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. 2012 Dec 5;41(2):827–841. doi: 10.1093/nar/gks1284

Figure 3.

Figure 3.

(A) Enrichment or depletion of GWAS SNPs (and several comparison SNP sets) in function-associated segments. The bars extend to the level of enrichment or depletion of each SNP set in the 25 segmentation classes from Segway (top) and ChromHMM (bottom) in GM12878. The results for 1000 random samplings of the SNPs matched to the phenotype-associated SNPs are displayed as a box plot, with the box extending from the 25th to the 75th percentiles, the whiskers extending to 1.5 times the interquartile range, and any outliers beyond shown as circles. If the enrichment for the phenotype associated, GWAS lead SNPs exceeded the 95th percentile of the results from the matched SNPs, then the bar is colored red (orange if otherwise). (B) An example of Crohn’s disease SNPs in non-coding sequences that could serve to regulate expression of NOD2. The figures show gene models from the GENCODE group (version 12), locations of SNPs associated with Crohn’s disease by GWAS, results of ChromHMM and Segway segmentations, selected histone modifications measured in GM12878 and HUVEC cells, locations of DNase hypersensitive sites in several cell types, and sites of occupancy by selected transcription factors. Regions discussed in the text are outlined by blue rectangles.