Figure 5
From: DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines
C21orf56 gene region. (a), (b), (c) Genotype at rs8133082 is associated with methylation (cg07747299) and gene expression at C21orf56, plotted per individual colored according to genotype at rs8133082 (GG = black, GT = green, TT = red) for directly genotyped (circles) and imputed (triangles) data. (d) Gene expression levels at C21orf56 after regressing out methylation. (e) Gene expression at C21orf56 (+/-2 kb) genomic region on chromosome 21. Distance is measured on the reverse strand relative to C21orf56 TSS at 46,428,697 bp. Barplots show average gene expression reads per million in the subsets of individuals from each of the three rs8133082-genotype classes. Middle panel shows histone-modification peaks in the region from Encode LCL GM12878. Bottom panel shows the gene-structure of C21orf56, where exons are in bold and the gene is expressed from the reverse strand. Green points indicate the location of four HapMap SNPs (rs8133205, rs6518275, rs8133082, and rs8134519) associated at FDR of 10% with both methylation and gene expression, and Figure S11 in Additional file 1 shows association results for this region with SNPs from the 1,000 Genomes Project. (f) Bisulphite-sequencing results for eight rs8133082-homozygote individuals (4 GG black, 4 TT red) validates the genome-wide methylation assay at cg07747299 and shows the extent of methylation in the surrounding 411 bp region.