Abstract Gene silencing via CpG island hypermethylation contributes to colorectal cancer (CRC). We previously demonstrated that genetic variants (single nucleotide polymorphisms, or SNPs) in the MLH1 gene promoter region are associated with MLH1 CpG island hypermethylation, MLH1 protein loss, and DNA mismatch repair deficiency in tumors. Recently, CpG-rich “shore” regions were identified flanking many CpG islands which exhibiting distinct methylation profiles among different tissues and in normal versus tumor states. To explore the role of MLH1 CpG island shore methylation, we performed global methylation profiling (Illumina 450K microarrays) to investigate DNA methylation in peripheral blood cell (PBC) DNA of over 800 CRC cases and 800 controls (Savio et al., 2012). We found that MLH1 CpG island shore hypomethylation occurred in PBC DNA of both cases and controls. Intriguingly, individuals carrying variant alleles of the MLH1 promoter SNP rs1800734 incur significant hypomethylation at the MLH1 CpG island shore, located 1.5 kb upstream irrespective of disease status. Based on these observations we sought to determine whether these SNP-associated epigenetic changes were apparent in other tissues, including CRC and normal colonic tissue. To address this, we investigated MLH1 CpG island shore methylation in matched PBC, normal colon, and tumor DNA of 349 CRC cases using the real-time PCR-based technique, MethyLight. Methylation was significantly lower in PBC DNA of CRC cases with variant SNP genotypes (both heterozygous and homozygous variant carriers) and this association was also observed in normal colonic DNA. The association between genotype and epigenotype was lost in tumor DNA, as no differences in methylation were seen among different genotypes. Hypermethylation in tumor DNA compared to normal tissues (PBC and colon) was also observed. This hypermethylation and lack of association between SNP genotype and shore methylation in tumors may indicate an epigenetic switch occurring. Bisulfite sequencing of DNA from fresh frozen tumors and paired normal colonic mucosa have recapitulated these results, with hypomethylation incurred in variant SNP carriers. Hypermethylation in tumor compared to normal DNA was also observed. Bisulfite sequencing of four CRC cell lines has also revealed SNP-dependent hypermethylation at the MLH1 CpG island shore. Taken together, we have integrated methylation data from a microarray platform, sensitive real-time PCR, and bisulfite sequencing for a comprehensive and systematic analysis of DNA methylation at the CpG island shore of MLH1 in multiple tissues of CRC cases, controls, and cell lines. These results indicate that static genetic variants can modulate dynamic epigenetic regulation at the MLH1 gene region, and may play a role in colorectal tumorigenesis. Citation Format: Andrea J. Savio, Mathieu Lemire, Miralem Mrkonjic, Steven Gallinger, Brent W. Zanke, Thomas J. Hudson, Bharati Bapat. Novel insights into the genetic and epigenetic regulation of the MLH1 CpG island and shore in colorectal cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1058. doi:10.1158/1538-7445.AM2015-1058