rs4761601

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

CEP83 : Intron Variant
PLXNC1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0104 (3145/29968,GnomAD)
A=0118 (3441/29118,TOPMED)
A=0099 (495/5008,1000G)
A=0131 (504/3854,ALSPAC)
A=0126 (467/3708,TWINSUK)

Position: chr12:94278226 (GRCh38.p7) (12q22)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 58 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.94278226G>A
GRCh37.p13 chr 12	NC_000012.11:g.94672002G>A

Gene: PLXNC1, plexin C1(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PLXNC1 transcript variant 1	NM_005761.2:c.	N/A	Intron Variant
PLXNC1 transcript variant 2	NR_037687.1:n.	N/A	Intron Variant
PLXNC1 transcript variant X1	XM_006719186.3:c.	N/A	Intron Variant
PLXNC1 transcript variant X3	XM_011537730.2:c.	N/A	Intron Variant
PLXNC1 transcript variant X2	XM_017018671.1:c.	N/A	Intron Variant
PLXNC1 transcript variant X4	XM_017018672.1:c.	N/A	Intron Variant
PLXNC1 transcript variant X5	XM_011537731.2:c.	N/A	Genic Downstream Transcript Variant

Gene: CEP83, centrosomal protein 83(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CEP83 transcript variant 2	NM_001042399.1:c.	N/A	Genic Downstream Transcript Variant
CEP83 transcript variant 1	NM_016122.2:c.	N/A	Genic Downstream Transcript Variant
CEP83 transcript variant X10	XM_006719437.2:c.	N/A	Genic Downstream Transcript Variant
CEP83 transcript variant X2	XM_011538424.1:c.	N/A	Genic Downstream Transcript Variant
CEP83 transcript variant X12	XM_011538427.2:c.	N/A	Genic Downstream Transcript Variant
CEP83 transcript variant X16	XM_011538429.2:c.	N/A	Genic Downstream Transcript Variant
CEP83 transcript variant X8	XM_017019385.1:c.	N/A	Genic Downstream Transcript Variant
CEP83 transcript variant X9	XM_017019386.1:c.	N/A	Genic Downstream Transcript Variant
CEP83 transcript variant X13	XM_017019387.1:c.	N/A	Genic Downstream Transcript Variant
CEP83 transcript variant X12	XM_017019388.1:c.	N/A	Genic Downstream Transcript Variant
CEP83 transcript variant X15	XM_017019389.1:c.	N/A	Genic Downstream Transcript Variant
CEP83 transcript variant X1	XR_001748731.1:n.	N/A	Intron Variant
CEP83 transcript variant X3	XR_001748732.1:n.	N/A	Intron Variant
CEP83 transcript variant X4	XR_001748733.1:n.	N/A	Intron Variant
CEP83 transcript variant X5	XR_001748734.1:n.	N/A	Intron Variant
CEP83 transcript variant X6	XR_001748735.1:n.	N/A	Intron Variant
CEP83 transcript variant X7	XR_001748736.1:n.	N/A	Intron Variant
CEP83 transcript variant X11	XR_001748737.1:n.	N/A	Genic Downstream Transcript Variant
CEP83 transcript variant X17	XR_001748738.1:n.	N/A	Genic Downstream Transcript Variant
CEP83 transcript variant X18	XR_001748739.1:n.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.938	A=0.062
1000Genomes	American	Sub	694	G=0.850	A=0.150
1000Genomes	East Asian	Sub	1008	G=0.878	A=0.122
1000Genomes	Europe	Sub	1006	G=0.862	A=0.138
1000Genomes	Global	Study-wide	5008	G=0.901	A=0.099
1000Genomes	South Asian	Sub	978	G=0.950	A=0.050
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.869	A=0.131
The Genome Aggregation Database	African	Sub	8726	G=0.934	A=0.066
The Genome Aggregation Database	American	Sub	836	G=0.810	A=0.190
The Genome Aggregation Database	East Asian	Sub	1618	G=0.883	A=0.117
The Genome Aggregation Database	Europe	Sub	18486	G=0.881	A=0.118
The Genome Aggregation Database	Global	Study-wide	29968	G=0.895	A=0.104
The Genome Aggregation Database	Other	Sub	302	G=0.860	A=0.140
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.881	A=0.118
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.874	A=0.126

PMID	Title	Author	Journal
19581569	Genome-wide association study of alcohol dependence.	Treutlein J	Arch Gen Psychiatry

P-Value

SNP ID	p-value	Traits	Study
rs4761601	4.05E-05	alcohol dependence	19581569

eQTL of rs4761601 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 rs4761601 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 )
chr12	94647857	94648091	E067	-23911
chr12	94648099	94648275	E067	-23727
chr12	94648292	94649295	E067	-22707
chr12	94683191	94684503	E067	11189
chr12	94636482	94636532	E068	-35470
chr12	94636538	94636636	E068	-35366
chr12	94636647	94636720	E068	-35282
chr12	94636722	94637202	E068	-34800
chr12	94671735	94671830	E068	-172
chr12	94679910	94680004	E068	7908
chr12	94680042	94680117	E068	8040
chr12	94680142	94680240	E068	8140
chr12	94680319	94680369	E068	8317
chr12	94680499	94681277	E068	8497
chr12	94640082	94640178	E069	-31824
chr12	94640316	94640400	E069	-31602
chr12	94640889	94641211	E069	-30791
chr12	94647857	94648091	E069	-23911
chr12	94648292	94649295	E069	-22707
chr12	94649309	94649581	E069	-22421
chr12	94654340	94655498	E069	-16504
chr12	94671735	94671830	E069	-172
chr12	94636647	94636720	E070	-35282
chr12	94671735	94671830	E070	-172
chr12	94671954	94672324	E070	0
chr12	94678718	94678982	E070	6716
chr12	94679030	94679078	E070	7028
chr12	94679156	94679258	E070	7154
chr12	94679317	94679371	E070	7315
chr12	94679403	94679471	E070	7401
chr12	94679801	94679849	E070	7799
chr12	94679910	94680004	E070	7908
chr12	94680042	94680117	E070	8040
chr12	94680142	94680240	E070	8140
chr12	94680319	94680369	E070	8317
chr12	94680499	94681277	E070	8497
chr12	94681360	94681533	E070	9358
chr12	94683191	94684503	E070	11189
chr12	94684662	94684799	E070	12660
chr12	94684829	94684877	E070	12827
chr12	94698030	94698114	E070	26028
chr12	94698292	94699706	E070	26290
chr12	94631203	94631435	E071	-40567
chr12	94649309	94649581	E071	-22421
chr12	94671735	94671830	E071	-172
chr12	94671954	94672324	E071	0
chr12	94649309	94649581	E072	-22421
chr12	94671735	94671830	E072	-172
chr12	94647857	94648091	E073	-23911
chr12	94648099	94648275	E073	-23727
chr12	94647649	94647766	E074	-24236
chr12	94671735	94671830	E074	-172
chr12	94683191	94684503	E074	11189
chr12	94683191	94684503	E081	11189
chr12	94680042	94680117	E082	8040
chr12	94680142	94680240	E082	8140
chr12	94680319	94680369	E082	8317
chr12	94680499	94681277	E082	8497