SNPs in DNase hypersensitive and histone marks sites

Question

[tonja.r]

I am investigating a role of SNPs in DNase hypersensitive sites and in the DNA regions of histone marks and have some questions about it.

SNPs in DNase hypersensitive sites might mean that those SNPs are in enhancer regions and might influence TF binding affinity what can influence a transcriptional output. Is it correct?

SNPs in histone marks sites I have the number of SNPs that fall in the peaks (chip-seq) for the following histone modifications of healthy patients: H3K27ac,H3K4me1,H3K4me3 (represent the active chromosome) H3K27me3, H3K9me3 (represent the repressed chromosome)

Histone modifications represent if the chromosome is active or repressed. A SNP might change the binding affinity of a histone. It means that if I have a SNP in data for active chromosome (H3K27ac,H3K4me1,H3K4me3), it might change the status of a chromosome, namely turn it into a repressed one or it might induce a histone not to bind at all(it means that this region is still active,no?) Is it right? I am not sure I understand the possible influences of a SNP histone marks sites.

[PoGibas]

Tonja, yes, everything is possible, but you have to check what was done before:

• Encode did a lot analysis on variation in regulatory sites.