rs7682973

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

C4orf50 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0288 (8630/29910,GnomAD)
G=0285 (8308/29118,TOPMED)
G=0240 (1202/5008,1000G)
G=0327 (1262/3854,ALSPAC)
G=0333 (1236/3708,TWINSUK)

Position: chr4:5943379 (GRCh38.p7) (4p16.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 73 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 4	NC_000004.12:g.5943379A>G
GRCh37.p13 chr 4	NC_000004.11:g.5945106A>G

Gene: C4orf50, uncharacterized C4orf50(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
C4orf50 transcript variant X6	XM_011513603.2:c.	N/A	Intron Variant
C4orf50 transcript variant X5	XM_011513604.2:c.	N/A	Intron Variant
C4orf50 transcript variant X1	XM_017008891.1:c.	N/A	Intron Variant
C4orf50 transcript variant X2	XM_017008892.1:c.	N/A	Intron Variant
C4orf50 transcript variant X3	XM_017008893.1:c.	N/A	Intron Variant
C4orf50 transcript variant X4	XM_017008894.1:c.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.763	G=0.237
1000Genomes	American	Sub	694	A=0.610	G=0.390
1000Genomes	East Asian	Sub	1008	A=0.931	G=0.069
1000Genomes	Europe	Sub	1006	A=0.654	G=0.346
1000Genomes	Global	Study-wide	5008	A=0.760	G=0.240
1000Genomes	South Asian	Sub	978	A=0.800	G=0.200
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.673	G=0.327
The Genome Aggregation Database	African	Sub	8706	A=0.745	G=0.255
The Genome Aggregation Database	American	Sub	838	A=0.590	G=0.410
The Genome Aggregation Database	East Asian	Sub	1620	A=0.958	G=0.042
The Genome Aggregation Database	Europe	Sub	18444	A=0.680	G=0.319
The Genome Aggregation Database	Global	Study-wide	29910	A=0.711	G=0.288
The Genome Aggregation Database	Other	Sub	302	A=0.660	G=0.340
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.714	G=0.285
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.667	G=0.333

PMID	Title	Author	Journal
24277619	ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.	Quillen EE	Am J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID	p-value	Traits	Study
rs7682973	0.000823	alcohol dependence	24277619

eQTL of rs7682973 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 rs7682973 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 )
chr4	5922941	5923462	E068	-21644
chr4	5934964	5935094	E068	-10012
chr4	5957202	5957577	E068	12096
chr4	5957683	5957763	E068	12577
chr4	5957973	5958073	E068	12867
chr4	5958075	5958130	E068	12969
chr4	5958197	5958660	E068	13091
chr4	5958738	5958923	E068	13632
chr4	5958938	5959008	E068	13832
chr4	5975890	5975930	E068	30784
chr4	5907474	5907977	E070	-37129
chr4	5908077	5908198	E070	-36908
chr4	5908262	5908406	E070	-36700
chr4	5914367	5914745	E070	-30361
chr4	5920475	5920586	E070	-24520
chr4	5922941	5923462	E070	-21644
chr4	5923543	5923631	E070	-21475
chr4	5925304	5925449	E070	-19657
chr4	5941509	5941660	E070	-3446
chr4	5941712	5941790	E070	-3316
chr4	5941839	5941940	E070	-3166
chr4	5942230	5942513	E070	-2593
chr4	5943467	5943550	E070	-1556
chr4	5943667	5943763	E070	-1343
chr4	5957202	5957577	E070	12096
chr4	5957683	5957763	E070	12577
chr4	5958197	5958660	E070	13091
chr4	5958738	5958923	E070	13632
chr4	5981659	5981753	E070	36553
chr4	5981793	5982016	E070	36687
chr4	5934964	5935094	E071	-10012
chr4	5924494	5924548	E072	-20558
chr4	5936074	5936150	E072	-8956
chr4	5957973	5958073	E072	12867
chr4	5958075	5958130	E072	12969
chr4	5958197	5958660	E072	13091
chr4	5965885	5965990	E072	20779
chr4	5922941	5923462	E073	-21644
chr4	5957973	5958073	E073	12867
chr4	5958075	5958130	E073	12969
chr4	5958197	5958660	E073	13091
chr4	5907474	5907977	E081	-37129
chr4	5908077	5908198	E081	-36908
chr4	5908262	5908406	E081	-36700
chr4	5913885	5914104	E081	-31002
chr4	5914367	5914745	E081	-30361
chr4	5914782	5915139	E081	-29967
chr4	5915342	5915392	E081	-29714
chr4	5922941	5923462	E081	-21644
chr4	5923543	5923631	E081	-21475
chr4	5924494	5924548	E081	-20558
chr4	5925586	5925636	E081	-19470
chr4	5957973	5958073	E081	12867
chr4	5958075	5958130	E081	12969
chr4	5958197	5958660	E081	13091
chr4	5958738	5958923	E081	13632
chr4	5958938	5959008	E081	13832
chr4	5981659	5981753	E081	36553
chr4	5981793	5982016	E081	36687
chr4	5982379	5982495	E081	37273
chr4	5907118	5907294	E082	-37812
chr4	5907474	5907977	E082	-37129
chr4	5908077	5908198	E082	-36908
chr4	5914367	5914745	E082	-30361
chr4	5914782	5915139	E082	-29967
chr4	5924494	5924548	E082	-20558
chr4	5941509	5941660	E082	-3446
chr4	5941712	5941790	E082	-3316
chr4	5941839	5941940	E082	-3166
chr4	5942230	5942513	E082	-2593
chr4	5957973	5958073	E082	12867
chr4	5958075	5958130	E082	12969
chr4	5958197	5958660	E082	13091