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 0.179 N/A 1 9.6e-05 2.0 PCs and sequencing center LOF
NG00065 European 2 0.179 N/A 1 9.6e-05 2.0 PCs and sequencing center VEP HIGH
NG00065 Meta 81 0.357 N/A 0 0.071 1528.0 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 81 0.409 N/A 0 0.071 1528.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 European 74 0.419 N/A 0 0.071 1484.0 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 74 0.462 N/A 0 0.071 1484.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 Meta 81 0.548 N/A 0 0.071 1528.0 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 European 2 0.611 N/A 1 9.6e-05 2.0 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 0.611 N/A 1 9.6e-05 2.0 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes LOF
NG00065 European 74 0.618 N/A 0 0.071 1484.0 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 European 2 0.625 N/A 1 9.6e-05 2.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP HIGH
NG00065 European 2 0.625 N/A 1 9.6e-05 2.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) LOF
NG00065 Caribbean Hispanic 11 0.801 N/A 1 0.056 44.1 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 Caribbean Hispanic 11 0.824 N/A 1 0.056 44.1 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 Caribbean Hispanic 11 0.852 N/A 1 0.056 44.1 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A

Genetic Variation and Variant-based Trait Associations (GWAS)

Variants contained within the GPC1 gene.

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The GPC1 gene contains 2,896 variants records (corresponding to 2,760 unique genomic positions).

The following variants, contained within ±100kb of GPC1, have been found to be associated with Alzheimer's disease in a GWAS study:

NIAGADS GWAS: Alzheimer's Disease

Variants contained within ±100kb of GPC1 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 6.2e-20 ADSP Single-Variant Risk Association: European (Model 1) NG00065
downstream N/A 6.2e-20 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
downstream N/A 6.2e-20 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
downstream N/A 4.1e-16 ADSP Single-Variant Risk Association: European (Model 2) NG00065
downstream N/A 4.1e-16 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 2) NG00065
downstream N/A 4.1e-16 ADSP Single-Variant Risk Association: meta analysis (Model 2) NG00065
in gene N/A 1.0e-8 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
in gene N/A 1.0e-8 ADSP Single-Variant Risk Association: European (Model 1) NG00065
in gene N/A 1.0e-8 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
in gene N/A 1.0e-8 ADSP Single-Variant Risk Association: European (Model 1) NG00065
in gene N/A 1.0e-8 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
in gene N/A 1.0e-8 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065

NHGRI GWAS: Alzheimer's Disease

Variants contained within ±100kb of GPC1 that are associated with Alzheimer's disease in the NHGRI GWAS Catalog.

The following variants, contained within ±100kb of GPC1, have been associated with AD-relevant neuropathologies in a GWAS study:

NIAGADS GWAS: AD biomarkers and related neuropathologies

Variants contained within ±100kb of GPC1 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 GPC1 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 GPC1 gene (chr2:241375088-241407493)

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:0007411 axon guidance TAS
BP GO:0006024 glycosaminoglycan biosynthetic process TAS
BP GO:0006027 glycosaminoglycan catabolic process TAS
BP GO:0030203 glycosaminoglycan metabolic process TAS
BP GO:0030200 heparan sulfate proteoglycan catabolic process IDA
BP GO:0050900 leukocyte migration TAS
BP GO:0032288 myelin assembly ISS
BP GO:0040037 negative regulation of fibroblast growth factor receptor signaling pathway IEA,ISS
BP GO:2001016 positive regulation of skeletal muscle cell differentiation ISS,IEA
BP GO:0001523 retinoid metabolic process TAS
BP GO:0014037 Schwann cell differentiation ISS
CC GO:0031225 anchored component of membrane IEA
CC GO:0005829 cytosol IDA
CC GO:0005768 endosome IEA
CC GO:0070062 extracellular exosome IDA
CC GO:0005576 extracellular region IEA
CC GO:0005615 extracellular space IEA,TAS
CC GO:0005796 Golgi lumen TAS
CC GO:0005887 integral component of plasma membrane TAS
CC GO:0043202 lysosomal lumen TAS
CC GO:0016020 membrane IEA
CC GO:0045121 membrane raft IDA,IEA,ISS
CC GO:0005654 nucleoplasm IDA
CC GO:0005886 plasma membrane IDA,TAS,IEA
CC GO:0005578 proteinaceous extracellular matrix ISS,IEA
MF GO:0005507 copper ion binding IDA
MF GO:0017134 fibroblast growth factor binding IEA,ISS
MF GO:0043395 heparan sulfate proteoglycan binding IEA
MF GO:0043236 laminin binding ISS,IEA

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.

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Pathway KEGG Accession Graph
Fluid shear stress and atherosclerosis hsa05418
Proteoglycans in cancer hsa05205