ArticleScientific reports2015
Re-annotation of presumed noncoding disease/trait-associated genetic variants by integrative analyses.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
8 citing papers in PubMed, 15 citations in OpenAlex.
- Comprehensive functional annotation of susceptibility variants associated with asthma.Human genetics · 2020Article
- An integrated transcriptional analysis of the developing human retina.Development (Cambridge, England) · 2019Article
- Mining the Unknown: Assigning Function to Noncoding Single Nucleotide Polymorphisms.Trends in genetics : TIG · 2017Review
- Expression profiling and functional annotation of noncoding genes across 11 distinct organs in rat development.Scientific reports · 2016Article
- An atlas of gene expression and gene co-regulation in the human retina.Nucleic acids research · 2016Article
- Identification of Tissue-Specific Protein-Coding and Noncoding Transcripts across 14 Human Tissues Using RNA-seq.Scientific reports · 2016Article
- Challenges, Solutions, and Quality Metrics of Personal Genome Assembly in Advancing Precision Medicine.Pharmaceutics · 2016Review
- Genome-wide DNA methylation profiling with MeDIP-seq using archived dried blood spots.Clinical epigenetics · 2016Article
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 2 countries.
Funding
Abstract
Using RefSeq annotations, most disease/trait-associated genetic variants identified by genome-wide association studies (GWAS) appear to be located within intronic or intergenic regions, which makes it difficult to interpret their functions. We reassessed GWAS-Associated single-nucleotide polymorphisms (herein termed as GASs) for their potential functionalities using integrative approaches. 8834 of 9184 RefSeq "noncoding" GASs were reassessed to have potential regulatory functionalities. As examples, 3 variants (rs3130320, rs3806932 and rs6890853) were shown to have regulatory properties in HepG2, A549 and 293T cells. Except rs3130320 as a known expression quantitative trait loci (eQTL), rs3806932 and rs6890853 were not reported as eQTLs in previous reports. 1999 of 9184 "noncoding" GASs were re-annotated to the promoters or intragenic regions using Ensembl, UCSC and AceView gene annotations but they were not annotated into corresponding regions in RefSeq database. Moreover, these GAS-harboring genes were broadly expressed across different tissues and a portion of them was expressed in a tissue-specific manner, suggesting that they could be functional. Collectively, our study demonstrates the benefits of using integrative analyses to interpret genetic variants and may help to predict or explain disease susceptibility more accurately and comprehensively.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.