SNPTracker: A Swift Tool for Comprehensive Tracking and Unifying dbSNP rs IDs and Genomic Coordinates of Massive Sequence Variants

Deng, Jiaen; Sham, Pak C.; Li, Miao-Xin

doi:10.1534/g3.115.021832

Cited by 15 publications

(13 citation statements)

References 2 publications

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“…SNP positions were back-translated from PheGenI’s GRCh38 annotation to GRCh37.p13 using SNPTracker (Deng et al, 2015), and the resulting catalog of SNP-trait associations included 14,321 significant associations (lead GWAS SNPs; defined as P < 5 × 10 −8 ) and 846 distinct phenotypes/traits.…”

Section: Methods Detailsmentioning

confidence: 99%

“…To define the collection of SNPs from GWAS studies, we downloaded the dataset of the Phenotype-Genotype Integrator (PheGenI) (Ramos et al, 2014), which merges NHGRI GWAS Catalog data with several databases of the National Center for Biotechnology Information (NCBI), including Gene, dbGaP, OMIM, eQTL and dbSNP (September 2017; https://www.ncbi.nlm.nih.gov/gap/phegeni). SNP positions were back-translated from PheGenI’s GRCh38 annotation to GRCh37.p13 using SNPTracker (Deng et al, 2015), and the resulting catalog of SNP-trait associations included 14,321 significant associations (lead GWAS SNPs; defined as P < 5 × 10 −8 ) and 846 distinct phenotypes/traits.…”

Section: Methods Detailsmentioning

confidence: 99%

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Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression

Schmiedel

Singh

Madrigal

et al. 2018

Cell

682

699

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SUMMARY While many genetic variants have been associated with risk for human diseases, how these variants affect gene expression in various cell types remains largely unknown. To address this gap, the DICE (Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics) project was established. Considering all human immune cell types and conditions studied, we identified cis-eQTLs for a total of 12,254 unique genes, which represent 61% of all protein-coding genes expressed in these cell types. Strikingly, a large fraction (41%) of these genes showed a strong cis-association with genotype only in a single cell type. We also found that biological sex is associated with major differences in immune cell gene expression in a highly cell-specific manner. These datasets will help reveal the effects of disease risk-associated genetic polymorphisms on specific immune cell types, providing mechanistic insights into how they might influence pathogenesis (http://dice-database.org).

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Section: Methods Detailsmentioning

confidence: 99%

Section: Methods Detailsmentioning

confidence: 99%

Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression

Schmiedel

Singh

Madrigal

et al. 2018

Cell

682

699

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“…However, the mechanism of regulation of Notch by Su(dx)/Itch remains unclear, they may function on internalization of membrane bound Notch, generation of NICD, and/or free cytoplasmic NICD (Qiu et al, 2000; McGill and McGlade, 2003). First identified in Caenorhabditis elegans , the Sel-10 gene encodes an F-box containing E3 ligase that targets NICD for ubiquitination and proteasomal degradation (Hubbard et al, 1997; Deng and Greenwald, 2016). The mammalian homolog of Sel-10, FBXW7, binds to NICD to promote its ubiquitination and subsequent rapid degradation (Gupta-Rossi et al, 2001; Öberg et al, 2001; Wu et al, 2001).…”

Section: Discussionmentioning

confidence: 99%

The ATPase TER94 regulates Notch signaling duringDrosophilawing development

Liu

Zhang

2018

Biology Open

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The evolutionarily conserved Notch signaling pathway plays crucial roles in various developmental contexts. Multiple mechanisms are involved in the regulation of Notch pathway activity. Identified through a genetic mosaic screen, we show that the ATPase TER94 acts as a positive regulator of Notch signaling during Drosophila wing development. Depletion of TER94 causes marginal notches in the adult wing and the reduction of Notch target genes wingless and cut during wing margin formation. We provide evidence that TER94 is likely required for proper Notch protein localization and activation. Furthermore, we show that knockdown of the TER94 adaptor p47 leads to similar Notch signaling defects. Although the TER94 complex is implicated in various cellular processes, its role in the regulation of Notch pathways was previously uncharacterized. Our study demonstrates that TER94 positively regulates Notch signaling and thus reveals a novel role of TER94 in development.

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“…GWAS4D accepts multiple variant description formats including VCF-like, dbSNP ID and coordinate-only. Variants not using the VCF-like format will be automatically lifted to dbSNP150 and assigned respective reference/1 st alternative alleles using SNPTracker ( 52 ). The web server will discard the variants not mapped onto dbSNP150 or 1000 Genomes Project unless the VCF-like format is used.…”

Section: Methods and Pipelinementioning

confidence: 99%

GWAS4D: multidimensional analysis of context-specific regulatory variant for human complex diseases and traits

Huang

Zhang

et al. 2018

Nucleic Acids Research

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Genome-wide association studies have generated over thousands of susceptibility loci for many human complex traits, and yet for most of these associations the true causal variants remain unknown. Tissue/cell type-specific prediction and prioritization of non-coding regulatory variants will facilitate the identification of causal variants and underlying pathogenic mechanisms for particular complex diseases and traits. By leveraging recent large-scale functional genomics/epigenomics data, we develop an intuitive web server, GWAS4D (http://mulinlab.tmu.edu.cn/gwas4d or http://mulinlab.org/gwas4d), that systematically evaluates GWAS signals and identifies context-specific regulatory variants. The updated web server includes six major features: (i) updates the regulatory variant prioritization method with our new algorithm; (ii) incorporates 127 tissue/cell type-specific epigenomes data; (iii) integrates motifs of 1480 transcriptional regulators from 13 public resources; (iv) uniformly processes Hi-C data and generates significant interactions at 5 kb resolution across 60 tissues/cell types; (v) adds comprehensive non-coding variant functional annotations; (vi) equips a highly interactive visualization function for SNP-target interaction. Using a GWAS fine-mapped set for 161 coronary artery disease risk loci, we demonstrate that GWAS4D is able to efficiently prioritize disease-causal regulatory variants.

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SNPTracker: A Swift Tool for Comprehensive Tracking and Unifying dbSNP rs IDs and Genomic Coordinates of Massive Sequence Variants

Cited by 15 publications

References 2 publications

Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression

Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression

The ATPase TER94 regulates Notch signaling duringDrosophilawing development

GWAS4D: multidimensional analysis of context-specific regulatory variant for human complex diseases and traits

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