I am currently running into a problem because I have insufficient amount of the data I need.
I have 81 sets of SNPs and I looked up if those SNPs fall into H3K27ac signal sites.
I am focusing on roadmap data of histone modification (section d (signal tracks), consolidated data, fold-enrichment) of the following cell types: Primary T helper cells PMA-I stimulated (E041-H3K27ac), Primary T helper naive cells from peripheral blood(E039-H3K27ac), Primary T helper 17 cells PMA-I stimulated (E042-H3K27ac).
(I was also wondering where from Fahr et al have RNA-seq data for Tnaive, Th stim and Th17)
My idea is to co-localize my SNPs not only with the histone mark sites but also with DNAse hypersensitivity and TFBS measured with CHiP-seq.
Unfortunately roadmap does not have DNase data of the the cells I mentioned, neither do they have a CHiP-seq.
My questions are: do I really need DNAse and CHiP-seq data of the cells above?
For DNAse I guess I need exactly the data from the cells I look at.
But can I use any CHIP-seq experiment as my goal is only to co-localize my SNPs with TFBS? Or is there any tool that can predict a TFBS from a given DNA sequence?