I am using the IlluminaHumanMethylation450kanno.ilmn12.hg19 Bioconductor package to get the annotation for some CpG sites. But I found that UCSC_RefGene_Name for some CpGs has more than one gene.
There are two scenarios.
1) The same gene is listed multiple times. For example,
UCSC_RefGene_Name of cg09315878 is "SDF4;SDF4". This is splice variants. I wonder if I could interpret this as cg09315878 is on SDF4 gene?
2) Different genes are listed for one CpG. For example,
UCSC_RefGene_Name of cg02716826 is "SUGT1P1;AQP3". I am not sure why and how to interpret this.