Hi,

I am almost sure at least few of you have solved this problem or have some ideas on how to proceed.

I have two sets of data, one set is SNP calls and the other one is DNA methylation calls. I want to identify the SNPs that may have direct impact on DNA methylation and on gene expression (also available). I am kind of lost, may be I should first take the SNPs that are present within the DNAmethylation regions and look at gene expression or see if the site is hypo or hyper methylated.

Unfortunately, I am unable to see a concrete way forward. Could anyone of you who has dealt with such a problem in the past, be kind enough to shed some light and guide.

Thank you