Biomedical Data Commons (BMDC) prioritizes B-lymphocyte non-coding genetic variants in Type 1 Diabetes
Fig 5
Novel genetic variant rs14004 is a candidate for gene expression regulation of HLA-DRB1 and HLA-DQB1.
A: Visualization of the portion of the genome that interacts with HLA-DRB1 and HLA-DQB1 (chr6: 32,100,000–33,100,000). ATAC-seq and CTCF, RAD21, STAT5, and TCF3 ChIP-seq raw read visualization (top panel). Cohesin (black) and H3K27ac (blue) HiChIP raw reads virtual 4C plots centered on the Notch 3’ UTR, rs14004, HLA-DRB1 TSS, HLA-DQB1 TSS, and rs9986640 (bottom panel). B: Schematic of the chromatin connectivity between the genetic variants and the genes as represented by the raw data for chr6: 32,100,000–33,100,000. C: Major (green) and minor (blue) allele frequencies from 1000 Genome Project for rs14004 and rs9986640. D: Primary whole blood RPKM values for NOTCH4, HLA-DRB1, and HLA-DQB1 of healthy and Type 1 Diabetes patients.