Protein-DNA interactions and DNA methylation control mammalian gene expression to determine cell fate. Heterochromatic regions of the genome are tethered to the nuclear lamina, repressing their transcription. In DamID the DNA adenine methylase (Dam) is fused to a protein-of-interest. Sites of DNA-protein interaction are identified by the methylation of adenines in GATC motifs at sites of interaction and their cleavage by the methylation-specific enzyme DpnI. DamID cannot currently identify endogenous DNA methylation modifications such as CpG methylation. Nanopore sequencing is a long-read sequencing approach that relies on current disruption by nucleotides from a DNA strand passing through a membrane-embedded nanopore. Nucleotide modifications such as CpG methylation have a distinguishable current disruption and can be directly detected. Nanopore-DamID combines these two techniques to profile genomic interactions while simultaneously identifying endogenous DNA modifications. Nanopore-DamID of transgenic neuroblastoma cells expressing the nuclear lamina protein LaminB1-Dam revealed distinctive CpG methylation patterns. Lamin Associated Domains (LADs) showed a low CpG methylation, however gene promotors in LADs show a high CpG methylation. Inversely, inter-Lamin Associated Domains (iLADs) showed a high CpG methylation but low CpG methylation at iLAD associated promotors. These results suggest that DNA methylation may be required to restrict activation of heterochromatic genes even when they are tethered at the nuclear periphery. Overall, Nanopore-DamID enables novel insights into the regulation of gene expression by DNA-protein interactions and DNA methylation.