rs583058

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

NENF : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0434 (12978/29896,GnomAD)
C=0463 (13483/29116,TOPMED)
C=0474 (2373/5008,1000G)
C=0410 (1582/3854,ALSPAC)
C=0425 (1575/3708,TWINSUK)

Position: chr1:212437413 (GRCh38.p7) (1q32.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 279 Enhancers around

Promoter: 27 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.212437413T>C
GRCh37.p13 chr 1	NC_000001.10:g.212610755T>C

Gene: NENF, neudesin neurotrophic factor(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
NENF transcript variant 1	NM_013349.4:c.	N/A	Intron Variant
NENF transcript variant 2	NR_026598.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.505	C=0.495
1000Genomes	American	Sub	694	T=0.440	C=0.560
1000Genomes	East Asian	Sub	1008	T=0.323	C=0.677
1000Genomes	Europe	Sub	1006	T=0.619	C=0.381
1000Genomes	Global	Study-wide	5008	T=0.526	C=0.474
1000Genomes	South Asian	Sub	978	T=0.730	C=0.270
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.590	C=0.410
The Genome Aggregation Database	African	Sub	8680	T=0.496	C=0.504
The Genome Aggregation Database	American	Sub	838	T=0.420	C=0.580
The Genome Aggregation Database	East Asian	Sub	1620	T=0.278	C=0.722
The Genome Aggregation Database	Europe	Sub	18456	T=0.631	C=0.368
The Genome Aggregation Database	Global	Study-wide	29896	T=0.565	C=0.434
The Genome Aggregation Database	Other	Sub	302	T=0.560	C=0.440
Trans-Omics for Precision Medicine	Global	Study-wide	29116	T=0.536	C=0.463
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.575	C=0.425

PMID	Title	Author	Journal
23089632	A genome-wide association study of alcohol-dependence symptom counts in extended pedigrees identifies C15orf53.	Wang JC	Mol Psychiatry

P-Value

SNP ID	p-value	Traits	Study
rs583058	0.0000142	alcohol dependence	23089632
rs583058	0.000944	alcohol dependence	23089632

eQTL of rs583058 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 rs583058 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	212585838	212585911	E067	-24844
chr1	212586277	212586356	E067	-24399
chr1	212586550	212586640	E067	-24115
chr1	212589400	212589501	E067	-21254
chr1	212589852	212589937	E067	-20818
chr1	212590008	212590058	E067	-20697
chr1	212590608	212590730	E067	-20025
chr1	212598790	212598900	E067	-11855
chr1	212603792	212604098	E067	-6657
chr1	212610759	212610817	E067	4
chr1	212610857	212611007	E067	102
chr1	212613925	212614122	E067	3170
chr1	212614181	212614231	E067	3426
chr1	212623785	212624377	E067	13030
chr1	212624418	212624619	E067	13663
chr1	212624742	212624786	E067	13987
chr1	212624945	212625001	E067	14190
chr1	212626030	212626100	E067	15275
chr1	212626181	212626678	E067	15426
chr1	212629021	212629061	E067	18266
chr1	212629134	212629795	E067	18379
chr1	212629847	212630004	E067	19092
chr1	212630469	212630519	E067	19714
chr1	212630580	212630642	E067	19825
chr1	212631674	212631724	E067	20919
chr1	212632275	212632399	E067	21520
chr1	212632618	212632748	E067	21863
chr1	212632856	212633543	E067	22101
chr1	212635446	212635501	E067	24691
chr1	212641105	212641501	E067	30350
chr1	212641537	212641766	E067	30782
chr1	212643169	212643907	E067	32414
chr1	212643984	212644072	E067	33229
chr1	212644131	212644215	E067	33376
chr1	212585838	212585911	E068	-24844
chr1	212586277	212586356	E068	-24399
chr1	212589400	212589501	E068	-21254
chr1	212589852	212589937	E068	-20818
chr1	212590008	212590058	E068	-20697
chr1	212604818	212604939	E068	-5816
chr1	212605052	212605197	E068	-5558
chr1	212610759	212610817	E068	4
chr1	212610857	212611007	E068	102
chr1	212613925	212614122	E068	3170
chr1	212614181	212614231	E068	3426
chr1	212623785	212624377	E068	13030
chr1	212624418	212624619	E068	13663
chr1	212624742	212624786	E068	13987
chr1	212624945	212625001	E068	14190
chr1	212625293	212625337	E068	14538
chr1	212625385	212625456	E068	14630
chr1	212626030	212626100	E068	15275
chr1	212626181	212626678	E068	15426
chr1	212629021	212629061	E068	18266
chr1	212629134	212629795	E068	18379
chr1	212629847	212630004	E068	19092
chr1	212630469	212630519	E068	19714
chr1	212630580	212630642	E068	19825
chr1	212631144	212631493	E068	20389
chr1	212631529	212631609	E068	20774
chr1	212631674	212631724	E068	20919
chr1	212632275	212632399	E068	21520
chr1	212632856	212633543	E068	22101
chr1	212635446	212635501	E068	24691
chr1	212636724	212636970	E068	25969
chr1	212640123	212641098	E068	29368
chr1	212641105	212641501	E068	30350
chr1	212641537	212641766	E068	30782
chr1	212641832	212641958	E068	31077
chr1	212642725	212642769	E068	31970
chr1	212643169	212643907	E068	32414
chr1	212643984	212644072	E068	33229
chr1	212644131	212644215	E068	33376
chr1	212575284	212575637	E069	-35118
chr1	212575641	212575812	E069	-34943
chr1	212586277	212586356	E069	-24399
chr1	212589400	212589501	E069	-21254
chr1	212589852	212589937	E069	-20818
chr1	212590008	212590058	E069	-20697
chr1	212590608	212590730	E069	-20025
chr1	212604818	212604939	E069	-5816
chr1	212605052	212605197	E069	-5558
chr1	212610759	212610817	E069	4
chr1	212610857	212611007	E069	102
chr1	212612251	212612538	E069	1496
chr1	212613925	212614122	E069	3170
chr1	212614181	212614231	E069	3426
chr1	212623785	212624377	E069	13030
chr1	212624418	212624619	E069	13663
chr1	212624742	212624786	E069	13987
chr1	212624945	212625001	E069	14190
chr1	212625293	212625337	E069	14538
chr1	212625385	212625456	E069	14630
chr1	212626030	212626100	E069	15275
chr1	212626181	212626678	E069	15426
chr1	212627378	212627428	E069	16623
chr1	212627532	212627665	E069	16777
chr1	212629021	212629061	E069	18266
chr1	212629134	212629795	E069	18379
chr1	212629847	212630004	E069	19092
chr1	212630469	212630519	E069	19714
chr1	212630580	212630642	E069	19825
chr1	212631144	212631493	E069	20389
chr1	212632275	212632399	E069	21520
chr1	212632618	212632748	E069	21863
chr1	212632856	212633543	E069	22101
chr1	212635446	212635501	E069	24691
chr1	212636724	212636970	E069	25969
chr1	212637025	212637317	E069	26270
chr1	212640123	212641098	E069	29368
chr1	212641105	212641501	E069	30350
chr1	212641537	212641766	E069	30782
chr1	212641832	212641958	E069	31077
chr1	212642725	212642769	E069	31970
chr1	212643169	212643907	E069	32414
chr1	212643984	212644072	E069	33229
chr1	212644131	212644215	E069	33376
chr1	212650411	212650881	E069	39656
chr1	212586277	212586356	E070	-24399
chr1	212586550	212586640	E070	-24115
chr1	212623785	212624377	E070	13030
chr1	212626030	212626100	E070	15275
chr1	212626181	212626678	E070	15426
chr1	212585838	212585911	E071	-24844
chr1	212586277	212586356	E071	-24399
chr1	212589400	212589501	E071	-21254
chr1	212589852	212589937	E071	-20818
chr1	212590008	212590058	E071	-20697
chr1	212603792	212604098	E071	-6657
chr1	212604214	212604297	E071	-6458
chr1	212604425	212604618	E071	-6137
chr1	212604676	212604749	E071	-6006
chr1	212604818	212604939	E071	-5816
chr1	212613925	212614122	E071	3170
chr1	212614181	212614231	E071	3426
chr1	212623785	212624377	E071	13030
chr1	212624418	212624619	E071	13663
chr1	212624742	212624786	E071	13987
chr1	212624945	212625001	E071	14190
chr1	212625293	212625337	E071	14538
chr1	212625385	212625456	E071	14630
chr1	212626030	212626100	E071	15275
chr1	212626181	212626678	E071	15426
chr1	212627378	212627428	E071	16623
chr1	212627532	212627665	E071	16777
chr1	212629021	212629061	E071	18266
chr1	212629134	212629795	E071	18379
chr1	212629847	212630004	E071	19092
chr1	212630469	212630519	E071	19714
chr1	212630580	212630642	E071	19825
chr1	212631144	212631493	E071	20389
chr1	212631529	212631609	E071	20774
chr1	212631674	212631724	E071	20919
chr1	212632275	212632399	E071	21520
chr1	212632618	212632748	E071	21863
chr1	212632856	212633543	E071	22101
chr1	212635446	212635501	E071	24691
chr1	212636724	212636970	E071	25969
chr1	212637025	212637317	E071	26270
chr1	212640123	212641098	E071	29368
chr1	212641105	212641501	E071	30350
chr1	212641537	212641766	E071	30782
chr1	212642725	212642769	E071	31970
chr1	212643169	212643907	E071	32414
chr1	212643984	212644072	E071	33229
chr1	212644131	212644215	E071	33376
chr1	212659088	212660111	E071	48333
chr1	212586277	212586356	E072	-24399
chr1	212589400	212589501	E072	-21254
chr1	212589852	212589937	E072	-20818
chr1	212590008	212590058	E072	-20697
chr1	212590608	212590730	E072	-20025
chr1	212612251	212612538	E072	1496
chr1	212613925	212614122	E072	3170
chr1	212614181	212614231	E072	3426
chr1	212623785	212624377	E072	13030
chr1	212624418	212624619	E072	13663
chr1	212624742	212624786	E072	13987
chr1	212624945	212625001	E072	14190
chr1	212625293	212625337	E072	14538
chr1	212625385	212625456	E072	14630
chr1	212626030	212626100	E072	15275
chr1	212626181	212626678	E072	15426
chr1	212629021	212629061	E072	18266
chr1	212629134	212629795	E072	18379
chr1	212629847	212630004	E072	19092
chr1	212630469	212630519	E072	19714
chr1	212630580	212630642	E072	19825
chr1	212632856	212633543	E072	22101
chr1	212635446	212635501	E072	24691
chr1	212636724	212636970	E072	25969
chr1	212640123	212641098	E072	29368
chr1	212641105	212641501	E072	30350
chr1	212641537	212641766	E072	30782
chr1	212643169	212643907	E072	32414
chr1	212643984	212644072	E072	33229
chr1	212644131	212644215	E072	33376
chr1	212645369	212645419	E072	34614
chr1	212650411	212650881	E072	39656
chr1	212651035	212651637	E072	40280
chr1	212659088	212660111	E072	48333
chr1	212660190	212660240	E072	49435
chr1	212585838	212585911	E073	-24844
chr1	212586277	212586356	E073	-24399
chr1	212589400	212589501	E073	-21254
chr1	212589852	212589937	E073	-20818
chr1	212590008	212590058	E073	-20697
chr1	212613925	212614122	E073	3170
chr1	212614181	212614231	E073	3426
chr1	212623785	212624377	E073	13030
chr1	212624418	212624619	E073	13663
chr1	212624742	212624786	E073	13987
chr1	212624945	212625001	E073	14190
chr1	212626030	212626100	E073	15275
chr1	212626181	212626678	E073	15426
chr1	212627378	212627428	E073	16623
chr1	212629021	212629061	E073	18266
chr1	212629134	212629795	E073	18379
chr1	212629847	212630004	E073	19092
chr1	212630469	212630519	E073	19714
chr1	212630580	212630642	E073	19825
chr1	212631144	212631493	E073	20389
chr1	212640123	212641098	E073	29368
chr1	212641105	212641501	E073	30350
chr1	212641537	212641766	E073	30782
chr1	212643169	212643907	E073	32414
chr1	212643984	212644072	E073	33229
chr1	212644131	212644215	E073	33376
chr1	212650411	212650881	E073	39656
chr1	212655386	212655668	E073	44631
chr1	212585838	212585911	E074	-24844
chr1	212586277	212586356	E074	-24399
chr1	212586550	212586640	E074	-24115
chr1	212589400	212589501	E074	-21254
chr1	212589852	212589937	E074	-20818
chr1	212590008	212590058	E074	-20697
chr1	212590608	212590730	E074	-20025
chr1	212613925	212614122	E074	3170
chr1	212614181	212614231	E074	3426
chr1	212615875	212615995	E074	5120
chr1	212623785	212624377	E074	13030
chr1	212624418	212624619	E074	13663
chr1	212624742	212624786	E074	13987
chr1	212624945	212625001	E074	14190
chr1	212625293	212625337	E074	14538
chr1	212625385	212625456	E074	14630
chr1	212626030	212626100	E074	15275
chr1	212626181	212626678	E074	15426
chr1	212629021	212629061	E074	18266
chr1	212629134	212629795	E074	18379
chr1	212629847	212630004	E074	19092
chr1	212630469	212630519	E074	19714
chr1	212630580	212630642	E074	19825
chr1	212631144	212631493	E074	20389
chr1	212632856	212633543	E074	22101
chr1	212635446	212635501	E074	24691
chr1	212636724	212636970	E074	25969
chr1	212640123	212641098	E074	29368
chr1	212641105	212641501	E074	30350
chr1	212641537	212641766	E074	30782
chr1	212643169	212643907	E074	32414
chr1	212643984	212644072	E074	33229
chr1	212644131	212644215	E074	33376
chr1	212645369	212645419	E074	34614
chr1	212650411	212650881	E074	39656
chr1	212651035	212651637	E074	40280
chr1	212586277	212586356	E081	-24399
chr1	212586550	212586640	E081	-24115
chr1	212624418	212624619	E081	13663
chr1	212626030	212626100	E081	15275
chr1	212626181	212626678	E081	15426
chr1	212627378	212627428	E081	16623
chr1	212629021	212629061	E081	18266
chr1	212629134	212629795	E081	18379
chr1	212629847	212630004	E081	19092
chr1	212643169	212643907	E081	32414
chr1	212626030	212626100	E082	15275
chr1	212626181	212626678	E082	15426
chr1	212629134	212629795	E082	18379

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	212587321	212589193	E067	-21562
chr1	212605917	212606595	E067	-4160
chr1	212606606	212607015	E067	-3740
chr1	212587321	212589193	E068	-21562
chr1	212605917	212606595	E068	-4160
chr1	212606606	212607015	E068	-3740
chr1	212587321	212589193	E069	-21562
chr1	212605917	212606595	E069	-4160
chr1	212606606	212607015	E069	-3740
chr1	212605917	212606595	E070	-4160
chr1	212606606	212607015	E070	-3740
chr1	212587321	212589193	E071	-21562
chr1	212605917	212606595	E071	-4160
chr1	212606606	212607015	E071	-3740
chr1	212587321	212589193	E072	-21562
chr1	212605917	212606595	E072	-4160
chr1	212606606	212607015	E072	-3740
chr1	212587321	212589193	E073	-21562
chr1	212605917	212606595	E073	-4160
chr1	212606606	212607015	E073	-3740
chr1	212587321	212589193	E074	-21562
chr1	212605917	212606595	E074	-4160
chr1	212606606	212607015	E074	-3740
chr1	212605917	212606595	E081	-4160
chr1	212587321	212589193	E082	-21562
chr1	212605917	212606595	E082	-4160
chr1	212606606	212607015	E082	-3740