I have been trying to use a pipeline for predicting gene expression for a target gene (Although you can do it for many) - the name of this method is epiXcan. Here is a link to the paper:
One of the very first steps in the pipeline is obtaining SNP 'annotations' from an epigenome reference consortium known as the REMC. In the methods paper they say:
"We first prepare eQTL statistics (computed with MatrixEQTL4) and SNP annotations (extracted from REMC https://egg2.wustl.edu/roadmap/web_portal/). For each eQTL tissue, we use the matched REMC tissue to extract the corresponding annotations".
I have completed the first step of obtaining eQTL statistics. However obtaining SNP annotations is where I am lost.
In my case, I am only trying to predict the expression of one gene (DRD4) and so my region of interest is the pre-frontal cortex. If you visit the website they provide though, it doesn't seem as though annotating a large list of SNPs - at least in the way they are presenting - is possible.
Can anyone provide some insight or direction on how to proceed? How does one obtain SNP annotations from the REMC? I have tried emailing the authors of the paper and they have not been responsive.