Insomnia predicted effector genes

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• Insomnia

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

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• Systolic blood pressure

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

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• Kidney function

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

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• Atrial fibrillation

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

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• Ascending aorta function

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

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• COVID-19 susceptibility and severity

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

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• Systemic lupus erythematosus (SLE)

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.

Estimated glomerular filtration rate (eGFRcrea) predicted effector genes

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• Estimated glomerular filtration rate (serum creatinine)

Method

This study integrated results from 8 methods to prioritize putative kidney function effector genes at loci genetically associated with eGFRcrea.

Cardiometabolic trait predicted effector genes

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• Cardiometabolic traits

Method

Candidate causal genes for cardiometabolic traits were predicted by integration of genetic association results, expression and splicing quantitative trait loci (eQTLs and sQTLs), transcriptional regulation by physiological and pharmacological cardiometabolic regulators, and protein-protein interaction

Type 1 diabetes predicted effector genes

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• Type 1 diabetes

Method

These predictions synthesize genetic, perturbational, and regulatory evidence to categorize potential T1D effector genes by the strength of their supporting evidence.

Reference:

Onengut-Gumuscu S and Rich SS. Unpublished, 2022.