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Systematic identification of human SNPs affecting regulatory element activity

ABSTRACT: Systematic identification of human SNPs affecting regulatory element activity

PROVIDER: PRJNA527132 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8730420_1.fastq.gz	Fastqsanger.gz
	SRR8730420_2.fastq.gz	Fastqsanger.gz
	SRR8730430_1.fastq.gz	Fastqsanger.gz
	SRR8730430_2.fastq.gz	Fastqsanger.gz
	SRR8730440_1.fastq.gz	Fastqsanger.gz

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Systematic identification of human SNPs affecting regulatory element activity

Project description:Most of the millions of single-nucleotide polymorphisms (SNPs) in the human genome are non-coding, and many overlap with putative regulatory elements. Genome-wide association studies have linked many of these SNPs to human traits or to gene expression levels, but rarely with sufficient resolution to identify the causal SNPs. Functional screens based on reporter assays have previously been of insufficient throughput to test the vast space of SNPs for possible effects on enhancer and promoter activity. Here, we have leveraged the throughput of the SuRE reporter technology to survey a total of 5.9 million SNPs, including 57% of the known common SNPs world-wide. We identified more than 30 thousand SNPs that alter the activity of putative regulatory elements, often in a cell-type specific manner. These data indicate that a large proportion of human non-coding SNPs may affect gene regulation. Integration of these SuRE data with genome-wide association studies may help to identify causal SNPs.

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High-throughput identification of human SNPs affecting regulatory element activity.

Project description:Most of the millions of SNPs in the human genome are non-coding, and many overlap with putative regulatory elements. Genome-wide association studies (GWAS) have linked many of these SNPs to human traits or to gene expression levels, but rarely with sufficient resolution to identify the causal SNPs. Functional screens based on reporter assays have previously been of insufficient throughput to test the vast space of SNPs for possible effects on regulatory element activity. Here we leveraged the throughput and resolution of the survey of regulatory elements (SuRE) reporter technology to survey the effect of 5.9 million SNPs, including 57% of the known common SNPs, on enhancer and promoter activity. We identified more than 30,000 SNPs that alter the activity of putative regulatory elements, partially in a cell-type-specific manner. Integration of this dataset with GWAS results may help to pinpoint SNPs that underlie human traits.

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