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C1QTNF4 - ENSG00000172247

C1q and tumor necrosis factor related protein 4

Also known as: CTRP4, ZACRP4

Location: chr11:47,611,216-47,616,211 reverse strand

Gene Type: protein coding

More information
NCBI Gene
114900
HUGO
HGNC:14346
Ensembl
ENSG00000172247
VEGA
OTTHUMG00000166895
OMIM
614911
UniProtKB
Q9BXJ3

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 20 0.040 N/A 1 2.2e-03 46.7 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 20 0.041 N/A 1 2.2e-03 46.7 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 Meta 21 0.055 N/A 1 2.5e-03 53.7 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 21 0.060 N/A 1 2.5e-03 53.7 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 European 20 0.104 N/A 1 2.2e-03 46.7 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 Meta 21 0.127 N/A 1 2.5e-03 53.7 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 Meta 1 0.159 N/A 0 2.3e-04 5.1 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 Meta 1 0.159 N/A 0 2.3e-04 5.0 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 1 0.162 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 1 0.162 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 LOF
NG00065 Meta 1 0.176 N/A 0 2.3e-04 5.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) LOF
NG00065 Meta 1 0.176 N/A 0 2.3e-04 5.1 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP HIGH
NG00065 European 1 0.180 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) LOF
NG00065 European 1 0.180 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 1 0.765 N/A 0 2.3e-04 5.0 PCs and sequencing center LOF
NG00065 Meta 1 0.765 N/A 0 2.3e-04 5.1 PCs and sequencing center VEP HIGH
NG00065 Caribbean Hispanic 1 0.770 N/A 0 1.3e-03 1.0 PCs and sequencing center VEP HIGH
NG00065 Caribbean Hispanic 1 0.770 N/A 0 1.3e-03 1.0 PCs and sequencing center LOF
NG00065 Caribbean Hispanic 1 0.793 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 0.793 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, and age at AD onset or last-known dementia-free age (for controls) LOF
NG00065 Caribbean Hispanic 1 0.800 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 European 1 0.820 N/A 0 1.9e-04 4.0 PCs and sequencing center LOF
NG00065 European 1 0.820 N/A 0 1.9e-04 4.0 PCs and sequencing center VEP HIGH
NG00065 Caribbean Hispanic 4 0.847 N/A 0 8.9e-03 7.0 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
NG00065 Caribbean Hispanic 4 0.857 N/A 0 8.9e-03 7.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH
NG00065 Caribbean Hispanic 4 0.870 N/A 1 8.9e-03 7.0 PCs and sequencing center VEP MOD-HIGH

Genetic Variation and Variant-based Trait Associations (GWAS)

Variants contained within the C1QTNF4 gene.

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The C1QTNF4 gene contains 403 variants records (corresponding to 382 unique genomic positions).

The following variants, contained within ±100kb of C1QTNF4, have been found to be associated with Alzheimer's disease in a GWAS study:

NIAGADS GWAS: Alzheimer's Disease

Variants contained within ±100kb of C1QTNF4 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 2.8e-15 ADSP Single-Variant Risk Association: European (Model 1) NG00065
downstream N/A 2.8e-15 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
downstream N/A 2.8e-15 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
downstream N/A 8.6e-14 ADSP Single-Variant Risk Association: European (Model 1) NG00065
downstream N/A 8.6e-14 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
downstream N/A 8.6e-14 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
downstream N/A 1.9e-13 ADSP Single-Variant Risk Association: meta analysis (Model 2) NG00065
downstream N/A 1.9e-13 ADSP Single-Variant Risk Association: European (Model 2) NG00065
downstream N/A 1.9e-13 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 2) NG00065
upstream C 1.1e-8 IGAP 2013: Stages 1 and 2 NG00036
upstream A 2.4e-8 IGAP 2013: Stages 1 and 2 NG00036

NHGRI GWAS: Alzheimer's Disease

Variants contained within ±100kb of C1QTNF4 that are associated with Alzheimer's disease in the NHGRI GWAS Catalog.

The following variants, contained within ±100kb of C1QTNF4, have been associated with AD-relevant neuropathologies in a GWAS study:

NIAGADS GWAS: AD biomarkers and related neuropathologies

Variants contained within ±100kb of C1QTNF4 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 C1QTNF4 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 C1QTNF4 gene (chr11:47611216-47616211)

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
CC GO:0005576 extracellular region IEA
CC GO:0005615 extracellular space IEA
MF GO:0005125 cytokine activity 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.