rs483954

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

NENF : 500B Downstream Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0385 (11504/29834,GnomAD)
G=0381 (11117/29116,TOPMED)
G=0384 (1924/5008,1000G)
G=0395 (1521/3854,ALSPAC)
G=0406 (1505/3708,TWINSUK)

Position: chr1:212446872 (GRCh38.p7) (1q32.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 300 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.212446872A>G
GRCh37.p13 chr 1	NC_000001.10:g.212620214A>G

Gene: NENF, neudesin neurotrophic factor(plus strand): 500B Downstream Variant

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

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.622	G=0.378
1000Genomes	American	Sub	694	A=0.550	G=0.450
1000Genomes	East Asian	Sub	1008	A=0.438	G=0.562
1000Genomes	Europe	Sub	1006	A=0.635	G=0.365
1000Genomes	Global	Study-wide	5008	A=0.616	G=0.384
1000Genomes	South Asian	Sub	978	A=0.820	G=0.180
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.605	G=0.395
The Genome Aggregation Database	African	Sub	8686	A=0.594	G=0.406
The Genome Aggregation Database	American	Sub	834	A=0.510	G=0.490
The Genome Aggregation Database	East Asian	Sub	1612	A=0.416	G=0.584
The Genome Aggregation Database	Europe	Sub	18402	A=0.646	G=0.353
The Genome Aggregation Database	Global	Study-wide	29834	A=0.614	G=0.385
The Genome Aggregation Database	Other	Sub	300	A=0.570	G=0.430
Trans-Omics for Precision Medicine	Global	Study-wide	29116	A=0.618	G=0.381
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.594	G=0.406

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
rs483954	0.0000039	alcohol dependence	23089632
rs483954	0.00063	alcohol dependence	23089632

eQTL of rs483954 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 rs483954 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	-34303
chr1	212586277	212586356	E067	-33858
chr1	212586550	212586640	E067	-33574
chr1	212589400	212589501	E067	-30713
chr1	212589852	212589937	E067	-30277
chr1	212590008	212590058	E067	-30156
chr1	212590608	212590730	E067	-29484
chr1	212598790	212598900	E067	-21314
chr1	212603792	212604098	E067	-16116
chr1	212610759	212610817	E067	-9397
chr1	212610857	212611007	E067	-9207
chr1	212613925	212614122	E067	-6092
chr1	212614181	212614231	E067	-5983
chr1	212623785	212624377	E067	3571
chr1	212624418	212624619	E067	4204
chr1	212624742	212624786	E067	4528
chr1	212624945	212625001	E067	4731
chr1	212626030	212626100	E067	5816
chr1	212626181	212626678	E067	5967
chr1	212629021	212629061	E067	8807
chr1	212629134	212629795	E067	8920
chr1	212629847	212630004	E067	9633
chr1	212630469	212630519	E067	10255
chr1	212630580	212630642	E067	10366
chr1	212631674	212631724	E067	11460
chr1	212632275	212632399	E067	12061
chr1	212632618	212632748	E067	12404
chr1	212632856	212633543	E067	12642
chr1	212635446	212635501	E067	15232
chr1	212641105	212641501	E067	20891
chr1	212641537	212641766	E067	21323
chr1	212643169	212643907	E067	22955
chr1	212643984	212644072	E067	23770
chr1	212644131	212644215	E067	23917
chr1	212661696	212662575	E067	41482
chr1	212662716	212662926	E067	42502
chr1	212669318	212669427	E067	49104
chr1	212585838	212585911	E068	-34303
chr1	212586277	212586356	E068	-33858
chr1	212589400	212589501	E068	-30713
chr1	212589852	212589937	E068	-30277
chr1	212590008	212590058	E068	-30156
chr1	212604818	212604939	E068	-15275
chr1	212605052	212605197	E068	-15017
chr1	212610759	212610817	E068	-9397
chr1	212610857	212611007	E068	-9207
chr1	212613925	212614122	E068	-6092
chr1	212614181	212614231	E068	-5983
chr1	212623785	212624377	E068	3571
chr1	212624418	212624619	E068	4204
chr1	212624742	212624786	E068	4528
chr1	212624945	212625001	E068	4731
chr1	212625293	212625337	E068	5079
chr1	212625385	212625456	E068	5171
chr1	212626030	212626100	E068	5816
chr1	212626181	212626678	E068	5967
chr1	212629021	212629061	E068	8807
chr1	212629134	212629795	E068	8920
chr1	212629847	212630004	E068	9633
chr1	212630469	212630519	E068	10255
chr1	212630580	212630642	E068	10366
chr1	212631144	212631493	E068	10930
chr1	212631529	212631609	E068	11315
chr1	212631674	212631724	E068	11460
chr1	212632275	212632399	E068	12061
chr1	212632856	212633543	E068	12642
chr1	212635446	212635501	E068	15232
chr1	212636724	212636970	E068	16510
chr1	212640123	212641098	E068	19909
chr1	212641105	212641501	E068	20891
chr1	212641537	212641766	E068	21323
chr1	212641832	212641958	E068	21618
chr1	212642725	212642769	E068	22511
chr1	212643169	212643907	E068	22955
chr1	212643984	212644072	E068	23770
chr1	212644131	212644215	E068	23917
chr1	212661696	212662575	E068	41482
chr1	212662716	212662926	E068	42502
chr1	212669318	212669427	E068	49104
chr1	212575284	212575637	E069	-44577
chr1	212575641	212575812	E069	-44402
chr1	212586277	212586356	E069	-33858
chr1	212589400	212589501	E069	-30713
chr1	212589852	212589937	E069	-30277
chr1	212590008	212590058	E069	-30156
chr1	212590608	212590730	E069	-29484
chr1	212604818	212604939	E069	-15275
chr1	212605052	212605197	E069	-15017
chr1	212610759	212610817	E069	-9397
chr1	212610857	212611007	E069	-9207
chr1	212612251	212612538	E069	-7676
chr1	212613925	212614122	E069	-6092
chr1	212614181	212614231	E069	-5983
chr1	212623785	212624377	E069	3571
chr1	212624418	212624619	E069	4204
chr1	212624742	212624786	E069	4528
chr1	212624945	212625001	E069	4731
chr1	212625293	212625337	E069	5079
chr1	212625385	212625456	E069	5171
chr1	212626030	212626100	E069	5816
chr1	212626181	212626678	E069	5967
chr1	212627378	212627428	E069	7164
chr1	212627532	212627665	E069	7318
chr1	212629021	212629061	E069	8807
chr1	212629134	212629795	E069	8920
chr1	212629847	212630004	E069	9633
chr1	212630469	212630519	E069	10255
chr1	212630580	212630642	E069	10366
chr1	212631144	212631493	E069	10930
chr1	212632275	212632399	E069	12061
chr1	212632618	212632748	E069	12404
chr1	212632856	212633543	E069	12642
chr1	212635446	212635501	E069	15232
chr1	212636724	212636970	E069	16510
chr1	212637025	212637317	E069	16811
chr1	212640123	212641098	E069	19909
chr1	212641105	212641501	E069	20891
chr1	212641537	212641766	E069	21323
chr1	212641832	212641958	E069	21618
chr1	212642725	212642769	E069	22511
chr1	212643169	212643907	E069	22955
chr1	212643984	212644072	E069	23770
chr1	212644131	212644215	E069	23917
chr1	212650411	212650881	E069	30197
chr1	212661696	212662575	E069	41482
chr1	212662716	212662926	E069	42502
chr1	212586277	212586356	E070	-33858
chr1	212586550	212586640	E070	-33574
chr1	212623785	212624377	E070	3571
chr1	212626030	212626100	E070	5816
chr1	212626181	212626678	E070	5967
chr1	212585838	212585911	E071	-34303
chr1	212586277	212586356	E071	-33858
chr1	212589400	212589501	E071	-30713
chr1	212589852	212589937	E071	-30277
chr1	212590008	212590058	E071	-30156
chr1	212603792	212604098	E071	-16116
chr1	212604214	212604297	E071	-15917
chr1	212604425	212604618	E071	-15596
chr1	212604676	212604749	E071	-15465
chr1	212604818	212604939	E071	-15275
chr1	212613925	212614122	E071	-6092
chr1	212614181	212614231	E071	-5983
chr1	212623785	212624377	E071	3571
chr1	212624418	212624619	E071	4204
chr1	212624742	212624786	E071	4528
chr1	212624945	212625001	E071	4731
chr1	212625293	212625337	E071	5079
chr1	212625385	212625456	E071	5171
chr1	212626030	212626100	E071	5816
chr1	212626181	212626678	E071	5967
chr1	212627378	212627428	E071	7164
chr1	212627532	212627665	E071	7318
chr1	212629021	212629061	E071	8807
chr1	212629134	212629795	E071	8920
chr1	212629847	212630004	E071	9633
chr1	212630469	212630519	E071	10255
chr1	212630580	212630642	E071	10366
chr1	212631144	212631493	E071	10930
chr1	212631529	212631609	E071	11315
chr1	212631674	212631724	E071	11460
chr1	212632275	212632399	E071	12061
chr1	212632618	212632748	E071	12404
chr1	212632856	212633543	E071	12642
chr1	212635446	212635501	E071	15232
chr1	212636724	212636970	E071	16510
chr1	212637025	212637317	E071	16811
chr1	212640123	212641098	E071	19909
chr1	212641105	212641501	E071	20891
chr1	212641537	212641766	E071	21323
chr1	212642725	212642769	E071	22511
chr1	212643169	212643907	E071	22955
chr1	212643984	212644072	E071	23770
chr1	212644131	212644215	E071	23917
chr1	212659088	212660111	E071	38874
chr1	212661410	212661509	E071	41196
chr1	212661696	212662575	E071	41482
chr1	212662716	212662926	E071	42502
chr1	212669318	212669427	E071	49104
chr1	212586277	212586356	E072	-33858
chr1	212589400	212589501	E072	-30713
chr1	212589852	212589937	E072	-30277
chr1	212590008	212590058	E072	-30156
chr1	212590608	212590730	E072	-29484
chr1	212612251	212612538	E072	-7676
chr1	212613925	212614122	E072	-6092
chr1	212614181	212614231	E072	-5983
chr1	212623785	212624377	E072	3571
chr1	212624418	212624619	E072	4204
chr1	212624742	212624786	E072	4528
chr1	212624945	212625001	E072	4731
chr1	212625293	212625337	E072	5079
chr1	212625385	212625456	E072	5171
chr1	212626030	212626100	E072	5816
chr1	212626181	212626678	E072	5967
chr1	212629021	212629061	E072	8807
chr1	212629134	212629795	E072	8920
chr1	212629847	212630004	E072	9633
chr1	212630469	212630519	E072	10255
chr1	212630580	212630642	E072	10366
chr1	212632856	212633543	E072	12642
chr1	212635446	212635501	E072	15232
chr1	212636724	212636970	E072	16510
chr1	212640123	212641098	E072	19909
chr1	212641105	212641501	E072	20891
chr1	212641537	212641766	E072	21323
chr1	212643169	212643907	E072	22955
chr1	212643984	212644072	E072	23770
chr1	212644131	212644215	E072	23917
chr1	212645369	212645419	E072	25155
chr1	212650411	212650881	E072	30197
chr1	212651035	212651637	E072	30821
chr1	212659088	212660111	E072	38874
chr1	212660190	212660240	E072	39976
chr1	212661696	212662575	E072	41482
chr1	212662716	212662926	E072	42502
chr1	212669318	212669427	E072	49104
chr1	212585838	212585911	E073	-34303
chr1	212586277	212586356	E073	-33858
chr1	212589400	212589501	E073	-30713
chr1	212589852	212589937	E073	-30277
chr1	212590008	212590058	E073	-30156
chr1	212613925	212614122	E073	-6092
chr1	212614181	212614231	E073	-5983
chr1	212623785	212624377	E073	3571
chr1	212624418	212624619	E073	4204
chr1	212624742	212624786	E073	4528
chr1	212624945	212625001	E073	4731
chr1	212626030	212626100	E073	5816
chr1	212626181	212626678	E073	5967
chr1	212627378	212627428	E073	7164
chr1	212629021	212629061	E073	8807
chr1	212629134	212629795	E073	8920
chr1	212629847	212630004	E073	9633
chr1	212630469	212630519	E073	10255
chr1	212630580	212630642	E073	10366
chr1	212631144	212631493	E073	10930
chr1	212640123	212641098	E073	19909
chr1	212641105	212641501	E073	20891
chr1	212641537	212641766	E073	21323
chr1	212643169	212643907	E073	22955
chr1	212643984	212644072	E073	23770
chr1	212644131	212644215	E073	23917
chr1	212650411	212650881	E073	30197
chr1	212655386	212655668	E073	35172
chr1	212661696	212662575	E073	41482
chr1	212662716	212662926	E073	42502
chr1	212585838	212585911	E074	-34303
chr1	212586277	212586356	E074	-33858
chr1	212586550	212586640	E074	-33574
chr1	212589400	212589501	E074	-30713
chr1	212589852	212589937	E074	-30277
chr1	212590008	212590058	E074	-30156
chr1	212590608	212590730	E074	-29484
chr1	212613925	212614122	E074	-6092
chr1	212614181	212614231	E074	-5983
chr1	212615875	212615995	E074	-4219
chr1	212623785	212624377	E074	3571
chr1	212624418	212624619	E074	4204
chr1	212624742	212624786	E074	4528
chr1	212624945	212625001	E074	4731
chr1	212625293	212625337	E074	5079
chr1	212625385	212625456	E074	5171
chr1	212626030	212626100	E074	5816
chr1	212626181	212626678	E074	5967
chr1	212629021	212629061	E074	8807
chr1	212629134	212629795	E074	8920
chr1	212629847	212630004	E074	9633
chr1	212630469	212630519	E074	10255
chr1	212630580	212630642	E074	10366
chr1	212631144	212631493	E074	10930
chr1	212632856	212633543	E074	12642
chr1	212635446	212635501	E074	15232
chr1	212636724	212636970	E074	16510
chr1	212640123	212641098	E074	19909
chr1	212641105	212641501	E074	20891
chr1	212641537	212641766	E074	21323
chr1	212643169	212643907	E074	22955
chr1	212643984	212644072	E074	23770
chr1	212644131	212644215	E074	23917
chr1	212645369	212645419	E074	25155
chr1	212650411	212650881	E074	30197
chr1	212651035	212651637	E074	30821
chr1	212661410	212661509	E074	41196
chr1	212661696	212662575	E074	41482
chr1	212662716	212662926	E074	42502
chr1	212669318	212669427	E074	49104
chr1	212586277	212586356	E081	-33858
chr1	212586550	212586640	E081	-33574
chr1	212624418	212624619	E081	4204
chr1	212626030	212626100	E081	5816
chr1	212626181	212626678	E081	5967
chr1	212627378	212627428	E081	7164
chr1	212629021	212629061	E081	8807
chr1	212629134	212629795	E081	8920
chr1	212629847	212630004	E081	9633
chr1	212643169	212643907	E081	22955
chr1	212626030	212626100	E082	5816
chr1	212626181	212626678	E082	5967
chr1	212629134	212629795	E082	8920

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	212587321	212589193	E067	-31021
chr1	212605917	212606595	E067	-13619
chr1	212606606	212607015	E067	-13199
chr1	212587321	212589193	E068	-31021
chr1	212605917	212606595	E068	-13619
chr1	212606606	212607015	E068	-13199
chr1	212587321	212589193	E069	-31021
chr1	212605917	212606595	E069	-13619
chr1	212606606	212607015	E069	-13199
chr1	212605917	212606595	E070	-13619
chr1	212606606	212607015	E070	-13199
chr1	212587321	212589193	E071	-31021
chr1	212605917	212606595	E071	-13619
chr1	212606606	212607015	E071	-13199
chr1	212587321	212589193	E072	-31021
chr1	212605917	212606595	E072	-13619
chr1	212606606	212607015	E072	-13199
chr1	212587321	212589193	E073	-31021
chr1	212605917	212606595	E073	-13619
chr1	212606606	212607015	E073	-13199
chr1	212587321	212589193	E074	-31021
chr1	212605917	212606595	E074	-13619
chr1	212606606	212607015	E074	-13199
chr1	212605917	212606595	E081	-13619
chr1	212587321	212589193	E082	-31021
chr1	212605917	212606595	E082	-13619
chr1	212606606	212607015	E082	-13199