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HLA-DQA1 - ENSG00000196735

major histocompatibility complex, class II, DQ alpha 1

Also known as: CELIAC1

Location: chr6:32,595,956-32,614,839

Gene Type: protein coding

More information

NCBI Gene: 3117
HUGO: HGNC:4942
Ensembl: ENSG00000196735
VEGA: OTTHUMG00000031106
OMIM: 146880
UniProtKB: P01909

Genomic Context
Gene-based Trait Associations
Genetic Variation and Variant-based Trait Associations
- Alzheimer's Disease GWAS
- Related Neuropathologies and Other Traits GWAS
Functional Genomics
Functional Annotation

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.

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Gene-based Trait Associations

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.

Accession	Population	N SNPs	p-value	Sign. Level	rho	CMAF	CMAC	Covariates	Variant Filter	Caveats
NG00065	European	1	0.359	N/A	0	4.8e-05	1.0	PCs and sequencing center	VEP HIGH
NG00065	European	1	0.359	N/A	0	4.8e-05	1.0	PCs and sequencing center	LOF
NG00065	European	11	0.507	N/A	1	0.095	1987.1	PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls)	VEP MOD-HIGH	N/A
NG00065	European	11	0.594	N/A	1	0.095	1987.1	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	1	0.598	N/A	0	4.8e-05	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	European	1	0.598	N/A	0	4.8e-05	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	Meta	11	0.658	N/A	1	0.095	2061.8	PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls)	VEP MOD-HIGH	N/A
NG00065	European	1	0.731	N/A	0	4.8e-05	1.0	PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls)	LOF
NG00065	European	1	0.731	N/A	0	4.8e-05	1.0	PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls)	VEP HIGH
NG00065	Meta	11	0.747	N/A	1	0.095	2061.8	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	5	0.874	N/A	1	0.094	74.6	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	5	0.889	N/A	1	0.094	74.6	PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls)	VEP MOD-HIGH	N/A
NG00065	European	11	0.894	N/A	1	0.095	1987.1	PCs and sequencing center	VEP MOD-HIGH	N/A
NG00065	Caribbean Hispanic	5	0.934	N/A	1	0.094	74.6	PCs and sequencing center	VEP MOD-HIGH	N/A
NG00065	Meta	11	0.966	N/A	1	0.095	2061.8	PCs and sequencing center	VEP MOD-HIGH	N/A

Genetic Variation and Variant-based Trait Associations (GWAS)

Variants contained within the HLA-DQA1 gene.

The HLA-DQA1 gene contains 3,478 variants records (corresponding to 3,000 unique genomic positions).

The following variants, contained within ±100kb of HLA-DQA1, 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-DQA1 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.

Relative Position	Variant	ADSP?	Allele	p-Value	Track	Accession
upstream	6:32578530:C:A (rs9271192)		C	2.9e-12	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32575406:A:T (rs9271058)		A	5.1e-12	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32580288:C:G (rs9271252)		C	1.2e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32580084:A:G (rs9271246)		A	1.3e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32571001:T:C (rs9270864)	N/A	T	2.5e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32576170:C:A (rs9271087)	N/A	C	2.5e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32579070:C:T (rs9271210)	N/A	C	2.7e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32578735:A:G (rs9271199)		A	2.8e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32580741:A:G (rs3997874)		A	2.8e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32570717:G:A (rs9270850)	N/A	G	2.9e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32520420:T:C (rs72492326)		T	3.3e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32575873:G:A (rs9271076)		G	3.5e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32570478:A:G (rs9270843)		A	3.5e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32569659:T:C (rs9270810)		T	3.7e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32570809:A:G (rs9270854)	N/A	A	3.7e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32578818:C:A (rs9271201)		C	4.0e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32571227:G:A (rs9270874)		G	4.0e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32571043:G:A (rs9270866)		G	4.1e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32520069:T:C (rs72844156)		T	4.2e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32570797:G:A (rs9270852)		G	4.2e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32578612:T:G (rs9271194)		T	4.2e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32575849:G:T (rs9271074)	N/A	G	4.2e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32569911:A:G (rs9270817)		A	4.3e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32578673:A:T (rs7451864)		A	4.3e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32572060:T:C (rs9270904)	N/A	T	4.4e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32576247:T:C (rs9271090)		T	4.9e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32570894:T:C (rs9270859)		T	5.0e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32573560:A:G (rs9270969)	N/A	A	5.1e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32575930:C:T (rs9271078)		C	5.2e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32576633:G:A (rs9271108)	N/A	G	5.2e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32576083:A:G (rs9271081)	N/A	A	5.3e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32578191:C:T (rs9271178)		C	5.5e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32578040:C:G (rs9271174)		C	5.5e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32578756:C:T (rs9271200)		C	5.6e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32570132:C:A (rs9270827)		C	5.6e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32570609:C:T (rs9270848)	N/A	C	5.9e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32578566:T:C (rs9271193)		T	6.5e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32576347:G:C (rs9271094)		G	6.7e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32579951:C:T (rs9271243)		C	6.8e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32576426:A:G (rs9271096)	N/A	A	7.0e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32576165:T:A (rs9271086)	N/A	T	7.1e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32578941:G:A (rs9271205)		G	7.6e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32577784:C:T (rs9271164)		C	8.0e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32572082:C:T (rs9270907)	N/A	C	8.1e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32570602:G:T (rs9270847)	N/A	G	8.3e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32575803:G:T (rs9271073)		G	8.5e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32572148:G:A (rs9270908)		G	8.6e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32572388:T:C (rs9270922)	N/A	T	8.9e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32578297:A:G (rs9271186)		A	9.3e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32573434:C:T (rs9270962)		C	9.7e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32577981:A:G (rs9271173)		A	9.8e-11	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32570238:T:C (rs9270833)		T	1.1e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32577785:A:G (rs9271165)		A	1.1e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32570550:T:G (rs9270844)	N/A	T	1.2e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32576177:T:G (rs9271089)	N/A	T	1.2e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32578196:G:A (rs9271179)		G	1.3e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32578209:C:T (rs9271180)		C	1.3e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32571201:G:A (rs9270873)		G	1.4e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32571962:A:G (rs9270902)	N/A	A	1.5e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32572952:G:A (rs9270946)	N/A	G	1.5e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32570055:T:G (rs9270824)	N/A	T	1.7e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32579940:T:C (rs9271242)		T	1.7e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32575290:T:C (rs9271051)	N/A	T	1.9e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32575852:A:G (rs9271075)		A	2.0e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32580241:C:A (rs9271251)		C	2.1e-10	IGAP 2013: Stages 1 and 2	NG00036
downstream	6:32652196:T:C (rs9275152)		C	2.2e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32574438:G:A (rs9270999)		G	2.2e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32574379:A:G (rs9270998)		A	2.4e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32580446:G:A (rs9271258)		G	2.4e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32569721:A:G (rs9270811)		A	2.5e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32569790:C:T (rs9270813)		C	2.5e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32573973:T:C (rs9270983)		T	2.6e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32550322:A:C (rs9269853)	N/A	A	2.7e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32574127:T:C (rs9270987)		T	3.2e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32576731:C:G (rs9271115)	N/A	C	3.3e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32509333:C:T (rs72492305)		C	3.3e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32560808:G:A (rs9270568)	N/A	G	3.7e-10	IGAP 2013: Stages 1 and 2	NG00036
downstream	6:32673574:A:T (rs9275495)		T	4.4e-10	IGAP 2013: Stages 1 and 2	NG00036
downstream	6:32682429:C:T (rs9275599)		T	4.4e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32571890:G:A (rs9270897)	N/A	G	4.8e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32580456:G:A (rs3997871)		G	5.6e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32570051:C:G (rs9270823)	N/A	C	5.8e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32560899:C:T (rs9270569)		C	5.9e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32578726:G:A (rs9271198)		G	6.0e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32560327:C:T (rs28366284)	N/A	C	6.5e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32564861:A:G (rs9270605)		A	6.8e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32571903:T:C (rs9270898)	N/A	T	6.9e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32561277:C:T (rs9270584)		C	7.1e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32565329:C:T (rs9270622)		C	8.0e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32576699:G:A (rs9271111)	N/A	G	8.6e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32572113:G:A (rs585669)	N/A	A	9.2e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32565854:C:T (rs9270650)		C	9.8e-10	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32575513:C:G (rs9271060)		C	1.1e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32561638:C:T (rs35371668)		T	1.1e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32561305:T:G (rs9270587)		T	1.2e-9	IGAP 2013: Stages 1 and 2	NG00036
downstream	6:32668411:G:A (rs9275373)		A	1.2e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32572948:A:C (rs9270945)	N/A	A	1.3e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32573027:T:A (rs9270950)	N/A	T	1.4e-9	IGAP 2013: Stages 1 and 2	NG00036
downstream	6:32682019:A:C (rs3998159)		C	1.4e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32572961:G:C (rs9270947)	N/A	G	1.5e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32574649:C:A (rs9271009)	N/A	C	1.6e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32565413:G:C (rs9270624)		G	1.6e-9	IGAP 2013: Stages 1 and 2	NG00036
in gene	6:32606885:G:T (rs9272545)	N/A	G	1.7e-9	IGAP 2013: Stages 1 and 2	NG00036
downstream	6:32681483:T:C (rs7454108)		C	1.9e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32586908:G:A (rs9271367)		G	2.0e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32567586:A:C (rs9270719)		A	2.2e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32579211:G:C (rs9271213)		G	2.3e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32559541:T:A (rs9270522)		T	2.4e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32576019:T:C (rs482162)		C	2.4e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32559825:A:G (rs34855541)		G	2.7e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32574652:T:C (rs9271010)	N/A	T	3.0e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32566149:G:A (rs9270664)		G	3.0e-9	IGAP 2013: Stages 1 and 2	NG00036
in gene	6:32606949:T:C (rs9272547)	N/A	T	3.1e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32574602:T:C (rs9271006)	N/A	T	3.2e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32561526:C:A (rs9270594)		C	3.2e-9	IGAP 2013: Stages 1 and 2	NG00036
downstream	6:32673385:C:G (rs9275490)		G	3.3e-9	IGAP 2013: Stages 1 and 2	NG00036
in gene	6:32607141:G:A (rs9272561)	N/A	A	3.4e-9	IGAP 2013: Stage 1	NG00036
upstream	6:32521785:T:G (rs72844190)	N/A	T	3.8e-9	IGAP 2013: Stage 1	NG00036
upstream	6:32510539:C:G (rs74290590)		C	3.9e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32574493:A:C (rs9271001)	N/A	A	3.9e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32511725:C:A (rs68148149)		C	3.9e-9	IGAP 2013: Stages 1 and 2	NG00036
downstream	6:32658335:T:C (rs9275213)		C	4.2e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32567007:A:G (rs9270693)		A	4.4e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32572972:C:T (rs9270948)	N/A	C	4.5e-9	IGAP 2013: Stages 1 and 2	NG00036
in gene	6:32606941:T:C (rs9272546)	N/A	T	4.7e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32519589:A:G (rs111609395)	N/A	A	5.2e-9	IGAP 2013: Stage 1	NG00036
upstream	6:32568448:G:A (rs35226637)		A	5.2e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32567502:A:T (rs9270716)		A	5.3e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32519600:A:T (rs73729117)	N/A	A	5.4e-9	IGAP 2013: Stage 1	NG00036
upstream	6:32590234:A:T (rs9271548)		A	5.4e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32579708:T:C (rs13207945)		C	5.6e-9	IGAP 2013: Stages 1 and 2	NG00036
downstream	6:32659099:T:C (rs9275221)		C	5.9e-9	IGAP 2013: Stages 1 and 2	NG00036
downstream	6:32666635:C:T (rs9275324)		T	6.0e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32578481:T:C (rs5021726)		C	6.1e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32572229:A:G (rs9270913)	N/A	A	6.3e-9	IGAP 2013: Stage 1	NG00036
upstream	6:32572224:A:G (rs9270912)	N/A	A	6.3e-9	IGAP 2013: Stage 1	NG00036
upstream	6:32570375:A:C (rs9270839)	N/A	A	6.6e-9	IGAP 2013: Stage 1	NG00036
downstream	6:32657565:A:G (rs9275206)		G	6.7e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32519600:A:T (rs73729117)	N/A	A	6.7e-9	IGAP 2013: Stages 1 and 2	NG00036
downstream	6:32649088:C:G (rs9275095)		G	6.8e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32573562:T:C (rs602457)		C	6.8e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32578209:C:T (rs9271180)		C	6.8e-9	IGAP 2013: Stage 1	NG00036
upstream	6:32572249:A:T (rs9270914)	N/A	A	7.1e-9	IGAP 2013: Stage 1	NG00036
upstream	6:32561334:C:G (rs35265698)		G	7.2e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32570377:C:T (rs9270840)	N/A	C	7.3e-9	IGAP 2013: Stage 1	NG00036
upstream	6:32587860:G:A (rs9271422)	N/A	G	7.3e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32566743:A:G (rs9270679)		A	7.4e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32580657:T:C (rs2395516)		C	7.8e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32570418:T:G (rs9270841)	N/A	T	7.9e-9	IGAP 2013: Stage 1	NG00036
upstream	6:32567488:A:T (rs9270714)		A	7.9e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32580366:G:T (rs2858860)		T	8.0e-9	IGAP 2013: Stages 1 and 2	NG00036
downstream	6:32666660:C:T (rs9275326)		T	8.0e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32561098:A:T (rs9270579)	N/A	A	8.1e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32580507:A:C (rs9271260)		A	8.4e-9	IGAP 2013: Stage 1	NG00036
downstream	6:32663431:T:C (rs9275296)		C	8.5e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32580241:C:A (rs9271251)		C	8.7e-9	IGAP 2013: Stage 1	NG00036
downstream	6:32667107:T:C (rs9275334)		C	8.8e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32570776:C:T (rs9270851)		C	9.2e-9	IGAP 2013: Stage 1	NG00036
upstream	6:32560523:A:G (rs9270553)		A	9.2e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32580741:A:G (rs3997874)		A	9.5e-9	IGAP 2013: Stage 1	NG00036
upstream	6:32578735:A:G (rs9271199)		A	9.6e-9	IGAP 2013: Stage 1	NG00036
upstream	6:32579743:T:A (rs13208027)		A	9.6e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32578726:G:A (rs9271198)		G	9.6e-9	IGAP 2013: Stage 1	NG00036
downstream	6:32665640:G:T (rs9275311)		T	9.7e-9	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32578756:C:T (rs9271200)		C	9.8e-9	IGAP 2013: Stage 1	NG00036
upstream	6:32575275:G:A (rs9271050)	N/A	G	9.9e-9	IGAP 2013: Stage 1	NG00036
upstream	6:32570717:G:A (rs9270850)	N/A	G	1.0e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32571771:G:A (rs9270885)	N/A	G	1.0e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32580288:C:G (rs9271252)		C	1.0e-8	IGAP 2013: Stage 1	NG00036
downstream	6:32713118:A:G		N/A	1.1e-8	ADSP Single-Variant Risk Association: European (Model 1)	NG00065
downstream	6:32713118:A:G		N/A	1.1e-8	ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1)	NG00065
downstream	6:32713118:A:G		N/A	1.1e-8	ADSP Single-Variant Risk Association: meta analysis (Model 1)	NG00065
upstream	6:32578673:A:T (rs7451864)		A	1.1e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32570797:G:A (rs9270852)		G	1.1e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32570353:C:T (rs9270838)		C	1.1e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32575265:T:C (rs9271049)	N/A	T	1.1e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32571777:G:A (rs9270886)	N/A	G	1.1e-8	IGAP 2013: Stage 1	NG00036
downstream	6:32680620:G:T (rs9275592)		T	1.1e-8	IGAP 2013: Stages 1 and 2	NG00036
downstream	6:32675634:C:G (rs9275532)		G	1.1e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32521594:A:T (rs112080536)	N/A	A	1.1e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32580084:A:G (rs9271246)		A	1.2e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32569659:T:C (rs9270810)		T	1.2e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32579070:C:T (rs9271210)	N/A	C	1.2e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32561283:C:A (rs35525122)		A	1.2e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32570461:C:T (rs9270842)		C	1.2e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32570478:A:G (rs9270843)		A	1.2e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32549782:C:T (rs9269819)	N/A	C	1.2e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32575309:T:C (rs9271052)	N/A	T	1.2e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32575290:T:C (rs9271051)	N/A	T	1.2e-8	IGAP 2013: Stage 1	NG00036
downstream	6:32680299:G:A (rs9275583)		A	1.2e-8	IGAP 2013: Stages 1 and 2	NG00036
downstream	6:32664126:A:G (rs9275300)		G	1.3e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32576633:G:A (rs9271108)	N/A	G	1.3e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32569879:T:G (rs9270816)		T	1.3e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32570809:A:G (rs9270854)	N/A	A	1.4e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32570281:G:A (rs9270835)		G	1.4e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32580880:G:A (rs2894378)		G	1.4e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32578941:G:A (rs9271205)		G	1.4e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32560631:C:T (rs35118762)		T	1.4e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32578818:C:A (rs9271201)		C	1.4e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32571001:T:C (rs9270864)	N/A	T	1.4e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32569911:A:G (rs9270817)		A	1.4e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32571227:G:A (rs9270874)		G	1.4e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32570800:G:A (rs9270853)	N/A	G	1.4e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32576440:T:G (rs9271098)	N/A	T	1.4e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32571011:G:C (rs9270865)	N/A	G	1.4e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32571043:G:A (rs9270866)		G	1.4e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32570325:A:G (rs9270836)		A	1.4e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32571201:G:A (rs9270873)		G	1.4e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32578837:A:C (rs9271202)		A	1.5e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32572079:T:C (rs9270906)	N/A	T	1.5e-8	IGAP 2013: Stage 1	NG00036
downstream	6:32675523:G:C (rs9275530)		C	1.5e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32572082:C:T (rs9270907)	N/A	C	1.5e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32573554:C:T (rs9270968)	N/A	C	1.5e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32577715:G:T (rs9271162)		G	1.5e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32573560:A:G (rs9270969)	N/A	A	1.5e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32569608:G:A (rs9270809)		G	1.5e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32577549:A:T (rs9271153)		A	1.5e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32569607:G:C (rs9270808)		G	1.5e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32576052:G:C (rs9271079)		G	1.6e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32580446:G:A (rs9271258)		G	1.6e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32578530:C:A (rs9271192)		C	1.6e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32580444:G:A (rs9271257)		G	1.6e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32573543:C:T (rs9270967)	N/A	C	1.6e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32572547:A:T (rs9270931)		A	1.6e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32518913:T:C (rs76566406)		T	1.6e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32576426:A:G (rs9271096)	N/A	A	1.6e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32577733:C:T (rs9271163)		C	1.6e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32578612:T:G (rs9271194)		T	1.7e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32569972:T:C (rs9270819)	N/A	T	1.7e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32580456:G:A (rs3997871)		G	1.7e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32549746:A:G (rs9269817)	N/A	A	1.7e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32549866:C:G (rs9269827)	N/A	C	1.7e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32577282:A:C (rs9271146)		A	1.7e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32572806:G:A (rs9270939)		G	1.7e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32571820:T:C (rs9270889)	N/A	T	1.7e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32567024:C:T (rs9270694)		C	1.7e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32573554:C:T (rs9270968)	N/A	C	1.7e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32576170:C:A (rs9271087)	N/A	C	1.7e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32579833:T:C (rs9271240)		T	1.7e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32579078:C:T (rs9271211)		C	1.7e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32572148:G:A (rs9270908)		G	1.7e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32579079:A:G (rs9271212)		A	1.8e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32572451:A:G (rs9270927)	N/A	A	1.8e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32575674:C:G (rs9271068)		C	1.8e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32572388:T:C (rs9270922)	N/A	T	1.8e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32575631:A:G (rs9271066)		A	1.8e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32576577:T:G (rs9271105)	N/A	T	1.8e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32575803:G:T (rs9271073)		G	1.8e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32570839:A:G (rs9270856)	N/A	A	1.8e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32578328:G:A (rs17204995)		A	1.8e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32587782:C:T (rs9271414)		C	1.8e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32576439:C:G (rs9271097)	N/A	C	1.8e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32572757:A:G (rs9270937)		A	1.8e-8	IGAP 2013: Stage 1	NG00036
downstream	6:32681530:T:C (rs3957146)		C	1.8e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32576083:A:G (rs9271081)	N/A	A	1.8e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32570849:G:A (rs9270857)	N/A	G	1.8e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32570859:C:T (rs9270858)		C	1.8e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32570894:T:C (rs9270859)		T	1.8e-8	IGAP 2013: Stage 1	NG00036
downstream	6:32664990:A:T (rs9275307)		T	1.8e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32575601:A:G (rs9271064)		A	1.9e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32570609:C:T (rs9270848)	N/A	C	1.9e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32570602:G:T (rs9270847)	N/A	G	1.9e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32575584:A:G (rs9271063)		A	1.9e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32576064:G:C (rs482044)		C	1.9e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32577474:T:G (rs9271151)		T	1.9e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32576561:G:A (rs9271104)		G	1.9e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32575930:C:T (rs9271078)		C	1.9e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32570025:C:T (rs9270822)	N/A	C	1.9e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32580617:T:A (rs3997872)		A	1.9e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32573415:A:G (rs601945)		G	1.9e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32573434:C:T (rs9270962)		C	1.9e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32576296:A:G (rs9271092)		A	1.9e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32571822:A:T (rs9270890)	N/A	A	1.9e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32576247:T:C (rs9271090)		T	1.9e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32570132:C:A (rs9270827)		C	2.0e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32576102:T:C (rs9271083)	N/A	T	2.0e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32576165:T:A (rs9271086)	N/A	T	2.0e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32549915:T:C (rs9269829)	N/A	T	2.0e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32578566:T:C (rs9271193)		T	2.0e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32578357:C:T (rs9271189)		C	2.0e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32520642:T:C (rs72844167)	N/A	T	2.0e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32561565:T:C (rs34553045)		C	2.0e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32575406:A:T (rs9271058)		A	2.1e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32520069:T:C (rs72844156)		T	2.1e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32575513:C:G (rs9271060)		C	2.1e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32514457:C:T (rs67426377)		C	2.1e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32577590:G:A (rs9271156)		G	2.1e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32578191:C:T (rs9271178)		C	2.1e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32578040:C:G (rs9271174)		C	2.1e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32579951:C:T (rs9271243)		C	2.1e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32578196:G:A (rs9271179)		G	2.1e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32579940:T:C (rs9271242)		T	2.1e-8	IGAP 2013: Stage 1	NG00036
downstream	6:32658665:G:A (rs9275214)		A	2.2e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32576604:A:T (rs9271107)	N/A	A	2.2e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32570311:T:G (rs34039593)		G	2.2e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32572060:T:C (rs9270904)	N/A	T	2.2e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32578297:A:G (rs9271186)		A	2.2e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32576493:C:T (rs9271101)		C	2.3e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32582189:A:C (rs3129751)		C	2.3e-8	IGAP 2013: Stages 1 and 2	NG00036
downstream	6:32639836:C:A (rs9274830)		A	2.3e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32572076:G:A (rs9270905)	N/A	G	2.3e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32577785:A:G (rs9271165)		A	2.3e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32577784:C:T (rs9271164)		C	2.3e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32569556:T:A (rs9270805)		T	2.4e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32550828:G:A (rs9269874)		G	2.4e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32519018:A:G (rs74217355)	N/A	A	2.5e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32580157:C:T (rs9271248)		C	2.5e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32561681:G:A (rs34647096)		A	2.6e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32570571:T:C (rs9270845)	N/A	T	2.6e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32567880:C:T (rs4341046)		C	2.6e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32570550:T:G (rs9270844)	N/A	T	2.6e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32574703:G:C (rs9271013)	N/A	G	2.6e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32576347:G:C (rs9271094)		G	2.6e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32550322:A:C (rs9269853)	N/A	A	2.7e-8	IGAP 2013: Stage 1	NG00036
downstream	6:32671755:G:A (rs9275442)		A	2.7e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32580112:A:G (rs9271247)		A	2.7e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32520632:G:A (rs72844166)	N/A	G	2.7e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32520642:T:C (rs72844167)	N/A	T	2.7e-8	IGAP 2013: Stage 1	NG00036
downstream	6:32671086:C:T (rs9275430)		T	2.7e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32565201:G:A (rs2760980)		A	2.7e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32520420:T:C (rs72492326)		T	2.7e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32559216:A:G (rs9270505)		A	2.7e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32570051:C:G (rs9270823)	N/A	C	2.7e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32570055:T:G (rs9270824)	N/A	T	2.7e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32575119:C:T (rs9271032)	N/A	C	2.8e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32518104:G:T (rs75515332)	N/A	G	2.8e-8	IGAP 2013: Stage 1	NG00036
downstream	6:32670912:T:C (rs9275426)		C	2.8e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32570649:C:T (rs9270849)	N/A	C	2.9e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32577455:A:G (rs9271149)		A	2.9e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32580507:A:C (rs9271260)		A	2.9e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32573574:C:T (rs9270970)		C	2.9e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32521735:T:A (rs75287767)	N/A	T	2.9e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32567897:G:A (rs28752490)		A	2.9e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32550331:T:G (rs9269854)		T	3.0e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32578958:G:A (rs502803)		A	3.0e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32512459:C:T (rs201885513)	N/A	C	3.2e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32512457:T:C (rs200696488)	N/A	T	3.2e-8	IGAP 2013: Stage 1	NG00036
downstream	6:32670548:G:A (rs9275422)		A	3.2e-8	IGAP 2013: Stages 1 and 2	NG00036
in gene	6:32612397:A:G (rs6927022)	N/A	G	3.3e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32570577:A:T (rs9270846)	N/A	A	3.4e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32570238:T:C (rs9270833)		T	3.4e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32574840:T:G (rs9271020)		T	3.5e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32570228:T:C (rs9270832)		T	3.5e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32570221:G:A (rs9270831)		G	3.5e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32576175:A:C (rs9271088)	N/A	A	3.5e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32576177:T:G (rs9271089)	N/A	T	3.5e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32577497:C:T (rs536810)		T	3.5e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32589158:A:G (rs9271493)		A	3.6e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32571789:C:A (rs9270887)	N/A	C	3.6e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32577981:A:G (rs9271173)		A	3.6e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32588985:G:T (rs9271487)		G	3.6e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32577975:C:T (rs9271172)		C	3.6e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32572695:G:C (rs9270934)		G	3.6e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32572701:A:G (rs9270935)		A	3.7e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32576175:A:C (rs9271088)	N/A	A	3.7e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32583357:A:T (rs6931277)		T	3.7e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32518151:G:C (rs112532723)	N/A	G	3.7e-8	IGAP 2013: Stage 1	NG00036
downstream	6:32659839:G:A (rs9275223)		A	3.7e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32576478:T:C (rs9271100)		T	3.7e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32572113:G:A (rs585669)	N/A	A	3.7e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32576687:T:C (rs9271109)	N/A	T	3.8e-8	IGAP 2013: Stage 1	NG00036
downstream	6:32671247:C:T (rs9275434)		T	4.0e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32576595:G:A (rs9271106)	N/A	G	4.1e-8	IGAP 2013: Stage 1	NG00036
downstream	6:32678491:T:C (rs4273728)		C	4.1e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32517646:T:G (rs111365964)		G	4.1e-8	IGAP 2013: Stages 1 and 2	NG00036
in gene	6:32609813:T:C (rs707951)		T	4.1e-8	IGAP 2013: Stages 1 and 2	NG00036
downstream	6:32671332:G:C (rs9275435)		C	4.1e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32517934:G:A (rs62405645)		G	4.2e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32571962:A:G (rs9270902)	N/A	A	4.2e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32575852:A:G (rs9271075)		A	4.3e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32575873:G:A (rs9271076)		G	4.3e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32561656:G:A (rs9270599)		G	4.3e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32579870:G:A (rs9271241)		G	4.4e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32575849:G:T (rs9271074)	N/A	G	4.4e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32569422:A:T (rs9270804)	N/A	A	4.5e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32569387:A:G (rs9270801)		A	4.5e-8	IGAP 2013: Stage 1	NG00036
downstream	6:32669483:A:G (rs9275395)		G	4.7e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32520526:G:T (rs67452113)	N/A	G	4.8e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32578127:A:G (rs9271176)		A	4.8e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32588882:G:T (rs9271483)		G	4.8e-8	IGAP 2013: Stages 1 and 2	NG00036
upstream	6:32569392:T:C (rs9270802)	N/A	T	4.8e-8	IGAP 2013: Stage 1	NG00036
upstream	6:32569556:T:A (rs9270805)		T	4.9e-8	IGAP 2013: Stages 1 and 2	NG00036

NHGRI GWAS: Alzheimer's Disease

Variants contained within ±100kb of HLA-DQA1 that are associated with Alzheimer's disease in the NHGRI GWAS Catalog.

Relative Position	Variant	ADSP?	Allele	Frequency	p-Value	Odds Ratio/Beta	Trait	Study Design	Study (Pubmed ID)
upstream	6:32578530:C:A (rs9271192)		C	0.276	3.0e-12	1.11	Alzheimers disease	8,572 European ancestry cases, 11,312 European ancestry controls	24162737

The following variants, contained within ±100kb of HLA-DQA1, have been associated with AD-relevant neuropathologies in a GWAS study:

NIAGADS GWAS: AD biomarkers and related neuropathologies

Variants contained within ±100kb of HLA-DQA1 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-DQA1 that are associated with a trait in the NHGRI GWAS Catalog.

Relative Position	Variant	ADSP?	Allele	Frequency	p-Value	Odds Ratio/Beta	Trait	Study Design	Study (PMID)
downstream	6:32663999:G:C (rs6457620)		?	0.500	4.0e-186	2.55	rheumatoid arthritis	3,929 European ancestry cases, 5,807 European ancestry controls	18794853
upstream	6:32586854:G:A (rs9271366)		G	0.150	7.0e-184	2.78	multiple sclerosis	2,256 European ancestry cases, 2,310 European ancestry controls	19525955
in gene	6:32604372:G:A (rs9272346)	N/A	G	0.610	5.0e-134	5.49	type I diabetes mellitus	(see Todd 2007)	17554300
in gene	6:32612397:A:G (rs6927022)	N/A	A	0.535	5.0e-133	1.444	ulcerative colitis	Up to 25,683 European ancestry cases, up to 17,015 European ancestry controls	23128233
in gene	6:32604372:G:A (rs9272346)	N/A	G	N/A	6.0e-129	N/A	type I diabetes mellitus	6,225 European ancestry cases, 6,946 European ancestry controls, 3,064 European ancestry trios from 2,828 families	18978792
upstream	6:32575658:G:C (rs3021304)		G	0.346	1.0e-118	2.97	Vogt-Koyanagi-Harada disease	764 Han Chinese ancestry cases, 3594 Han Chinese ancestry controls	25108386
upstream	6:32577380:A:G (rs660895)		?	0.210	1.0e-108	3.62	rheumatoid arthritis	1,053 European ancestry cases, 1,858 European ancestry controls	17804836
upstream	6:32576478:T:C (rs9271100)		T	0.217	8.0e-95	1.68	leprosy	6,765 Chinese ancestry cases, 9,505 Chinese ancestry controls	25642632
upstream	6:32576478:T:C (rs9271100)		?	N/A	2.0e-94	N/A	ulcerative colitis	10,679 European ancestry cases, 26,715 European ancestry controls, 397 Iranian ancestry cases, 342 Iranian ancestry controls, 1,239 Indian ancestry cases, 990 Indian ancestry controls, 1,134 East Asian ancestry cases, 3,719 East Asian ancestry controls	26192919
downstream	6:32682135:C:T (rs3957147)		T	N/A	3.0e-93	2.0	systemic lupus erythematosus	N/A	26502338
in gene	6:32605884:C:T (rs2187668)		A	0.130	8.0e-93	4.32	membranous glomerulonephritis	N/A	21323541
downstream	6:32626272:C:A (rs9273363)		C	0.730	1.0e-86	1.3593605	ulcerative colitis	10,679 European ancestry cases, 26,715 European ancestry controls, 397 Iranian ancestry cases, 342 Iranian ancestry controls, 1,239 Indian ancestry cases, 990 Indian ancestry controls, 1,134 East Asian ancestry cases, 3,719 East Asian ancestry controls	26192919
upstream	6:32579035:G:A (rs9271209)		?	N/A	2.0e-85	N/A	ulcerative colitis	10,679 European ancestry cases, 26,715 European ancestry controls, 397 Iranian ancestry cases, 342 Iranian ancestry controls, 1,239 Indian ancestry cases, 990 Indian ancestry controls, 1,134 East Asian ancestry cases, 3,719 East Asian ancestry controls	26192919
in gene	6:32605884:C:T (rs2187668)		?	0.150	2.0e-78	2.9	autoimmune hepatits type 1	451 European ancestry cases, 4,103 European ancestry controls	24768677
downstream	6:32663851:C:T (rs6457617)		T	0.490	5.0e-75	2.36	rheumatoid arthritis	N/A	17554300
upstream	6:32586854:G:A (rs9271366)		C	0.210	2.0e-70	4.44	ulcerative colitis	607 Japanese ancestry Crohn's disease cases, 376 Japanese ancestry ulcerative colitis cases	21699788
upstream	6:32586854:G:A (rs9271366)		C	0.210	2.0e-70	4.44	Crohn's disease	607 Japanese ancestry Crohn's disease cases, 376 Japanese ancestry ulcerative colitis cases	21699788
downstream	6:32680928:T:G (rs7765379)		G	N/A	9.0e-59	1.93	Crohn's disease	Up to 1,151 Japanese ancestry cases, up to 15,800 Japanese ancestry controls	23266558
downstream	6:32671103:T:C (rs13192471)		G	0.220	2.0e-58	1.97	rheumatoid arthritis	4,768 Japanese ancestry cases, 17,359 Japanese ancestry controls	20453841
downstream	6:32626272:C:A (rs9273363)		C	0.730	3.0e-58	1.213039	inflammatory bowel disease	25,273 European ancestry cases, 26,715 European ancestry controls, 548 Iranian ancestry cases, 342 Iranian ancestry control, 1,423 Indian ancestry cases, 990 Indian ancestry controls, 2,824 East Asian ancestry cases, 3,719 East Asian ancestry controls	26192919
downstream	6:32657578:T:C (rs7774434)		C	0.470	2.0e-56	1.68	primary biliary cirrhosis	3,716 European ancestry cases, 4,261 European ancestry controls	26394269
downstream	6:32669156:T:C (rs9275390)		?	0.250	3.0e-54	2.38	systemic scleroderma	3,175 European ancestry cases, 4,210 European ancestry controls	21779181
upstream	6:32501144:C:T (rs2157337)	N/A	?	N/A	9.0e-52	N/A	rheumatoid arthritis	887 European ancestry ACPA positive RA cases, 1,218 European ancestry controls	21156761
in gene	6:32605884:C:T (rs2187668)		A	0.260	1.0e-50	6.23	celiac disease	4,918 European ancestry cases, 5,684 European ancestry controls	20190752
in gene	6:32609594:G:A (rs9272729)		A	0.200	2.0e-39	7.07	membranous glomerulonephritis	137 European ancestry cases, 379 European ancestry controls	27333618
downstream	6:32663851:C:T (rs6457617)		T	0.500	2.0e-37	1.61	systemic scleroderma	1,682 European ancestry cases, 3,926 European ancestry controls	21750679
downstream	6:32670255:C:T (rs2856718)		A	0.480	4.0e-37	1.56	hepatitis B infection	2,209 Japanese ancestry cases, 4,440 Japanese ancestry controls	21750111
upstream	6:32590953:T:C (rs9271588)		T	0.532	9.0e-37	1.75	Sjogren syndrome	1,303 Han Chinese ancestry cases, 2,727 Han Chinese ancestry controls	24097066
downstream	6:32678999:A:G (rs9275572)		G	0.590	1.0e-35	2.21	alopecia areata	N/A	20596022
downstream	6:32657578:T:C (rs7774434)		C	0.380	4.0e-34	1.6	biliary liver cirrhosis	620 European ancestry cases, 2,514 European ancestry controls	21399635
in gene	6:32605884:C:T (rs2187668)		A	0.130	2.0e-33	2.53	protein measurement	342 European ancestry cases, 886 European ancestry controls	20694011
upstream	6:32586854:G:A (rs9271366)		?	0.850	3.0e-33	7.69	protein measurement	342 European ancestry cases, 886 European ancestry controls	20694011
downstream	6:32663851:C:T (rs6457617)		T	0.450	7.0e-33	1.4	Graves disease	3,994 Chinese ancestry cases, 3,510 Chinese ancestry controls	21841780
downstream	6:32681631:C:T (rs9275596)		T	0.650	3.0e-31	1.44	IGA glomerulonephritis	2,491 East Asian ancestry cases, 1,780 East Asian ancestry controls, 2,420 European ancestry cases, 7,222 European ancestry controls	25305756
downstream	6:32659878:A:G (rs9275224)		G	0.510	6.0e-30	1.36	IGA glomerulonephritis	2,491 East Asian ancestry cases, 1,780 East Asian ancestry controls, 2,420 European ancestry cases, 7,222 European ancestry controls	25305756
downstream	6:32665420:T:G (rs10484561)		G	0.110	1.0e-29	1.95	neoplasm of mature B-cells	up to 3,164 European ancestry cases, 6,208 European ancestry controls	20639881
in gene	6:32605884:C:T (rs2187668)		A	0.120	6.0e-28	2.23	systemic lupus erythematosus	N/A	21408207
downstream	6:32670255:C:T (rs2856718)		C	0.550	7.0e-28	1.28	chronic hepatitis B infection	6,600 Chinese ancestry cases, 8,127 Chinese ancestry controls	25802187
upstream	6:32573629:A:G (rs602875)		A	0.680	5.0e-27	1.61	leprosy	3,254 Chinese ancestry cases, 5,955 Chinese ancestry controls	20018961
upstream	6:32574171:G:C (rs615672)		?	N/A	8.0e-27	N/A	rheumatoid arthritis	N/A	17554300
downstream	6:32681631:C:T (rs9275596)		?	0.730	2.0e-26	1.59	kidney disease	712 Han Chinese ancestry cases, 748 Han Chinese ancestry controls, 1,238 European ancestry cases, 1,172 European ancestry controls	21399633

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HLA-DQA1 - ENSG00000196735

major histocompatibility complex, class II, DQ alpha 1

Contents

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

Genetic Variation and Variant-based Trait Associations (GWAS)

Variants contained within the HLA-DQA1 gene.

NHGRI GWAS: Alzheimer's Disease

Variants contained within ±100kb of HLA-DQA1 that are associated with Alzheimer's disease in the NHGRI GWAS Catalog.

NHGRI GWAS: Other Traits (incl. related neuropathologies and AD biomarkers)

Variants contained within ±100kb of HLA-DQA1 that are associated with a trait in the NHGRI GWAS Catalog.

HLA-DQA1 - ENSG00000196735

major histocompatibility complex, class II, DQ alpha 1

Contents

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

Genetic Variation and Variant-based Trait Associations (GWAS) Variants contained within the HLA-DQA1 gene.

NHGRI GWAS: Alzheimer's Disease Variants contained within ±100kb of HLA-DQA1 that are associated with Alzheimer's disease in the NHGRI GWAS Catalog.

NHGRI GWAS: Other Traits (incl. related neuropathologies and AD biomarkers) Variants contained within ±100kb of HLA-DQA1 that are associated with a trait in the NHGRI GWAS Catalog.

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.

Genetic Variation and Variant-based Trait Associations (GWAS)

Variants contained within the HLA-DQA1 gene.

NHGRI GWAS: Alzheimer's Disease

Variants contained within ±100kb of HLA-DQA1 that are associated with Alzheimer's disease in the NHGRI GWAS Catalog.

NHGRI GWAS: Other Traits (incl. related neuropathologies and AD biomarkers)

Variants contained within ±100kb of HLA-DQA1 that are associated with a trait in the NHGRI GWAS Catalog.