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SLC39A13 - ENSG00000165915

solute carrier family 39 member 13

Also known as: FLJ25785

Location: chr11:47,428,683-47,438,047

Gene Type: protein coding

More information
NCBI Gene
91252
HUGO
HGNC:20859
Ensembl
ENSG00000165915
VEGA
OTTHUMG00000166890
OMIM
608735
UniProtKB
Q96H72

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 Caribbean Hispanic 8 0.032 N/A 0 0.024 19.0 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 Caribbean Hispanic 8 0.032 N/A 0 0.024 19.0 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 8 0.034 N/A 0 0.024 19.0 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 Meta 36 0.054 N/A 1 0.030 657.2 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 36 0.079 N/A 1 0.030 657.2 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 Meta 36 0.097 N/A 1 0.030 657.2 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 European 31 0.248 N/A 1 0.028 583.2 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 European 31 0.337 N/A 1 0.028 583.2 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 European 31 0.344 N/A 1 0.028 583.2 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 European 3 0.378 N/A 1 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 3 0.382 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 3 0.568 N/A 0 1.4e-04 3.0 PCs and sequencing center VEP HIGH
NG00065 European 3 0.570 N/A 0 1.4e-04 3.0 PCs and sequencing center LOF
NG00065 European 3 0.611 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 3 0.611 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

Genetic Variation and Variant-based Trait Associations (GWAS)

Variants contained within the SLC39A13 gene.

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The SLC39A13 gene contains 878 variants records (corresponding to 827 unique genomic positions).

The following variants, contained within ±100kb of SLC39A13, have been found to be associated with Alzheimer's disease in a GWAS study:

NIAGADS GWAS: Alzheimer's Disease

Variants contained within ±100kb of SLC39A13 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
upstream N/A 1.3e-8 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
upstream N/A 1.3e-8 ADSP Single-Variant Risk Association: European (Model 1) NG00065
upstream G 1.4e-8 IGAP 2013: Stages 1 and 2 NG00036
downstream A 1.9e-8 IGAP 2013: Stages 1 and 2 NG00036
downstream A 2.4e-8 IGAP 2013: Stages 1 and 2 NG00036
downstream A 2.9e-8 IGAP 2013: Stages 1 and 2 NG00036
upstream T 3.0e-8 IGAP 2013: Stages 1 and 2 NG00036
downstream G 3.0e-8 IGAP 2013: Stages 1 and 2 NG00036
downstream C 3.2e-8 IGAP 2013: Stages 1 and 2 NG00036
upstream A 3.5e-8 IGAP 2013: Stages 1 and 2 NG00036
in gene N/A A 3.6e-8 IGAP 2013: Stages 1 and 2 NG00036
in gene A 3.9e-8 IGAP 2013: Stages 1 and 2 NG00036
in gene G 4.3e-8 IGAP 2013: Stages 1 and 2 NG00036

NHGRI GWAS: Alzheimer's Disease

Variants contained within ±100kb of SLC39A13 that are associated with Alzheimer's disease in the NHGRI GWAS Catalog.

The following variants, contained within ±100kb of SLC39A13, have been associated with AD-relevant neuropathologies in a GWAS study:

NIAGADS GWAS: AD biomarkers and related neuropathologies

Variants contained within ±100kb of SLC39A13 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 SLC39A13 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 SLC39A13 gene (chr11:47428683-47438047)

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:0006882 cellular zinc ion homeostasis ISS,IEA,IDA
BP GO:0061448 connective tissue development IEA,IMP
BP GO:0006811 ion transport IEA
BP GO:0030001 metal ion transport IEA
BP GO:0010043 response to zinc ion IEA
BP GO:0055085 transmembrane transport IEA
BP GO:0006810 transport IEA
BP GO:0071577 zinc II ion transmembrane transport IEA,ISS,IDA
BP GO:0006829 zinc II ion transport IEA
CC GO:0005783 endoplasmic reticulum IEA
CC GO:0005794 Golgi apparatus IDA,IEA,ISS
CC GO:0000139 Golgi membrane IEA
CC GO:0030173 integral component of Golgi membrane IC
CC GO:0016021 integral component of membrane IEA,IDA
CC GO:0016020 membrane IEA
CC GO:0048471 perinuclear region of cytoplasm IEA,ISS
MF GO:0046873 metal ion transmembrane transporter activity IEA
MF GO:0005515 protein binding IPI
MF GO:0042803 protein homodimerization activity IPI
MF GO:0005385 zinc ion transmembrane transporter activity IC,IDA

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.