We identified a CNV (CNVR2845.27 at chrom6:32710664–32743652) in perfect LD with the replicated type 1 diabetes SNP rs9272346 predicting the expression of at least 20 transcripts, mostly in the HLA region; a CNV (CNVR2845.40 at chrom6:32735154–32737954) is tagged (r2 = 0.95) by the same type 1 diabetes SNP. A tCNV CNVR2845.46 is also in strong LD (r2 = 0.93) with a replicated multiple sclerosis SNP rs3135388 and predicts the expression of 20 transcripts (of which the largest expression association p value is ∼10−33).
