GLGC HDL cholesterol predicted effector genes
GLGC HDL cholesterol predicted effector genes
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Method
The PoPS and DEPICT genome-wide methods and four locus-specific methods were used to predict the effector gene(s) at each locus.
Metabolite level predicted effector genes
Metabolite level predicted effector genes
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Method
In this unpublished work from Eric Fauman, putative causal genes at GWAS significant loci for metabolite levels or metabolite ratios were identified based on experimental characterizations in the biomedical literature.
Reference:
Fauman E. Unpublished, 2022.
GLGC log-triglyceride predicted effector genes
GLGC log-triglyceride predicted effector genes
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Method
The PoPS and DEPICT genome-wide methods and four locus-specific methods were used to predict the effector gene(s) at each locus.
Insomnia predicted effector genes
Insomnia predicted effector genes
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Method:
Potential effector genes for insomnia were prioritized based on coding variant evidence, colocalization of eQTLs and GWAS signals, and protein-protein interactions.
Systolic blood pressure (SBP) predicted effector genes
Systolic blood pressure (SBP) predicted effector genes
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Method:
This prioritization of potential systolic blood pressure (SBP) effectors was based on colocalization of genetic association signals for SBP with cell fraction adjusted kidney eQTLs.
Kidney function predicted effector genes
Kidney function predicted effector genes
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Method:
This prioritization of potential kidney function effectors was based on colocalization of genetic association signals for six kidney function traits with cell fraction adjusted kidney eQTLs.
Atrial fibrillation predicted effector genes
Atrial fibrillation predicted effector genes
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Method:
Potential effector genes for atrial fibrillation were prioritized at GWAS loci using six types of evidence, including eQTLs, gene set enrichment analysis, and MetaXcan analysis.
Ascending aorta function predicted effector genes
Ascending aorta function predicted effector genes
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Method:
Genes were prioritized at loci genetically associated with three aortic properties, based on three evidence types: results from DEPICT (Data-driven Expression Prioritized Integration for Complex Traits); presence of a coding variant in high LD with the lead SNP; and proximity of a gene to the lea
COVID-19 susceptibility and severity predicted effector genes
COVID-19 susceptibility and severity predicted effector genes
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Method:
This study applied the COGS (Capture Hi-C Omnibus Gene Score) pipeline to promoter capture Hi-C data (PCHi-C) data, along with genetic associations from four different analyses performed by the COVID-19 Host Genetics
Systemic lupus erythematosus (SLE) predicted effector genes
Systemic lupus erythematosus (SLE) predicted effector genes
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Method:
This study generated effector gene predictions for SLE using genome-wide association results and promoter-focused Capture-C analysis in follicular helper T-cells from human tonsil to link genetically associated variants to the genes they may regulate.