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. 2017 Dec 8;5(1):e414. doi: 10.1212/NXI.0000000000000414

Figure 1. SNAP plot of the chromatin state overlapping the SNPs in LD with the AHI1 cis-eQTL and MS susceptibility variant, rs4896153 in CD4+ T cells.

Figure 1

(A) Naive (CD4+CD25−CDRA+) and memory (CD4+CD25−CDRA−) CD4+ T cell–specific chromatin state mapping was generated using the chromHMM algorithm in 1-Mb and 100-kb views surrounding the AHI1 locus. ChIP-seq data generated by the ENCODE/ROADMAP project reveal various chromatin marks including enhancers, heterochromatin, and polycomb, and various transcription marks are color coded. All the discovered SNPs from dbGAP137 are listed including their p value of association to MS, the recombination rate. The LD structure is represented in the r-square value calculated from the Broad SNAP server and is assigned in red. The strongest MS-associated variant rs4896153 (green) and the strongest eQTL variant rs6908428 are labeled. (B) Zoom in of the region overlapping the rs13197384 showing the chromatin state in naive and memory T cells. eQTL = expression quantitative trait locus; LD = linkage disequilibrium; TSS = transcription start site.