Fig. 5

rs1476679 spatially contacts many eQTL genes via CTCF-mediated chromatin loops and affects their expression levels. a Chromatin interactions of the rs1476679 locus as determined by TCC experiments. Red and blue lines represent significant chromatin interactions from rs1476679 in SK-N-SH and U-251 MG cells, respectively. b Zoom-in region of the rs1476679 locus. The upper panel indicates chromatin interactions of the s1476679 locus. The orange and green bands indicate gene bodies on the positive and negative strands, respectively. Gene symbols in red indicate the eQTL genes of rs1476679. Asterisks indicate chromatin interactions of the rs1476679 locus with the GATS, PILRB, and PILRA genes. In the bottom panel, the color plot indicates the peak scores from ChIP-seq data for CTCF or RNA polymerase II (RNAPII) and DNase-seq data showing DNase I-hypersensitive sites (DHSs). Each row in the colored plot represents different brain tissues or neuronal cell lines (18 experiments (rows) including nine tissues or cell lines based on CTCF ChIP-seq, 21 experiments including 10 cell lines based on RNAPII ChIP-seq, and 82 experiments including 31 cell lines based on DNase-seq; Additional file 1: Table S11). c GATS, PILRB, and PILRA expression levels in the hippocampus and entorhinal cortex from GSE5281. Boxes represent the interquartile range between the first and third quartiles and median (internal line). Whiskers denote the lowest and highest values within 1.5 times the range of the 1 first and third quartiles, respectively; dotsrepresent GATS, PILRB, and PILRA expression levels in each sample