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. 2015 Apr;33(4):345-6.
doi: 10.1038/nbt.3158.

Epigenomic annotation of genetic variants using the Roadmap Epigenome Browser

Xin Zhou, Daofeng Li, Bo Zhang, Rebecca F Lowdon, Nicole B Rockweiler, Renee L Sears, Pamela A F Madden, Ivan Smirnov, Joseph F Costello, Ting Wang

Epigenomic annotation of genetic variants using the Roadmap Epigenome Browser

Xin Zhou et al. Nat Biotechnol. 2015 Apr.
No abstract available

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Figures

Figure 1
Figure 1
Multiple sclerosis-associated GWAS SNPs are annotated using epigenomic and expression data from 31 primary human tissues (orange) and cells (light green). H3K4me1 ChIP-seq read density (in green) is shown for a 6-kb region centered on each SNP. RNA-seq read density (in blue) is shown over the 5’ end of genes that are closest to these SNPs. Hierarchical clustering is applied to both H3K4me1 and RNA-seq data. The region associated with rs756699 has H3K4me1 mostly confined to immune-related cell types (solid black box). The closest gene TCF7 (3.8 kb downstream) also shows strong expression in the same group of cell types (solid blue box, Supplementary Fig. 9). The region surrounding rs307896 has H3K4me1 signal in all tissues/cell types (dashed black box). rs307896 lies in an intron of SAE1, a gene which is also expressed in all the samples (dashed blue box). Normalized gene expression values (RPKM) for TCF7 and SAE1 are included in Supplementary Fig. 5.
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