rs1932933

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

NOS1AP : Intron Variant
LOC105371475 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T==0499 (14913/29884,GnomAD)
C=0453 (13217/29118,TOPMED)
C=0362 (1815/5008,1000G)
T==0365 (1407/3854,ALSPAC)
T==0369 (1367/3708,TWINSUK)

Position: chr1:162148256 (GRCh38.p7) (1q23.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 6 publication(s)

Genomic View: See rs on genome

Enhancer: 290 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.162148256T>C
GRCh37.p13 chr 1	NC_000001.10:g.162118046T>C
NOS1AP RefSeqGene	NG_015979.1:g.83466T>C

Gene: NOS1AP, nitric oxide synthase 1 adaptor protein(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
NOS1AP transcript variant 3	NM_001164757.1:c.	N/A	Intron Variant
NOS1AP transcript variant 1	NM_014697.2:c.	N/A	Intron Variant
NOS1AP transcript variant 2	NM_001126060.1:c.	N/A	Genic Upstream Transcript Variant

Gene: LOC105371475, uncharacterized LOC105371475(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105371475 transcript variant X3	XR_001738271.1:n.	N/A	Intron Variant
LOC105371475 transcript variant X5	XR_001738272.1:n.	N/A	Intron Variant
LOC105371475 transcript variant X1	XR_922216.2:n.	N/A	Genic Downstream Transcript Variant
LOC105371475 transcript variant X2	XR_922218.2:n.	N/A	Genic Downstream Transcript Variant
LOC105371475 transcript variant X4	XR_922222.2:n.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.812	C=0.188
1000Genomes	American	Sub	694	T=0.410	C=0.590
1000Genomes	East Asian	Sub	1008	T=0.775	C=0.225
1000Genomes	Europe	Sub	1006	T=0.372	C=0.628
1000Genomes	Global	Study-wide	5008	T=0.638	C=0.362
1000Genomes	South Asian	Sub	978	T=0.700	C=0.300
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.365	C=0.635
The Genome Aggregation Database	African	Sub	8694	T=0.752	C=0.248
The Genome Aggregation Database	American	Sub	836	T=0.380	C=0.620
The Genome Aggregation Database	East Asian	Sub	1614	T=0.753	C=0.247
The Genome Aggregation Database	Europe	Sub	18438	T=0.363	C=0.636
The Genome Aggregation Database	Global	Study-wide	29884	T=0.499	C=0.501
The Genome Aggregation Database	Other	Sub	302	T=0.490	C=0.510
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.546	C=0.453
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.369	C=0.631

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res
20031603	A genome-wide association scan of RR and QT interval duration in 3 European genetically isolated populations: the EUROSPAN project.	Marroni F	Circ Cardiovasc Genet
20819849	The p.M292T NDUFS2 mutation causes complex I-deficient Leigh syndrome in multiple families.	Tuppen HA	Brain
23347024	Associations between NOS1AP single nucleotide polymorphisms (SNPs) and QT interval duration in four racial/ethnic groups in the Multi-Ethnic Study of Atherosclerosis (MESA).	Shah SA	Ann Noninvasive Electrocardiol
23691058	Dosage transmission disequilibrium test (dTDT) for linkage and association detection.	Zhang Z	PLoS One
17903306	Genome-wide association study of electrocardiographic and heart rate variability traits: the Framingham Heart Study.	Newton-Cheh C	BMC Med Genet

P-Value

SNP ID	p-value	Traits	Study
rs1932933	0.00000582	alcohol dependence	23691058
rs1932933	0.00084	alcohol dependence	20201924

eQTL of rs1932933 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

meQTL of rs1932933 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

Genomic View

Chromatin Interaction

There is no significant Hi-C chromatin interaction data for this SNP.

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr1	162086694	162086736	E067	-31310
chr1	162086836	162086925	E067	-31121
chr1	162087139	162087372	E067	-30674
chr1	162087638	162087705	E067	-30341
chr1	162088045	162088113	E067	-29933
chr1	162104855	162104957	E067	-13089
chr1	162106349	162106421	E067	-11625
chr1	162106656	162106860	E067	-11186
chr1	162106917	162107075	E067	-10971
chr1	162114207	162114257	E067	-3789
chr1	162114431	162115027	E067	-3019
chr1	162115105	162116116	E067	-1930
chr1	162116128	162116384	E067	-1662
chr1	162117642	162117856	E067	-190
chr1	162117928	162118177	E067	0
chr1	162118727	162118767	E067	681
chr1	162127156	162127246	E067	9110
chr1	162127286	162127340	E067	9240
chr1	162127357	162127495	E067	9311
chr1	162129367	162129561	E067	11321
chr1	162135178	162135232	E067	17132
chr1	162135472	162135580	E067	17426
chr1	162135783	162135891	E067	17737
chr1	162137844	162137889	E067	19798
chr1	162138157	162138320	E067	20111
chr1	162138655	162138749	E067	20609
chr1	162138876	162139412	E067	20830
chr1	162139546	162139683	E067	21500
chr1	162157440	162158172	E067	39394
chr1	162158298	162158460	E067	40252
chr1	162087139	162087372	E068	-30674
chr1	162088045	162088113	E068	-29933
chr1	162089391	162089435	E068	-28611
chr1	162106917	162107075	E068	-10971
chr1	162107405	162107483	E068	-10563
chr1	162109120	162109451	E068	-8595
chr1	162114431	162115027	E068	-3019
chr1	162115105	162116116	E068	-1930
chr1	162126976	162127111	E068	8930
chr1	162127156	162127246	E068	9110
chr1	162127286	162127340	E068	9240
chr1	162127357	162127495	E068	9311
chr1	162135178	162135232	E068	17132
chr1	162135472	162135580	E068	17426
chr1	162135783	162135891	E068	17737
chr1	162137844	162137889	E068	19798
chr1	162138157	162138320	E068	20111
chr1	162138655	162138749	E068	20609
chr1	162157440	162158172	E068	39394
chr1	162081273	162081323	E069	-36723
chr1	162083034	162083261	E069	-34785
chr1	162083298	162083459	E069	-34587
chr1	162084095	162084274	E069	-33772
chr1	162086694	162086736	E069	-31310
chr1	162086836	162086925	E069	-31121
chr1	162087139	162087372	E069	-30674
chr1	162087638	162087705	E069	-30341
chr1	162088045	162088113	E069	-29933
chr1	162107669	162107713	E069	-10333
chr1	162109120	162109451	E069	-8595
chr1	162114431	162115027	E069	-3019
chr1	162116128	162116384	E069	-1662
chr1	162127156	162127246	E069	9110
chr1	162127286	162127340	E069	9240
chr1	162127357	162127495	E069	9311
chr1	162135178	162135232	E069	17132
chr1	162135472	162135580	E069	17426
chr1	162135783	162135891	E069	17737
chr1	162136724	162136816	E069	18678
chr1	162136866	162136910	E069	18820
chr1	162136939	162137011	E069	18893
chr1	162137033	162137194	E069	18987
chr1	162137224	162137290	E069	19178
chr1	162137844	162137889	E069	19798
chr1	162138157	162138320	E069	20111
chr1	162138655	162138749	E069	20609
chr1	162138876	162139412	E069	20830
chr1	162139546	162139683	E069	21500
chr1	162157440	162158172	E069	39394
chr1	162158298	162158460	E069	40252
chr1	162162620	162163329	E069	44574
chr1	162163364	162163537	E069	45318
chr1	162163729	162163838	E069	45683
chr1	162164234	162164308	E069	46188
chr1	162164374	162164498	E069	46328
chr1	162114207	162114257	E070	-3789
chr1	162115105	162116116	E070	-1930
chr1	162116128	162116384	E070	-1662
chr1	162126684	162126792	E070	8638
chr1	162126976	162127111	E070	8930
chr1	162127156	162127246	E070	9110
chr1	162127286	162127340	E070	9240
chr1	162127357	162127495	E070	9311
chr1	162135178	162135232	E070	17132
chr1	162135472	162135580	E070	17426
chr1	162135783	162135891	E070	17737
chr1	162136724	162136816	E070	18678
chr1	162138157	162138320	E070	20111
chr1	162138655	162138749	E070	20609
chr1	162138876	162139412	E070	20830
chr1	162145217	162145485	E070	27171
chr1	162145553	162145671	E070	27507
chr1	162150366	162150447	E070	32320
chr1	162150456	162150839	E070	32410
chr1	162157440	162158172	E070	39394
chr1	162158298	162158460	E070	40252
chr1	162162620	162163329	E070	44574
chr1	162163364	162163537	E070	45318
chr1	162163729	162163838	E070	45683
chr1	162166846	162167039	E070	48800
chr1	162167088	162167288	E070	49042
chr1	162167311	162167414	E070	49265
chr1	162167426	162167627	E070	49380
chr1	162077840	162078073	E071	-39973
chr1	162081273	162081323	E071	-36723
chr1	162083034	162083261	E071	-34785
chr1	162083298	162083459	E071	-34587
chr1	162084095	162084274	E071	-33772
chr1	162086694	162086736	E071	-31310
chr1	162086836	162086925	E071	-31121
chr1	162087139	162087372	E071	-30674
chr1	162087638	162087705	E071	-30341
chr1	162088045	162088113	E071	-29933
chr1	162089391	162089435	E071	-28611
chr1	162089524	162089602	E071	-28444
chr1	162089683	162089838	E071	-28208
chr1	162109120	162109451	E071	-8595
chr1	162114207	162114257	E071	-3789
chr1	162114431	162115027	E071	-3019
chr1	162115105	162116116	E071	-1930
chr1	162116128	162116384	E071	-1662
chr1	162127156	162127246	E071	9110
chr1	162127286	162127340	E071	9240
chr1	162127357	162127495	E071	9311
chr1	162135178	162135232	E071	17132
chr1	162135472	162135580	E071	17426
chr1	162135783	162135891	E071	17737
chr1	162138157	162138320	E071	20111
chr1	162138655	162138749	E071	20609
chr1	162138876	162139412	E071	20830
chr1	162157440	162158172	E071	39394
chr1	162158298	162158460	E071	40252
chr1	162161205	162161534	E071	43159
chr1	162161565	162162265	E071	43519
chr1	162162620	162163329	E071	44574
chr1	162163364	162163537	E071	45318
chr1	162163729	162163838	E071	45683
chr1	162077840	162078073	E072	-39973
chr1	162081273	162081323	E072	-36723
chr1	162086836	162086925	E072	-31121
chr1	162087139	162087372	E072	-30674
chr1	162087638	162087705	E072	-30341
chr1	162088045	162088113	E072	-29933
chr1	162106917	162107075	E072	-10971
chr1	162107405	162107483	E072	-10563
chr1	162107669	162107713	E072	-10333
chr1	162109120	162109451	E072	-8595
chr1	162116128	162116384	E072	-1662
chr1	162126976	162127111	E072	8930
chr1	162127156	162127246	E072	9110
chr1	162127286	162127340	E072	9240
chr1	162127357	162127495	E072	9311
chr1	162135178	162135232	E072	17132
chr1	162135472	162135580	E072	17426
chr1	162135783	162135891	E072	17737
chr1	162137033	162137194	E072	18987
chr1	162137224	162137290	E072	19178
chr1	162137844	162137889	E072	19798
chr1	162138655	162138749	E072	20609
chr1	162138876	162139412	E072	20830
chr1	162139546	162139683	E072	21500
chr1	162157440	162158172	E072	39394
chr1	162158298	162158460	E072	40252
chr1	162163364	162163537	E072	45318
chr1	162163729	162163838	E072	45683
chr1	162081273	162081323	E073	-36723
chr1	162083034	162083261	E073	-34785
chr1	162086694	162086736	E073	-31310
chr1	162087638	162087705	E073	-30341
chr1	162114431	162115027	E073	-3019
chr1	162115105	162116116	E073	-1930
chr1	162116128	162116384	E073	-1662
chr1	162117642	162117856	E073	-190
chr1	162117928	162118177	E073	0
chr1	162135472	162135580	E073	17426
chr1	162135783	162135891	E073	17737
chr1	162137224	162137290	E073	19178
chr1	162137844	162137889	E073	19798
chr1	162138157	162138320	E073	20111
chr1	162138655	162138749	E073	20609
chr1	162138876	162139412	E073	20830
chr1	162157440	162158172	E073	39394
chr1	162163364	162163537	E073	45318
chr1	162163729	162163838	E073	45683
chr1	162077840	162078073	E074	-39973
chr1	162078366	162078483	E074	-39563
chr1	162083034	162083261	E074	-34785
chr1	162083298	162083459	E074	-34587
chr1	162084095	162084274	E074	-33772
chr1	162086694	162086736	E074	-31310
chr1	162086836	162086925	E074	-31121
chr1	162087139	162087372	E074	-30674
chr1	162087638	162087705	E074	-30341
chr1	162088045	162088113	E074	-29933
chr1	162101295	162101509	E074	-16537
chr1	162101543	162101715	E074	-16331
chr1	162101730	162102105	E074	-15941
chr1	162107405	162107483	E074	-10563
chr1	162107669	162107713	E074	-10333
chr1	162108003	162108199	E074	-9847
chr1	162109120	162109451	E074	-8595
chr1	162110054	162110144	E074	-7902
chr1	162114207	162114257	E074	-3789
chr1	162114431	162115027	E074	-3019
chr1	162115105	162116116	E074	-1930
chr1	162116128	162116384	E074	-1662
chr1	162127156	162127246	E074	9110
chr1	162127286	162127340	E074	9240
chr1	162127357	162127495	E074	9311
chr1	162128769	162128903	E074	10723
chr1	162129020	162129121	E074	10974
chr1	162129367	162129561	E074	11321
chr1	162135178	162135232	E074	17132
chr1	162135472	162135580	E074	17426
chr1	162135783	162135891	E074	17737
chr1	162136724	162136816	E074	18678
chr1	162136866	162136910	E074	18820
chr1	162136939	162137011	E074	18893
chr1	162137033	162137194	E074	18987
chr1	162137224	162137290	E074	19178
chr1	162137844	162137889	E074	19798
chr1	162138157	162138320	E074	20111
chr1	162138655	162138749	E074	20609
chr1	162138876	162139412	E074	20830
chr1	162139546	162139683	E074	21500
chr1	162157440	162158172	E074	39394
chr1	162158298	162158460	E074	40252
chr1	162162620	162163329	E074	44574
chr1	162163364	162163537	E074	45318
chr1	162163729	162163838	E074	45683
chr1	162164234	162164308	E074	46188
chr1	162164374	162164498	E074	46328
chr1	162107405	162107483	E081	-10563
chr1	162114431	162115027	E081	-3019
chr1	162115105	162116116	E081	-1930
chr1	162116128	162116384	E081	-1662
chr1	162126976	162127111	E081	8930
chr1	162127156	162127246	E081	9110
chr1	162127286	162127340	E081	9240
chr1	162127357	162127495	E081	9311
chr1	162132524	162132610	E081	14478
chr1	162133260	162133828	E081	15214
chr1	162133901	162134038	E081	15855
chr1	162138157	162138320	E081	20111
chr1	162138655	162138749	E081	20609
chr1	162145217	162145485	E081	27171
chr1	162145553	162145671	E081	27507
chr1	162157440	162158172	E081	39394
chr1	162158298	162158460	E081	40252
chr1	162162620	162163329	E081	44574
chr1	162163364	162163537	E081	45318
chr1	162163729	162163838	E081	45683
chr1	162164234	162164308	E081	46188
chr1	162164374	162164498	E081	46328
chr1	162166327	162166443	E081	48281
chr1	162166846	162167039	E081	48800
chr1	162167088	162167288	E081	49042
chr1	162167311	162167414	E081	49265
chr1	162105196	162105285	E082	-12761
chr1	162114431	162115027	E082	-3019
chr1	162115105	162116116	E082	-1930
chr1	162116128	162116384	E082	-1662
chr1	162126976	162127111	E082	8930
chr1	162127156	162127246	E082	9110
chr1	162127286	162127340	E082	9240
chr1	162127357	162127495	E082	9311
chr1	162135472	162135580	E082	17426
chr1	162135783	162135891	E082	17737
chr1	162138157	162138320	E082	20111
chr1	162138655	162138749	E082	20609
chr1	162157440	162158172	E082	39394
chr1	162158298	162158460	E082	40252
chr1	162162620	162163329	E082	44574
chr1	162163364	162163537	E082	45318
chr1	162163729	162163838	E082	45683
chr1	162164234	162164308	E082	46188
chr1	162164374	162164498	E082	46328
chr1	162167088	162167288	E082	49042
chr1	162167311	162167414	E082	49265
chr1	162167426	162167627	E082	49380