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HLA-DPA1 - ENSG00000231389

major histocompatibility complex, class II, DP alpha 1

Location: chr6:33,032,346-33,048,552 reverse strand

Gene Type: protein coding

More information
NCBI Gene
3113
HUGO
HGNC:4938
Ensembl
ENSG00000231389
VEGA
OTTHUMG00000031058
OMIM
142880
UniProtKB
P20036

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 22 0.264 N/A 1 0.020 422.9 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 22 0.292 N/A 1 0.020 422.9 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 European 2 0.367 N/A 0 9.7e-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 0.368 N/A 0 9.7e-05 2.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) LOF
NG00065 European 2 0.372 N/A 1 9.7e-05 2.0 PCs and sequencing center VEP HIGH
NG00065 European 2 0.375 N/A 0 9.7e-05 2.0 PCs and sequencing center LOF
NG00065 European 2 0.376 N/A 0 9.7e-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 0.377 N/A 0 9.7e-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 Meta 26 0.462 N/A 1 0.028 604.2 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 26 0.511 N/A 1 0.028 604.2 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 6 0.579 N/A 1 0.083 65.5 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 6 0.579 N/A 1 0.083 65.5 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 6 0.609 N/A 1 0.083 65.5 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 Meta 3 0.815 N/A 0 3.4e-04 7.4 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP HIGH
NG00065 Meta 3 0.822 N/A 0 3.4e-04 7.4 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 3 0.829 N/A 1 3.4e-04 7.4 PCs and sequencing center VEP HIGH
NG00065 Caribbean Hispanic 1 0.835 N/A 0 6.8e-03 5.4 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP HIGH
NG00065 Caribbean Hispanic 1 0.842 N/A 0 6.8e-03 5.4 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 0.872 N/A 0 6.8e-03 5.4 PCs and sequencing center VEP HIGH
NG00065 European 22 0.980 N/A 0 0.020 422.9 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 Meta 26 0.996 N/A 0 0.028 604.2 PCs and sequencing center VEP MOD-HIGH N/A

Genetic Variation and Variant-based Trait Associations (GWAS)

Variants contained within the HLA-DPA1 gene.

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The HLA-DPA1 gene contains 1,621 variants records (corresponding to 1,462 unique genomic positions).

The following variants, contained within ±100kb of HLA-DPA1, have been found to be associated with Alzheimer's disease in a GWAS study:

NIAGADS GWAS: Alzheimer's Disease

Variants contained within ±100kb of HLA-DPA1 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.

NHGRI GWAS: Alzheimer's Disease

Variants contained within ±100kb of HLA-DPA1 that are associated with Alzheimer's disease in the NHGRI GWAS Catalog.

The following variants, contained within ±100kb of HLA-DPA1, have been associated with AD-relevant neuropathologies in a GWAS study:

NIAGADS GWAS: AD biomarkers and related neuropathologies

Variants contained within ±100kb of HLA-DPA1 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 HLA-DPA1 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 HLA-DPA1 gene (chr6:33032346-33048552)

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:0019882 antigen processing and presentation IEA
BP GO:0002504 antigen processing and presentation of peptide or polysaccharide antigen via MHC class II IEA
BP GO:0006955 immune response IEA
BP GO:0002376 immune system process IEA
CC GO:0016021 integral component of membrane IEA
CC GO:0043231 intracellular membrane-bounded organelle IDA
CC GO:0016020 membrane IEA
CC GO:0042613 MHC class II protein complex 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
Allograft rejection hsa05330
Antigen processing and presentation hsa04612
Asthma hsa05310
Autoimmune thyroid disease hsa05320
Cell adhesion molecules (CAMs) hsa04514
Epstein-Barr virus infection hsa05169
Graft-versus-host disease hsa05332
Hematopoietic cell lineage hsa04640
Herpes simplex infection hsa05168
HTLV-I infection hsa05166
Inflammatory bowel disease (IBD) hsa05321
Influenza A hsa05164
Intestinal immune network for IgA production hsa04672
Leishmaniasis hsa05140
Phagosome hsa04145
Rheumatoid arthritis hsa05323
Staphylococcus aureus infection hsa05150
Systemic lupus erythematosus hsa05322
Th17 cell differentiation hsa04659
Th1 and Th2 cell differentiation hsa04658
Toxoplasmosis hsa05145
Tuberculosis hsa05152
Type I diabetes mellitus hsa04940
Viral myocarditis hsa05416