I study autoimmune disease. Recently, several groups have reported that T-cell enhancer regions are particularly enriched for candidate causal variants of Rheumatoid Arthritis and other autoimmune diseases.
I did covariate controlled gene burden testing on T-cell enhancer regions near to genes of interest in RA, and obtained some interesting results.
However, I want to run gene burden testing on a series of control regions.
My thought was that these control regions should be non-immune cell enhancer regions near non-immune cells, but in areas matching the loci I selected in other respects.
Does anyone have suggests on what to match for in selecting controls to see if there is inflation in test statistics?
Thank you very much!