Results: 3

1.
FIGURE 3.

FIGURE 3. From: Genome-wide Epigenetic Data Facilitate Understanding of Disease Susceptibility Association Studies.

GWAS variants associated with Crohn disease and other autoimmune diseases found in potential regulatory regions marked by epigenetic features. A, fine mapping of genetic variants in a 2-Mb interval on human chromosome 5 (chr5). The red vertical lines demarcate a LD block. This figure was reprinted with permission from the supplement to Ref. . B, current view of genomic data for the same interval as in A, showing from top to bottom genetic variants from the GWAS Catalog, followed by signal tracks for GATA2 occupancy in HUVECs and DHSs in HUVECs and T-helper 1 (Th1) and T-helper 2 (Ths) cells, with gene annotation at the bottom. The signal tracks are from the ENCODE Consortium (, ). C, view focused on a 50-kb region containing a cluster of variants associated with autoimmune diseases. The different disease associations are marked by the color of the circle at the top of the vertical green lines. This figure was reprinted with permission from Ref. .

Ross C. Hardison. J Biol Chem. 2012 September 7;287(37):30932-30940.
2.
FIGURE 2.

FIGURE 2. From: Genome-wide Epigenetic Data Facilitate Understanding of Disease Susceptibility Association Studies.

GWAS variants associated with high levels of fetal hemoglobin in adults found in an enhancer marked by epigenetic features. A, fine mapping of genetic variants between the genes HBS1L and MYB on human chromosome 6 (chr6), with the position of SNPs along the x axis (assembly GRCh37/hg19) and the logarithm (base 10) of the 1/p value for the association with the trait on the y axis. This figure was adapted with permission from Fig. 4 in Ref. . B, current view of genomic data for the same 148-kb interval as in A, showing from top to bottom the position of the 3-bp deletion implicated in the trait (HMIPdel); genetic variants from the GWAS Catalog (vertical green lines); gene annotation; and signal tracks for DHSs in K562 cells, GATA1 occupancy in peripheral blood-derived erythroblasts, TAL1 occupancy in K562 cells, and GATA2 occupancy in K562 cells. The signal tracks are from the ENCODE Consortium (, , ). C, view focused on a 3-kb region containing the 3-bp deletion implicated in the trait and an enhancer bound by GATA factors and TAL1. PBDE, peripheral blood derived erythroblasts.

Ross C. Hardison. J Biol Chem. 2012 September 7;287(37):30932-30940.
3.
FIGURE 1.

FIGURE 1. From: Genome-wide Epigenetic Data Facilitate Understanding of Disease Susceptibility Association Studies.

Epigenetic data link GWAS results to hypotheses about how specific SNPs affect a phenotype. A, in a GWAS, individuals are grouped into cases or controls, denoted by different colors for stick figures. DNA samples from each person are genotyped at a large number of polymorphic sites, illustrated as panels of gray or colored circles. SNPs for which the frequency of one allele is significantly different between the groups (e.g. the yellow allele at one SNP is more frequent in cases, whereas red is more frequent in controls) are identified, and those passing stringent filters and replication are analyzed further as lead SNPs. B, epigenetic features in chromosomal regions containing the lead SNP and linked SNPs are examined for evidence of CRMs. In this illustration, a SNP in LD with the lead SNP is in chromatin that is hypersensitive to DNase, monomethylated at histone H3 lysine 4, and bound by a transcription factor (TF). C, combining the genetic and epigenetic information leads to testable hypotheses such as allele-specific binding by a transcription factor causes differential expression of a target gene.

Ross C. Hardison. J Biol Chem. 2012 September 7;287(37):30932-30940.

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