Chunk #25 — Transcriptional effects of enhancer variants

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Enhancer variants: evaluating functions in common disease.

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binding motif disruptionQT intervalKapoor et al. [32]rs12143842rs7539120 NOS1AP eQTL gene, genetic associationCardiac tissuesAllele-specific luciferase activity, eQTL, enhancer assay (zebrafish embryos)Restless leg syndromeSpieler et al. [37]rs12469063rs13469063 MEIS1 PreSTIGE prediction method, ChIA-PET, Hi-CTelencephalonAllele-specific expression of reporter gene in zebrafish, Allele-specific LacZ (mouse), EMSA, binding motif disruption, effect of decreased gene expression on phenotypeSystemic lupus erythematosusWang et al. [40]rs2230926rs148314165, rs200820567 TNFAIP3 3CLCLsEMSA, allele-specific luciferase activity, allele-specific 3CType 2 diabetesGaulton et al. [76]rs7903146rs7903146 TCF7L2 Nearest genePancreatic islet cellsAllele-specific luciferase activity, allele-specific FAIRE3C, chromosome conformation capture; 4C-seq, circular chromosome conformation capture followed by sequencing; ChIA-PET, chromatin interaction analysis by paired-end tag sequencing; ChIP, chromatin immunoprecipitation; EMSA, electrophoretic mobility shift assay; eQTL, expression quantitative trait loci; FAIRE, formaldehyde-assisted isolation of regulatory elements; FISH, fluorescence in situ hybridization; LCLs, lymphoblastoid cell lines; NA, not applicable; SNP, single nucleotide polymorphism.