Genomic Context

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Gene-based Trait Associations

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ADSP WES: Alzheimer's Disease ADSP

Results from gene-level rare and functional variant aggregation tests for association to AD supported by significane of p < 0.5 / #genes.

Individual score test statistics for rare, predicted functional, and loss of function variants colocated with the gene were aggregated to compute gene level p-values.

See NIAGADS Accession NG00065 for more information.

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Accession Population N SNPs p-value Sign. Level rho CMAF CMAC Covariates Variant Filter Caveats
NG00065 European 2 0.159 N/A 0 1.4e-04 3.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP HIGH
NG00065 European 2 0.159 N/A 0 1.4e-04 3.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) LOF
NG00065 European 2 0.168 N/A 0 1.4e-04 3.0 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes VEP HIGH
NG00065 European 2 0.168 N/A 0 1.4e-04 3.0 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes LOF
NG00065 Meta 3 0.177 N/A 0 1.9e-04 4.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP HIGH
NG00065 Meta 3 0.188 N/A 0 1.9e-04 4.0 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes VEP HIGH
NG00065 European 2 0.239 N/A 0 1.4e-04 3.0 PCs and sequencing center VEP HIGH
NG00065 European 2 0.239 N/A 0 1.4e-04 3.0 PCs and sequencing center LOF
NG00065 European 23 0.261 N/A 1 0.011 230.2 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 Meta 3 0.264 N/A 0 1.9e-04 4.0 PCs and sequencing center VEP HIGH
NG00065 Meta 27 0.315 N/A 0 0.012 267.8 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 Caribbean Hispanic 6 0.328 N/A 1 0.048 37.6 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 Caribbean Hispanic 6 0.332 N/A 1 0.048 37.6 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 Caribbean Hispanic 6 0.369 N/A 1 0.048 37.6 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes VEP MOD-HIGH N/A
NG00065 European 23 0.587 N/A 0 0.011 230.2 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes VEP MOD-HIGH N/A
NG00065 Meta 27 0.645 N/A 0 0.012 267.8 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes VEP MOD-HIGH N/A
NG00065 European 23 0.671 N/A 0 0.011 230.2 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 Meta 27 0.692 N/A 0 0.012 267.8 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 Caribbean Hispanic 1 0.797 N/A 0 1.3e-03 1.0 PCs and sequencing center VEP HIGH
NG00065 Caribbean Hispanic 1 0.797 N/A 0 1.3e-03 1.0 PCs and sequencing center LOF
NG00065 Caribbean Hispanic 1 0.800 N/A 0 1.3e-03 1.0 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes LOF
NG00065 Caribbean Hispanic 1 0.800 N/A 0 1.3e-03 1.0 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes VEP HIGH
NG00065 Caribbean Hispanic 1 0.805 N/A 0 1.3e-03 1.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP HIGH
NG00065 Caribbean Hispanic 1 0.805 N/A 0 1.3e-03 1.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) LOF

Genetic Variation and Variant-based Trait Associations (GWAS)

Variants contained within the AGFG2 gene.

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The AGFG2 gene contains 1,752 variants records (corresponding to 1,686 unique genomic positions).

The following variants, contained within ±100kb of AGFG2, have been found to be associated with Alzheimer's disease in a GWAS study:

NIAGADS GWAS: Alzheimer's Disease

Variants contained within ±100kb of AGFG2 that have genome-wide significance in a NIAGADS Alzheimer's Disease GWAS summary statistics dataset; supported by a p-value < 5 x 10-8. For exome array studies, a cutoff of p-value < 1 x 10-3 was used.

Click on accession numbers to view a detailed report about the dataset or to request access to the data.

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Relative Position Variant ADSP? Allele p-Value Track Accession
downstream N/A 8.4e-20 ADSP Single-Variant Risk Association: European (Model 1) NG00065
downstream N/A 8.4e-20 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
downstream N/A 8.4e-20 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
downstream N/A 4.5e-17 ADSP Single-Variant Risk Association: meta analysis (Model 2) NG00065
downstream N/A 4.5e-17 ADSP Single-Variant Risk Association: European (Model 2) NG00065
downstream N/A 4.5e-17 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 2) NG00065
upstream N/A 6.2e-12 ADSP Single-Variant Risk Association: European (Model 1) NG00065
upstream N/A 6.2e-12 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
upstream N/A 6.2e-12 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
downstream N/A 6.1e-11 ADSP Single-Variant Risk Association: European (Model 2) NG00065
downstream N/A 6.1e-11 ADSP Single-Variant Risk Association: meta analysis (Model 2) NG00065
downstream N/A 6.1e-11 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 2) NG00065
upstream N/A 8.7e-11 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 2) NG00065
upstream N/A 8.7e-11 ADSP Single-Variant Risk Association: meta analysis (Model 2) NG00065
upstream N/A 8.7e-11 ADSP Single-Variant Risk Association: European (Model 2) NG00065
downstream N/A 1.4e-10 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
downstream N/A 1.4e-10 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
downstream N/A 1.4e-10 ADSP Single-Variant Risk Association: European (Model 1) NG00065
upstream T 6.0e-10 IGAP 2013: Stages 1 and 2 NG00036
upstream A 6.1e-10 IGAP 2013: Stages 1 and 2 NG00036
downstream N/A 1.0e-9 ADSP Single-Variant Risk Association: meta analysis (Model 2) NG00065
downstream N/A 1.0e-9 ADSP Single-Variant Risk Association: European (Model 2) NG00065
downstream N/A 1.0e-9 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 2) NG00065
downstream N/A 1.4e-8 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
downstream N/A 1.4e-8 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
downstream N/A 1.4e-8 ADSP Single-Variant Risk Association: European (Model 1) NG00065
downstream N/A 1.6e-8 ADSP Single-Variant Risk Association: European (Model 1) NG00065
downstream N/A 1.6e-8 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
downstream N/A 1.6e-8 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065

NHGRI GWAS: Alzheimer's Disease

Variants contained within ±100kb of AGFG2 that are associated with Alzheimer's disease in the NHGRI GWAS Catalog.

The following variants, contained within ±100kb of AGFG2, have been associated with AD-relevant neuropathologies in a GWAS study:

NIAGADS GWAS: AD biomarkers and related neuropathologies

Variants contained within ±100kb of AGFG2 that have genome-wide significance in a NIAGADS GWAS summary statistics dataset; supported by a p-value < 5 x 10-8. For exome array studies, a cutoff of p-value < 1 x 10-3 was used.

Click on accession numbers to view a detailed report about the dataset or to request access to the data.

NHGRI GWAS: Other Traits (incl. related neuropathologies and AD biomarkers)

Variants contained within ±100kb of AGFG2 that are associated with a trait in the NHGRI GWAS Catalog.

Functional Genomics

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Explore all functional genomics annotations within the region of the AGFG2 gene (chr7:100136834-100165842)

Transcription Factor Binding Site Overlap in Gene Promoter Region (ENCODE ChIP-SEQ)

ChIP-Seq sites for transcription factor binding (from selected brain-relevant ENCODE tracks) within the promoter region of this gene. See methods for more information.

Functional Annotation

Gene Ontology

Functional annotations were obtained from UniProt-GOA gene association files.

Click on a term accession number to view term details at the Gene Ontology Consortium.

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Ontology GO Accession Term Evidence Code
BP GO:0008150 biological_process ND
BP GO:0043547 positive regulation of GTPase activity IEA
CC GO:0016020 membrane IDA
MF GO:0005096 GTPase activator activity IEA
MF GO:0046872 metal ion binding IEA
MF GO:0003674 molecular_function ND

KEGG Pathways

Click on a pathway accession number to view term details at KEGG.

Click on the number in the Find Similar column to get a list of genes annotated by the associated pathway.