Figure 2
An example of a putative candidate cis -regulatory SNP affecting transcription in mouse F 2 population. A. cis-acting LOD scores for Casc4 on chromosome 2 in multiple tissues and sample sets (male, female or combined/all) in the BXH cross. x-axis – genomic location in Mb, y-axis – LOD score from interval mapping. Physical location of the gene is indicated with a red arrow-head. Only LODs scores >10 are shown. B. Association of expression levels of Casc4 with genotypes of the promoter SNP, mCV23866990. The distribution of the expression levels in brain (left) and adipose (right) is shown according to the genotypes of this SNP in the F2 animals. A_A represents the DBA and C3H allele, and C_C the B6 allele. C. A binding site for transcription factor Hand1 is affected by SNP mCV23866990. The polymorphism changes a highly conserved base in the binding site (T→C change on the reverse strand, boxed and shaded). The frequency matrix and a sequence logo of the profile representing the binding site are shown. D. Scatter plot of Casc4 (x-axis) versus Hand1 expression levels in the body atlas data set [49, 50]. Hand1 expression is correlated to that of Casc4 with a p-value of < 10-6 (Spearman rank order correlation -0.58).