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ZKSCAN1 - ENSG00000106261

zinc finger with KRAB and SCAN domains 1

Also known as: KOX18, PHZ-37, ZSCAN33

Location: chr7:99,613,204-99,639,312

Gene Type: protein coding

More information
NCBI Gene
7586
HUGO
HGNC:13101
Ensembl
ENSG00000106261
VEGA
OTTHUMG00000156534
OMIM
601260
UniProtKB
P17029

Genomic Context

The genome browser snapshot is fully interactive. Mouse over track elements for more information. Click and drag to move tracks. Click and drag on top positional guide to zoom to a sub-region.

To add tracks, use the provided link to switch to the full genome browser view.

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 3 0.014 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 4 0.015 N/A 1 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 European 3 0.016 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 European 4 0.018 N/A 1 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 Caribbean Hispanic 4 0.180 N/A 0 7.6e-03 6.0 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 0.187 N/A 0 7.6e-03 6.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH
NG00065 Caribbean Hispanic 4 0.203 N/A 0 7.6e-03 6.0 PCs and sequencing center VEP MOD-HIGH
NG00065 European 38 0.268 N/A 1 0.013 263.7 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 40 0.290 N/A 1 0.012 269.7 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 38 0.304 N/A 1 0.013 263.7 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 Meta 40 0.325 N/A 1 0.012 269.7 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 European 38 0.365 N/A 1 0.013 263.7 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 Meta 40 0.378 N/A 1 0.012 269.7 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 European 4 0.415 N/A 1 1.9e-04 4.0 PCs and sequencing center VEP HIGH
NG00065 European 3 0.517 N/A 0 1.4e-04 3.0 PCs and sequencing center LOF

Genetic Variation and Variant-based Trait Associations (GWAS)

Variants contained within the ZKSCAN1 gene.

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The ZKSCAN1 gene contains 1,594 variants records (corresponding to 1,536 unique genomic positions).

The following variants, contained within ±100kb of ZKSCAN1, have been found to be associated with Alzheimer's disease in a GWAS study:

NIAGADS GWAS: Alzheimer's Disease

Variants contained within ±100kb of ZKSCAN1 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 6.4e-15 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
downstream N/A 6.4e-15 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
downstream N/A 6.4e-15 ADSP Single-Variant Risk Association: European (Model 1) NG00065
in gene N/A 1.5e-14 ADSP Single-Variant Risk Association: European (Model 1) NG00065
in gene N/A 1.5e-14 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
in gene N/A 1.5e-14 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
downstream N/A 8.8e-14 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
downstream N/A 8.8e-14 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
downstream N/A 8.8e-14 ADSP Single-Variant Risk Association: European (Model 1) NG00065
downstream N/A 5.8e-13 ADSP Single-Variant Risk Association: meta analysis (Model 2) NG00065
downstream N/A 5.8e-13 ADSP Single-Variant Risk Association: European (Model 2) NG00065
downstream N/A 5.8e-13 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 2) NG00065
in gene N/A 7.2e-13 ADSP Single-Variant Risk Association: European (Model 2) NG00065
in gene N/A 7.2e-13 ADSP Single-Variant Risk Association: meta analysis (Model 2) NG00065
in gene N/A 7.2e-13 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 2) NG00065
in gene N/A 1.6e-8 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
in gene N/A 1.6e-8 ADSP Single-Variant Risk Association: European (Model 1) NG00065
in gene 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 ZKSCAN1 that are associated with Alzheimer's disease in the NHGRI GWAS Catalog.

The following variants, contained within ±100kb of ZKSCAN1, have been associated with AD-relevant neuropathologies in a GWAS study:

NIAGADS GWAS: AD biomarkers and related neuropathologies

Variants contained within ±100kb of ZKSCAN1 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 ZKSCAN1 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 ZKSCAN1 gene (chr7:99613204-99639312)

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:0006355 regulation of transcription, DNA-templated NAS,IEA
BP GO:0006351 transcription, DNA-templated IEA
CC GO:0005622 intracellular IEA
CC GO:0005634 nucleus IBA,IEA,NAS
MF GO:0003677 DNA binding IEA
MF GO:0046872 metal ion binding IEA
MF GO:0003676 nucleic acid binding IEA
MF GO:0005515 protein binding IPI
MF GO:0043565 sequence-specific DNA binding IBA
MF GO:0003700 transcription factor activity, sequence-specific DNA binding NAS,IEA,IBA

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.