Export Methylation Score (β) vs. Genotype Plots


Summary:

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. http://hapmap.ncbi.nlm.nih.gov

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 set of SNP’s and all CpG sites on the corresponding chromosome, rather than a single SNP and CpG sites nearby as in the Generate Methylation Plots page. An analysis job will be run on a cluster, and the results and plots for significant SNP/CpG pairs will be emailed to you.

If you have already generated a list of SNP’s in the current session via the ASM SNP Search page it should be in the SNP list field below.

Please note that as of 2016-06-02 this service has been temporarily disabled while the underlying computational cluster is under a period of high load. Apologies for the inconvenience.




Run analysis on this list of SNP’s (specified by rs #):

Only return results where the significance p-value of the genotype‐methylation plot is ≤
Using HapMap sample populations:
Plots and results will be emailed to: