RT Journal Article
SR Electronic
T1 Systematic identification of human SNPs affecting regulatory element activity
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 460402
DO 10.1101/460402
A1 Joris van Arensbergen
A1 Ludo Pagie
A1 Vincent FitzPatrick
A1 Marcel de Haas
A1 Marijke Baltissen
A1 Federico Comoglio
A1 Robin van der Weide
A1 Hans Teunissen
A1 Urmo Võsa
A1 Lude Franke
A1 Elzo de Wit
A1 Michiel Vermeulen
A1 Harmen Bussemaker
A1 Bas van Steensel
YR 2018
UL http://biorxiv.org/content/early/2018/11/04/460402.abstract
AB 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. 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 pinpoint SNPs that underlie human traits.