Generate Methylation Score (β) vs. Genotype Plots


In a recent paper, the UBC Kobor lab investigated cytosine methylation patterns in a total of 180 European and African (Yoruban) samples, using the Infinium HumanMethylation27 BeadChip assay (Illumina, San Diego, CA, USA).

We have developed a tool for investigating the methylation patterns of these samples in the context of their genotypic architecture. This tool allows us to assess whether methylation patterns differ by genotype, either in cis or in trans, for selected SNP’s and CpG sites.

HapMap: Genotypes from HapMap release 3, build 36 are used. The data was retrieved from the International HapMap Project website.

A total of 165 samples from the 180 samples assessed in the Kobor methylation study had genotype information available. Of these, 81 were European and 84 were African. A total of 27,578 CpG sites were assessed in the Kobor paper, and a total of 1,457,897 HapMap SNP genotypes are available.

This form allows you to test a single SNP and CpG sites nearby, and displays all generated plots of methylation versus genotype score in the browser. To investigate multiple SNP’s at once, using chromosome-wide CpG site data, please use the Export Methylation Plots page. The export tool requires you to specify a cut-off p-value for the returned results.

Generate plots for CpG sites within:

kilobases (kb)
of this SNP (specified by rs #):
Using HapMap sample populations: