a hard time trying to wrap my head around it.