Studies of liver tissue identifies functional gene regulatory elements associated to gene expression, type 2 diabetes and other metabolic diseases

Genome wide association studies (GWAS) of diseases and traits have found associations to gene regions but not the functional SNP or the gene mediating the effect. Difference in gene regulatory signals can be detected using chromatin immunoprecipitation and next gen sequencing (ChIP-seq) of transcription factors or histone modifications by aligning reads to known polymorphisms in individual genomes. The aim was to identify such regulatory elements in human liver to understand the genetics behind type 2 diabetes and metabolic diseases.The genome of liver tissue was sequenced using 10x genomics technology to call polymorphic positions. Using ChIP-seq for two histone modifications: H3K4me3, H3K27ac and the transcription factor CTCF, and our established bioinformatics pipeline we detected sites with significant difference in signal between the alleles.