Epigenomic annotation of genetic variants using the Roadmap Epigenome Browser.

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.

LLM interpretation

This figure presents a genomic track visualization comparing H3K4me1 ChIP-seq (green) and RNA-seq (blue) read densities across 31 human tissues and cells, organized by hierarchical clustering. For SNP rs756699, H3K4me1 signal and expression of the nearby gene *TCF7* are concentrated in immune-related cell types (solid boxes). In contrast, SNP rs307896 and the gene *SAE1* exhibit H3K4me1 signal and expression across nearly all sampled tissues and cells (dashed boxes).