nstd163 (Gupta et al. 2020)
- Organism:
- Human
- Study Type:
- Collection
- Submitter:
- Khyati Chandratre
- Description:
- Core promoter controls transcription initiation. However, little is known for core promoter diversity in the humans and its relationship with diseases. Applying the “Exome-based Variant Detection in Core-promoters” method (Kim et al. Scientific Report 6:31716, 2016), we analyzed human core-promoter diversity using the 2,682 exome data sets of 25 worldwide human populations collected by the 1000 Genome Project, and identified 31,996 variants in the core promoters of 12,509 human genes. We observed substantial differences of variant distribution between the core promoter and the entire genome, identified the genes with highly variable core promoters and their involved functional pathways, revealed preferential localization of variation in core promoter motifs. eQTL test revealed that 12% of core promoter variants can significantly alter gene expression level. GWAS data matching identified 163 core promoter variants as the GWAS identified traits associated with multiple diseases. The data reveals the highly diversified nature of core promoter in the humans, and highlights that core promoter can play more important roles than thought in gene expression regulation and diseases. See Variant Summary counts for nstd163 in dbVar Variant Summary.
- Publication(s):
- Gupta et al. 2020