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ABCA7 - ENSG00000064687

ATP binding cassette subfamily A member 7

Also known as: ABCX

Location: chr19:1,040,102-1,065,571

Gene Type: protein coding

Genetic evidence for a gene-level association to AD has been reported for this gene in exonic rare-variant aggregation tests by the ADSP.

See the Gene-based Trait Association section of this page for more information and to browse the test results.

Genetic Evidence for AD ADSP

More information
NCBI Gene
10347
HUGO
HGNC:37
Ensembl
ENSG00000064687
VEGA
OTTHUMG00000167547
OMIM
605414
UniProtKB
Q8IZY2

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 Meta 43 2.1e-06 p ≤ 0.05 1 8.6e-03 186.0 PCs and sequencing center LOF
NG00065 European 38 3.0e-06 p ≤ 0.05 1 7.8e-03 163.0 PCs and sequencing center LOF
NG00065 Meta 43 7.5e-04 N/A 1 8.6e-03 186.0 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes LOF N/A
NG00065 Meta 43 1.0e-03 N/A 0 8.6e-03 186.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) LOF N/A
NG00065 European 40 1.2e-03 N/A 1 0.049 1026.2 PCs and sequencing center VEP HIGH
NG00065 Meta 45 1.2e-03 N/A 1 0.049 1063.2 PCs and sequencing center VEP HIGH
NG00065 Meta 45 1.3e-03 N/A 1 0.049 1063.2 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes VEP HIGH N/A
NG00065 European 38 1.4e-03 N/A 0 7.8e-03 163.0 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes LOF N/A
NG00065 European 38 1.4e-03 N/A 0 7.8e-03 163.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) LOF N/A
NG00065 Meta 45 1.9e-03 N/A 1 0.049 1063.2 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP HIGH N/A
NG00065 European 40 2.8e-03 N/A 1 0.049 1026.2 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes VEP HIGH N/A
NG00065 European 40 4.2e-03 N/A 1 0.049 1026.2 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP HIGH N/A
NG00065 Meta 285 0.036 N/A 1 0.229 4955.9 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 European 263 0.041 N/A 1 0.198 4134.9 PCs and sequencing center VEP MOD-HIGH
NG00065 European 263 0.045 N/A 1 0.198 4134.9 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 Meta 285 0.049 N/A 1 0.229 4955.9 PCs and sequencing center VEP MOD-HIGH
NG00065 Meta 285 0.050 N/A 1 0.229 4955.9 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 263 0.066 N/A 1 0.198 4134.9 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 0.196 N/A 0 0.030 23.0 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes LOF N/A
NG00065 Caribbean Hispanic 8 0.198 N/A 0 0.030 23.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) LOF N/A
NG00065 Caribbean Hispanic 8 0.236 N/A 0 0.030 23.0 PCs and sequencing center LOF N/A
NG00065 Caribbean Hispanic 9 0.365 N/A 0 0.047 36.8 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes VEP HIGH N/A
NG00065 Caribbean Hispanic 9 0.373 N/A 0 0.047 36.8 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP HIGH N/A
NG00065 Caribbean Hispanic 9 0.425 N/A 0 0.047 36.8 PCs and sequencing center VEP HIGH N/A
NG00065 Caribbean Hispanic 47 0.935 N/A 0 0.300 236.7 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 47 0.938 N/A 0 0.300 236.7 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 Caribbean Hispanic 47 0.939 N/A 0 0.300 236.7 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

Genetic Variation and Variant-based Trait Associations (GWAS)

Variants contained within the ABCA7 gene.

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The ABCA7 gene contains 4,270 variants records (corresponding to 3,818 unique genomic positions).

The following variants, contained within ±100kb of ABCA7, have been found to be associated with Alzheimer's disease in a GWAS study:

NIAGADS GWAS: Alzheimer's Disease

Variants contained within ±100kb of ABCA7 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 6.0e-25 ADSP Single-Variant Risk Association: European (Model 1) NG00065
upstream N/A 6.0e-25 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
upstream N/A 6.0e-25 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
downstream N/A 8.2e-20 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
downstream N/A 8.2e-20 ADSP Single-Variant Risk Association: European (Model 1) NG00065
downstream N/A 8.2e-20 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
downstream N/A 4.4e-17 ADSP Single-Variant Risk Association: European (Model 2) NG00065
downstream N/A 4.4e-17 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 2) NG00065
downstream N/A 4.4e-17 ADSP Single-Variant Risk Association: meta analysis (Model 2) NG00065
downstream N/A 8.6e-17 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
downstream N/A 8.6e-17 ADSP Single-Variant Risk Association: European (Model 1) NG00065
downstream N/A 8.6e-17 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
in gene A 1.1e-15 IGAP 2013: Stages 1 and 2 NG00036
in gene G 1.4e-15 IGAP 2013: Stages 1 and 2 NG00036
downstream N/A 1.2e-14 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 2) NG00065
downstream N/A 1.2e-14 ADSP Single-Variant Risk Association: European (Model 2) NG00065
downstream N/A 1.2e-14 ADSP Single-Variant Risk Association: meta analysis (Model 2) NG00065
in gene G 4.2e-13 IGAP 2013: Stages 1 and 2 NG00036
in gene G 5.2e-13 IGAP 2013: Stages 1 and 2 NG00036
upstream N/A 6.0e-13 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 2) NG00065
upstream N/A 6.0e-13 ADSP Single-Variant Risk Association: European (Model 2) NG00065
upstream N/A 6.0e-13 ADSP Single-Variant Risk Association: meta analysis (Model 2) NG00065
in gene G 1.9e-12 IGAP 2013: Stages 1 and 2 NG00036
in gene A 5.5e-12 IGAP 2013: Stages 1 and 2 NG00036
in gene T 4.9e-11 IGAP 2013: Stages 1 and 2 NG00036
downstream A 4.5e-10 IGAP 2013: Stages 1 and 2 NG00036
downstream T 7.8e-10 IGAP 2013: Stages 1 and 2 NG00036
downstream C 1.3e-9 IGAP 2013: Stages 1 and 2 NG00036
in gene G 1.5e-9 IGAP 2013: Stages 1 and 2 NG00036
in gene A 1.7e-9 IGAP 2013: Stage 1 NG00036
upstream C 1.7e-9 IGAP 2013: Stages 1 and 2 NG00036
downstream A 1.9e-9 IGAP 2013: Stages 1 and 2 NG00036
in gene A 2.2e-9 ADGC African Americans 2013: APOE Adj NG00039
upstream A 2.3e-9 IGAP 2013: Stages 1 and 2 NG00036
downstream T 2.9e-9 IGAP 2013: Stages 1 and 2 NG00036
in gene G 4.3e-9 IGAP 2013: Stage 1 NG00036
downstream A 4.7e-9 IGAP 2013: Stages 1 and 2 NG00036
in gene A 4.7e-9 IGAP 2013: Stage 1 NG00036
in gene C 9.2e-9 IGAP 2013: Stages 1 and 2 NG00036
upstream N/A 1.1e-8 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
upstream N/A 1.1e-8 ADSP Single-Variant Risk Association: European (Model 1) NG00065
upstream N/A 1.1e-8 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
in gene G 1.2e-8 IGAP 2013: Stage 1 NG00036
in gene G 1.3e-8 IGAP 2013: Stage 1 NG00036
in gene G 1.3e-8 IGAP 2013: Stage 1 NG00036
downstream G 1.5e-8 IGAP 2013: Stages 1 and 2 NG00036
in gene T 1.7e-8 IGAP 2013: Stage 1 NG00036
in gene A 1.8e-8 IGAP 2013: Stage 1 NG00036
in gene G 2.0e-8 IGAP 2013: Stages 1 and 2 NG00036
downstream N/A 2.0e-8 ADSP Single-Variant Risk Association: European (Model 1) NG00065
downstream N/A 2.0e-8 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
downstream N/A 2.0e-8 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
downstream A 3.1e-8 IGAP 2013: Stages 1 and 2 NG00036
downstream T 3.1e-8 ADGC African Americans 2013: APOE Adj NG00039

NHGRI GWAS: Alzheimer's Disease

Variants contained within ±100kb of ABCA7 that are associated with Alzheimer's disease in the NHGRI GWAS Catalog.

The following variants, contained within ±100kb of ABCA7, have been associated with AD-relevant neuropathologies in a GWAS study:

NIAGADS GWAS: AD biomarkers and related neuropathologies

Variants contained within ±100kb of ABCA7 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 ABCA7 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 ABCA7 gene (chr19:1040102-1065571)

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:0015917 aminophospholipid transport IEA
BP GO:0038027 apolipoprotein A-I-mediated signaling pathway IEA,IDA
BP GO:0033344 cholesterol efflux IDA
BP GO:0034380 high-density lipoprotein particle assembly IDA
BP GO:0007613 memory ISS,IEA
BP GO:0042985 negative regulation of amyloid precursor protein biosynthetic process ISS,IEA
BP GO:1902430 negative regulation of beta-amyloid formation IEA,ISS
BP GO:0018149 peptide cross-linking IEA,ISS
BP GO:0006909 phagocytosis IEA
BP GO:0033700 phospholipid efflux IEA,IDA
BP GO:0045332 phospholipid translocation IDA
BP GO:1900223 positive regulation of beta-amyloid clearance ISS,IEA
BP GO:0010875 positive regulation of cholesterol efflux IEA,ISS
BP GO:1901076 positive regulation of engulfment of apoptotic cell IEA,ISS
BP GO:0070374 positive regulation of ERK1 and ERK2 cascade IEA,ISS
BP GO:0050766 positive regulation of phagocytosis ISS,IEA
BP GO:1902995 positive regulation of phospholipid efflux ISS,IEA
BP GO:0034504 protein localization to nucleus ISS,IEA
BP GO:0055085 transmembrane transport TAS
BP GO:0006810 transport IEA
CC GO:0016324 apical plasma membrane IEA
CC GO:0043190 ATP-binding cassette (ABC) transporter complex TAS
CC GO:0030054 cell junction IDA
CC GO:0009986 cell surface IEA,ISS
CC GO:0031901 early endosome membrane IEA
CC GO:0005768 endosome IEA
CC GO:0005794 Golgi apparatus IDA,IEA
CC GO:0000139 Golgi membrane IEA
CC GO:0016021 integral component of membrane TAS,IEA
CC GO:0005622 intracellular IEA
CC GO:0043231 intracellular membrane-bounded organelle IBA
CC GO:0016020 membrane IEA
CC GO:0001891 phagocytic cup IEA,ISS
CC GO:0005886 plasma membrane TAS,IEA,IDA
CC GO:0032587 ruffle membrane ISS,IEA
MF GO:0034188 apolipoprotein A-I receptor activity IDA,IEA
MF GO:0016887 ATPase activity IDA,IEA
MF GO:0042626 ATPase activity, coupled to transmembrane movement of substances IBA
MF GO:0005524 ATP binding IEA,TAS
MF GO:0000166 nucleotide binding IEA
MF GO:0090554 phosphatidylcholine-translocating ATPase activity IDA
MF GO:0090556 phosphatidylserine-translocating ATPase activity IDA
MF GO:0005548 phospholipid transporter activity IEA
MF GO:0005215 transporter activity TAS,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
ABC transporters hsa02010