rs1756871

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0408 (12224/29912,GnomAD)
G==0450 (13109/29118,TOPMED)
G==0398 (1992/5008,1000G)
G==0325 (1254/3854,ALSPAC)
G==0335 (1243/3708,TWINSUK)

Position: chr9:4758022 (GRCh38.p7) (9p24.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 75 Enhancers around

Promoter: 19 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 9	NC_000009.12:g.4758022G>A
GRCh37.p13 chr 9	NC_000009.11:g.4758022G>A

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.603	A=0.397
1000Genomes	American	Sub	694	G=0.440	A=0.560
1000Genomes	East Asian	Sub	1008	G=0.235	A=0.765
1000Genomes	Europe	Sub	1006	G=0.354	A=0.646
1000Genomes	Global	Study-wide	5008	G=0.398	A=0.602
1000Genomes	South Asian	Sub	978	G=0.300	A=0.700
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.325	A=0.675
The Genome Aggregation Database	African	Sub	8698	G=0.555	A=0.445
The Genome Aggregation Database	American	Sub	838	G=0.510	A=0.490
The Genome Aggregation Database	East Asian	Sub	1618	G=0.203	A=0.797
The Genome Aggregation Database	Europe	Sub	18456	G=0.355	A=0.644
The Genome Aggregation Database	Global	Study-wide	29912	G=0.408	A=0.591
The Genome Aggregation Database	Other	Sub	302	G=0.280	A=0.720
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.450	A=0.549
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.335	A=0.665

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs1756871	0.000228	alcohol dependence	20201924

eQTL of rs1756871 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 rs1756871 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 )
chr9	4717885	4718084	E067	-39938
chr9	4718290	4718360	E067	-39662
chr9	4743124	4743811	E067	-14211
chr9	4797361	4798268	E067	39339
chr9	4798346	4798515	E067	40324
chr9	4798576	4798704	E067	40554
chr9	4798724	4798764	E067	40702
chr9	4798789	4798958	E067	40767
chr9	4799014	4799100	E067	40992
chr9	4799186	4799253	E067	41164
chr9	4722502	4722568	E068	-35454
chr9	4722579	4722804	E068	-35218
chr9	4797361	4798268	E068	39339
chr9	4798346	4798515	E068	40324
chr9	4798576	4798704	E068	40554
chr9	4798724	4798764	E068	40702
chr9	4798789	4798958	E068	40767
chr9	4799014	4799100	E068	40992
chr9	4799186	4799253	E068	41164
chr9	4804195	4804301	E068	46173
chr9	4717885	4718084	E069	-39938
chr9	4718290	4718360	E069	-39662
chr9	4762172	4763668	E069	4150
chr9	4797361	4798268	E069	39339
chr9	4798346	4798515	E069	40324
chr9	4804195	4804301	E069	46173
chr9	4794827	4794933	E070	36805
chr9	4797361	4798268	E070	39339
chr9	4798346	4798515	E070	40324
chr9	4798576	4798704	E070	40554
chr9	4798724	4798764	E070	40702
chr9	4798789	4798958	E070	40767
chr9	4799014	4799100	E070	40992
chr9	4799186	4799253	E070	41164
chr9	4717885	4718084	E071	-39938
chr9	4738822	4738894	E071	-19128
chr9	4742614	4742698	E071	-15324
chr9	4742740	4742796	E071	-15226
chr9	4742885	4742987	E071	-15035
chr9	4743124	4743811	E071	-14211
chr9	4797361	4798268	E071	39339
chr9	4798346	4798515	E071	40324
chr9	4798576	4798704	E071	40554
chr9	4798724	4798764	E071	40702
chr9	4798789	4798958	E071	40767
chr9	4799014	4799100	E071	40992
chr9	4799186	4799253	E071	41164
chr9	4799517	4799573	E071	41495
chr9	4799821	4800050	E071	41799
chr9	4717885	4718084	E072	-39938
chr9	4718290	4718360	E072	-39662
chr9	4731760	4731815	E072	-26207
chr9	4797361	4798268	E072	39339
chr9	4798346	4798515	E072	40324
chr9	4804195	4804301	E072	46173
chr9	4798346	4798515	E073	40324
chr9	4798576	4798704	E073	40554
chr9	4798724	4798764	E073	40702
chr9	4798789	4798958	E073	40767
chr9	4805315	4805861	E073	47293
chr9	4717885	4718084	E074	-39938
chr9	4718290	4718360	E074	-39662
chr9	4762172	4763668	E074	4150
chr9	4770605	4770716	E074	12583
chr9	4797361	4798268	E074	39339
chr9	4798346	4798515	E074	40324
chr9	4798576	4798704	E074	40554
chr9	4798724	4798764	E074	40702
chr9	4798789	4798958	E074	40767
chr9	4799014	4799100	E074	40992
chr9	4799186	4799253	E074	41164
chr9	4799517	4799573	E074	41495
chr9	4799821	4800050	E074	41799
chr9	4738822	4738894	E081	-19128
chr9	4738822	4738894	E082	-19128

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr9	4739872	4742568	E067	-15454
chr9	4791960	4794016	E067	33938
chr9	4739872	4742568	E068	-15454
chr9	4791960	4794016	E068	33938
chr9	4739872	4742568	E069	-15454
chr9	4791960	4794016	E069	33938
chr9	4739872	4742568	E070	-15454
chr9	4791960	4794016	E070	33938
chr9	4739872	4742568	E071	-15454
chr9	4791960	4794016	E071	33938
chr9	4739872	4742568	E072	-15454
chr9	4791960	4794016	E072	33938
chr9	4739872	4742568	E073	-15454
chr9	4791960	4794016	E073	33938
chr9	4739872	4742568	E074	-15454
chr9	4791960	4794016	E074	33938
chr9	4791960	4794016	E081	33938
chr9	4739872	4742568	E082	-15454
chr9	4791960	4794016	E082	33938