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. Author manuscript; available in PMC: 2014 Nov 7.
Published in final edited form as: Cell. 2013 Oct 10;155(4):10.1016/j.cell.2013.09.053. doi: 10.1016/j.cell.2013.09.053

Figure 5. Examples of disease-associated SNPs in super-enhancers.

Figure 5

A) (top left) Radar plots showing the density of non-coding SNPs linked to Alzheimer’s disease (AD) in the super-enhancer domains and typical enhancers identified in 12 human cell and tissue types. The center of the plot is 0, and a colored dot on the respective axis indicates the SNP density (SNP/10MB sequence) in the super-enhancer domains or typical enhancers of each cell and tissue type. Lines connecting the density values to the origin of the plot are added to improve visualization. (top right) Distribution of non-coding SNPs linked to AD in the typical enhancers and super-enhancers of brain tissue. (bottom left) List of genes associated with AD SNP-containing super-enhancers in brain tissue. (bottom right) ChIP-Seq binding profile for H3K27ac at the BIN1 locus in brain tissue. The positions of AD-SNPs are highlighted as red bars, and the super-enhancers are highlighted as black bars above the binding profile. Indel rs59335482 (a three base pair insertion) is also highlighted. (rpm/bp: reads per million per base pair)

B) (top left) Radar plots showing the density of non-coding SNPs linked to type 1 diabetes (T1D) in the super-enhancer domains and typical enhancers identified in 12 human cell and tissue types. The center of the plot is 0, and a colored dot on the respective axis indicates the SNP density (SNP/10MB sequence) in the super-enhancer domains or typical enhancers of each cell and tissue type. Lines connecting the density values to the origin of the plot are added to improve visualization. (top right) Distribution of non-coding SNPs linked to T1D in the typical enhancers and super-enhancers of Th cells. (bottom left) List of genes associated with T1D SNP-containing super-enhancers in Th cells. (bottom right) ChIP-Seq binding profile for H3K27ac at the IL2RA locus in Th cells. The positions of T1D SNPs are highlighted as red bars, and the super-enhancers are highlighted as black bars above the binding profile.

C) (top left) Radar plots showing the density of non-coding SNPs linked to systemic lupus erythematosus (SLE) in the super-enhancer domains and typical enhancers identified in 12 human cell and tissue types. The center of the plot is 0, and a colored dot on the respective axis indicates the SNP density (SNP/10MB sequence) in the super-enhancer domains or typical enhancers of each cell and tissue type. Lines connecting the density values to the origin of the plot are added to improve visualization. (top right) Distribution of non-coding SNPs linked to SLE in the typical enhancers and super-enhancers of B cells. (bottom left) List of genes associated with SLE SNP-containing super-enhancers in B cells. (bottom right) ChIP-Seq binding profile for H3K27ac at the HLA-DRB1 and HLA-DQA1 loci in B cells. The positions of SLE SNPs are highlighted as red bars, and the super-enhancers are highlighted as black bars above the binding profile.

See also Figure S5.