GLGC HDL cholesterol predicted effector genes

View predictions from the Global Lipids Genetics Consortium for:

• HDL cholesterol

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

View predictions for:

• Multiple metabolite levels

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In this unpublished work from Eric Fauman, putative causal genes at GWAS significant loci for metabolite levels or metabolite ratios were identified based on experimental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Fauman E. Unpublished, 2022.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

View predictions from the Global Lipids Genetics Consortium for:

• Log-triglyceride levels

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

View predictions for:

• 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

View predictions for:

• 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

View predictions for:

• 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

View predictions for:

• 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

View predictions for:

• 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

View predictions for:

• 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

View predictions for:

• 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.