Figure 4

Cis , but not local -eQTLs correlate to polymorphisms in regions hypersensitive to DNase I. ENCODE DNase I hypersensitivity data for mouse gonadal fat was obtained from UCSC genome browser. Conserved peaks were defined as overlapping peaks in the two replicates, and only these were used for the analysis. Genes were divided into three groups – eQTLs overexpressing the B allele (labeled B), eQTLs overexpressing the D allele in F1 study or the non B allele in the HMDP study, and genes that had no significant eQTL in the study (labeled NS). Intact peaks were defined as DNase I peaks that do not carry a polymorphism (SNP or indel) between B and D strains. For each gene we counted 1) total number of peaks 2) total number of intact peaks that overlap with the gene 3) sum of DNase I signal that comes from all peaks overlapping the gene and 4) sum of DNase I signal that comes only from intact peaks overlapping the gene. A and C show proportions of number of intact peaks per gene in F1 and HMDP data respectively. B and D show the average amount of DNase I signal obtained from those intact peaks. E and F illustrate cis-eQTLs that either overexpress the D allele (E, Usp38) or the B allele (F, Tmem159). Gene structure is shown in blue, conserved DNase I hypersensitive peaks are shown in red. Dots indicate SNPs that either overlap a conserved DNase I peak (cyan) or were used to produce allele specific counts (yellow). Original DNase I signal of replicates 1 and 2 is shown in black and grey, respectively. Allele specific counts for D and B are shown in brown and black on the top.