rs4804

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

NENF : Synonymous Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0428 (52006/121316,ExAC)
C=0432 (12935/29918,GnomAD)
C=0462 (13472/29116,TOPMED)
T==0432 (5623/13006,GO-ESP)
C=0479 (2400/5008,1000G)
C=0408 (1574/3854,ALSPAC)
C=0422 (1566/3708,TWINSUK)

Position: chr1:212445997 (GRCh38.p7) (1q32.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 295 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.212445997T>C
GRCh37.p13 chr 1	NC_000001.10:g.212619339T>C

Gene: NENF, neudesin neurotrophic factor(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
NENF transcript variant 1	NM_013349.4:c.510T>C	D [GAT]> D [GAC]	Coding Sequence Variant
neudesin precursor	NP_037481.1:p.Asp...NP_037481.1:p.Asp170=	D [Asp]> D [Asp]	Synonymous Variant
NENF transcript variant 2	NR_026598.1:n.506T>C	T>C	Non Coding Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.506	C=0.494
1000Genomes	American	Sub	694	T=0.440	C=0.560
1000Genomes	East Asian	Sub	1008	T=0.325	C=0.675
1000Genomes	Europe	Sub	1006	T=0.619	C=0.381
1000Genomes	Global	Study-wide	5008	T=0.521	C=0.479
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=0.592	C=0.408
The Exome Aggregation Consortium	American	Sub	21974	T=0.421	C=0.578
The Exome Aggregation Consortium	Asian	Sub	25128	T=0.570	C=0.429
The Exome Aggregation Consortium	Europe	Sub	73308	T=0.616	C=0.384
The Exome Aggregation Consortium	Global	Study-wide	121316	T=0.571	C=0.428
The Exome Aggregation Consortium	Other	Sub	906	T=0.610	C=0.390
The Genome Aggregation Database	African	Sub	8706	T=0.497	C=0.503
The Genome Aggregation Database	American	Sub	838	T=0.420	C=0.580
The Genome Aggregation Database	East Asian	Sub	1612	T=0.283	C=0.717
The Genome Aggregation Database	Europe	Sub	18462	T=0.632	C=0.367
The Genome Aggregation Database	Global	Study-wide	29918	T=0.567	C=0.432
The Genome Aggregation Database	Other	Sub	300	T=0.560	C=0.440
Trans-Omics for Precision Medicine	Global	Study-wide	29116	T=0.537	C=0.462
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.578	C=0.422

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
rs4804	0.00000836	alcohol dependence	23089632
rs4804	0.000715	alcohol dependence	23089632

eQTL of rs4804 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 rs4804 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	-33428
chr1	212586277	212586356	E067	-32983
chr1	212586550	212586640	E067	-32699
chr1	212589400	212589501	E067	-29838
chr1	212589852	212589937	E067	-29402
chr1	212590008	212590058	E067	-29281
chr1	212590608	212590730	E067	-28609
chr1	212598790	212598900	E067	-20439
chr1	212603792	212604098	E067	-15241
chr1	212610759	212610817	E067	-8522
chr1	212610857	212611007	E067	-8332
chr1	212613925	212614122	E067	-5217
chr1	212614181	212614231	E067	-5108
chr1	212623785	212624377	E067	4446
chr1	212624418	212624619	E067	5079
chr1	212624742	212624786	E067	5403
chr1	212624945	212625001	E067	5606
chr1	212626030	212626100	E067	6691
chr1	212626181	212626678	E067	6842
chr1	212629021	212629061	E067	9682
chr1	212629134	212629795	E067	9795
chr1	212629847	212630004	E067	10508
chr1	212630469	212630519	E067	11130
chr1	212630580	212630642	E067	11241
chr1	212631674	212631724	E067	12335
chr1	212632275	212632399	E067	12936
chr1	212632618	212632748	E067	13279
chr1	212632856	212633543	E067	13517
chr1	212635446	212635501	E067	16107
chr1	212641105	212641501	E067	21766
chr1	212641537	212641766	E067	22198
chr1	212643169	212643907	E067	23830
chr1	212643984	212644072	E067	24645
chr1	212644131	212644215	E067	24792
chr1	212661696	212662575	E067	42357
chr1	212662716	212662926	E067	43377
chr1	212585838	212585911	E068	-33428
chr1	212586277	212586356	E068	-32983
chr1	212589400	212589501	E068	-29838
chr1	212589852	212589937	E068	-29402
chr1	212590008	212590058	E068	-29281
chr1	212604818	212604939	E068	-14400
chr1	212605052	212605197	E068	-14142
chr1	212610759	212610817	E068	-8522
chr1	212610857	212611007	E068	-8332
chr1	212613925	212614122	E068	-5217
chr1	212614181	212614231	E068	-5108
chr1	212623785	212624377	E068	4446
chr1	212624418	212624619	E068	5079
chr1	212624742	212624786	E068	5403
chr1	212624945	212625001	E068	5606
chr1	212625293	212625337	E068	5954
chr1	212625385	212625456	E068	6046
chr1	212626030	212626100	E068	6691
chr1	212626181	212626678	E068	6842
chr1	212629021	212629061	E068	9682
chr1	212629134	212629795	E068	9795
chr1	212629847	212630004	E068	10508
chr1	212630469	212630519	E068	11130
chr1	212630580	212630642	E068	11241
chr1	212631144	212631493	E068	11805
chr1	212631529	212631609	E068	12190
chr1	212631674	212631724	E068	12335
chr1	212632275	212632399	E068	12936
chr1	212632856	212633543	E068	13517
chr1	212635446	212635501	E068	16107
chr1	212636724	212636970	E068	17385
chr1	212640123	212641098	E068	20784
chr1	212641105	212641501	E068	21766
chr1	212641537	212641766	E068	22198
chr1	212641832	212641958	E068	22493
chr1	212642725	212642769	E068	23386
chr1	212643169	212643907	E068	23830
chr1	212643984	212644072	E068	24645
chr1	212644131	212644215	E068	24792
chr1	212661696	212662575	E068	42357
chr1	212662716	212662926	E068	43377
chr1	212575284	212575637	E069	-43702
chr1	212575641	212575812	E069	-43527
chr1	212586277	212586356	E069	-32983
chr1	212589400	212589501	E069	-29838
chr1	212589852	212589937	E069	-29402
chr1	212590008	212590058	E069	-29281
chr1	212590608	212590730	E069	-28609
chr1	212604818	212604939	E069	-14400
chr1	212605052	212605197	E069	-14142
chr1	212610759	212610817	E069	-8522
chr1	212610857	212611007	E069	-8332
chr1	212612251	212612538	E069	-6801
chr1	212613925	212614122	E069	-5217
chr1	212614181	212614231	E069	-5108
chr1	212623785	212624377	E069	4446
chr1	212624418	212624619	E069	5079
chr1	212624742	212624786	E069	5403
chr1	212624945	212625001	E069	5606
chr1	212625293	212625337	E069	5954
chr1	212625385	212625456	E069	6046
chr1	212626030	212626100	E069	6691
chr1	212626181	212626678	E069	6842
chr1	212627378	212627428	E069	8039
chr1	212627532	212627665	E069	8193
chr1	212629021	212629061	E069	9682
chr1	212629134	212629795	E069	9795
chr1	212629847	212630004	E069	10508
chr1	212630469	212630519	E069	11130
chr1	212630580	212630642	E069	11241
chr1	212631144	212631493	E069	11805
chr1	212632275	212632399	E069	12936
chr1	212632618	212632748	E069	13279
chr1	212632856	212633543	E069	13517
chr1	212635446	212635501	E069	16107
chr1	212636724	212636970	E069	17385
chr1	212637025	212637317	E069	17686
chr1	212640123	212641098	E069	20784
chr1	212641105	212641501	E069	21766
chr1	212641537	212641766	E069	22198
chr1	212641832	212641958	E069	22493
chr1	212642725	212642769	E069	23386
chr1	212643169	212643907	E069	23830
chr1	212643984	212644072	E069	24645
chr1	212644131	212644215	E069	24792
chr1	212650411	212650881	E069	31072
chr1	212661696	212662575	E069	42357
chr1	212662716	212662926	E069	43377
chr1	212586277	212586356	E070	-32983
chr1	212586550	212586640	E070	-32699
chr1	212623785	212624377	E070	4446
chr1	212626030	212626100	E070	6691
chr1	212626181	212626678	E070	6842
chr1	212585838	212585911	E071	-33428
chr1	212586277	212586356	E071	-32983
chr1	212589400	212589501	E071	-29838
chr1	212589852	212589937	E071	-29402
chr1	212590008	212590058	E071	-29281
chr1	212603792	212604098	E071	-15241
chr1	212604214	212604297	E071	-15042
chr1	212604425	212604618	E071	-14721
chr1	212604676	212604749	E071	-14590
chr1	212604818	212604939	E071	-14400
chr1	212613925	212614122	E071	-5217
chr1	212614181	212614231	E071	-5108
chr1	212623785	212624377	E071	4446
chr1	212624418	212624619	E071	5079
chr1	212624742	212624786	E071	5403
chr1	212624945	212625001	E071	5606
chr1	212625293	212625337	E071	5954
chr1	212625385	212625456	E071	6046
chr1	212626030	212626100	E071	6691
chr1	212626181	212626678	E071	6842
chr1	212627378	212627428	E071	8039
chr1	212627532	212627665	E071	8193
chr1	212629021	212629061	E071	9682
chr1	212629134	212629795	E071	9795
chr1	212629847	212630004	E071	10508
chr1	212630469	212630519	E071	11130
chr1	212630580	212630642	E071	11241
chr1	212631144	212631493	E071	11805
chr1	212631529	212631609	E071	12190
chr1	212631674	212631724	E071	12335
chr1	212632275	212632399	E071	12936
chr1	212632618	212632748	E071	13279
chr1	212632856	212633543	E071	13517
chr1	212635446	212635501	E071	16107
chr1	212636724	212636970	E071	17385
chr1	212637025	212637317	E071	17686
chr1	212640123	212641098	E071	20784
chr1	212641105	212641501	E071	21766
chr1	212641537	212641766	E071	22198
chr1	212642725	212642769	E071	23386
chr1	212643169	212643907	E071	23830
chr1	212643984	212644072	E071	24645
chr1	212644131	212644215	E071	24792
chr1	212659088	212660111	E071	39749
chr1	212661410	212661509	E071	42071
chr1	212661696	212662575	E071	42357
chr1	212662716	212662926	E071	43377
chr1	212586277	212586356	E072	-32983
chr1	212589400	212589501	E072	-29838
chr1	212589852	212589937	E072	-29402
chr1	212590008	212590058	E072	-29281
chr1	212590608	212590730	E072	-28609
chr1	212612251	212612538	E072	-6801
chr1	212613925	212614122	E072	-5217
chr1	212614181	212614231	E072	-5108
chr1	212623785	212624377	E072	4446
chr1	212624418	212624619	E072	5079
chr1	212624742	212624786	E072	5403
chr1	212624945	212625001	E072	5606
chr1	212625293	212625337	E072	5954
chr1	212625385	212625456	E072	6046
chr1	212626030	212626100	E072	6691
chr1	212626181	212626678	E072	6842
chr1	212629021	212629061	E072	9682
chr1	212629134	212629795	E072	9795
chr1	212629847	212630004	E072	10508
chr1	212630469	212630519	E072	11130
chr1	212630580	212630642	E072	11241
chr1	212632856	212633543	E072	13517
chr1	212635446	212635501	E072	16107
chr1	212636724	212636970	E072	17385
chr1	212640123	212641098	E072	20784
chr1	212641105	212641501	E072	21766
chr1	212641537	212641766	E072	22198
chr1	212643169	212643907	E072	23830
chr1	212643984	212644072	E072	24645
chr1	212644131	212644215	E072	24792
chr1	212645369	212645419	E072	26030
chr1	212650411	212650881	E072	31072
chr1	212651035	212651637	E072	31696
chr1	212659088	212660111	E072	39749
chr1	212660190	212660240	E072	40851
chr1	212661696	212662575	E072	42357
chr1	212662716	212662926	E072	43377
chr1	212585838	212585911	E073	-33428
chr1	212586277	212586356	E073	-32983
chr1	212589400	212589501	E073	-29838
chr1	212589852	212589937	E073	-29402
chr1	212590008	212590058	E073	-29281
chr1	212613925	212614122	E073	-5217
chr1	212614181	212614231	E073	-5108
chr1	212623785	212624377	E073	4446
chr1	212624418	212624619	E073	5079
chr1	212624742	212624786	E073	5403
chr1	212624945	212625001	E073	5606
chr1	212626030	212626100	E073	6691
chr1	212626181	212626678	E073	6842
chr1	212627378	212627428	E073	8039
chr1	212629021	212629061	E073	9682
chr1	212629134	212629795	E073	9795
chr1	212629847	212630004	E073	10508
chr1	212630469	212630519	E073	11130
chr1	212630580	212630642	E073	11241
chr1	212631144	212631493	E073	11805
chr1	212640123	212641098	E073	20784
chr1	212641105	212641501	E073	21766
chr1	212641537	212641766	E073	22198
chr1	212643169	212643907	E073	23830
chr1	212643984	212644072	E073	24645
chr1	212644131	212644215	E073	24792
chr1	212650411	212650881	E073	31072
chr1	212655386	212655668	E073	36047
chr1	212661696	212662575	E073	42357
chr1	212662716	212662926	E073	43377
chr1	212585838	212585911	E074	-33428
chr1	212586277	212586356	E074	-32983
chr1	212586550	212586640	E074	-32699
chr1	212589400	212589501	E074	-29838
chr1	212589852	212589937	E074	-29402
chr1	212590008	212590058	E074	-29281
chr1	212590608	212590730	E074	-28609
chr1	212613925	212614122	E074	-5217
chr1	212614181	212614231	E074	-5108
chr1	212615875	212615995	E074	-3344
chr1	212623785	212624377	E074	4446
chr1	212624418	212624619	E074	5079
chr1	212624742	212624786	E074	5403
chr1	212624945	212625001	E074	5606
chr1	212625293	212625337	E074	5954
chr1	212625385	212625456	E074	6046
chr1	212626030	212626100	E074	6691
chr1	212626181	212626678	E074	6842
chr1	212629021	212629061	E074	9682
chr1	212629134	212629795	E074	9795
chr1	212629847	212630004	E074	10508
chr1	212630469	212630519	E074	11130
chr1	212630580	212630642	E074	11241
chr1	212631144	212631493	E074	11805
chr1	212632856	212633543	E074	13517
chr1	212635446	212635501	E074	16107
chr1	212636724	212636970	E074	17385
chr1	212640123	212641098	E074	20784
chr1	212641105	212641501	E074	21766
chr1	212641537	212641766	E074	22198
chr1	212643169	212643907	E074	23830
chr1	212643984	212644072	E074	24645
chr1	212644131	212644215	E074	24792
chr1	212645369	212645419	E074	26030
chr1	212650411	212650881	E074	31072
chr1	212651035	212651637	E074	31696
chr1	212661410	212661509	E074	42071
chr1	212661696	212662575	E074	42357
chr1	212662716	212662926	E074	43377
chr1	212586277	212586356	E081	-32983
chr1	212586550	212586640	E081	-32699
chr1	212624418	212624619	E081	5079
chr1	212626030	212626100	E081	6691
chr1	212626181	212626678	E081	6842
chr1	212627378	212627428	E081	8039
chr1	212629021	212629061	E081	9682
chr1	212629134	212629795	E081	9795
chr1	212629847	212630004	E081	10508
chr1	212643169	212643907	E081	23830
chr1	212626030	212626100	E082	6691
chr1	212626181	212626678	E082	6842
chr1	212629134	212629795	E082	9795

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	212587321	212589193	E067	-30146
chr1	212605917	212606595	E067	-12744
chr1	212606606	212607015	E067	-12324
chr1	212587321	212589193	E068	-30146
chr1	212605917	212606595	E068	-12744
chr1	212606606	212607015	E068	-12324
chr1	212587321	212589193	E069	-30146
chr1	212605917	212606595	E069	-12744
chr1	212606606	212607015	E069	-12324
chr1	212605917	212606595	E070	-12744
chr1	212606606	212607015	E070	-12324
chr1	212587321	212589193	E071	-30146
chr1	212605917	212606595	E071	-12744
chr1	212606606	212607015	E071	-12324
chr1	212587321	212589193	E072	-30146
chr1	212605917	212606595	E072	-12744
chr1	212606606	212607015	E072	-12324
chr1	212587321	212589193	E073	-30146
chr1	212605917	212606595	E073	-12744
chr1	212606606	212607015	E073	-12324
chr1	212587321	212589193	E074	-30146
chr1	212605917	212606595	E074	-12744
chr1	212606606	212607015	E074	-12324
chr1	212605917	212606595	E081	-12744
chr1	212587321	212589193	E082	-30146
chr1	212605917	212606595	E082	-12744
chr1	212606606	212607015	E082	-12324