rs2857839

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

GRK4 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T==0362 (10852/29918,GnomAD)
T==0327 (9539/29118,TOPMED)
T==0328 (1643/5008,1000G)
T==0424 (1633/3854,ALSPAC)
T==0413 (1531/3708,TWINSUK)

Position: chr4:3034903 (GRCh38.p7) (4p16.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 23 Enhancers around

Promoter: 38 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 4	NC_000004.12:g.3034903T>C
GRCh37.p13 chr 4	NC_000004.11:g.3036630T>C
GRK4 RefSeqGene	NG_029102.1:g.76288T>C

Gene: GRK4, G protein-coupled receptor kinase 4(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
GRK4 transcript variant 2	NM_001004056.1:c.	N/A	Intron Variant
GRK4 transcript variant 3	NM_001004057.1:c.	N/A	Intron Variant
GRK4 transcript variant 4	NM_005307.2:c.	N/A	Intron Variant
GRK4 transcript variant 1	NM_182982.2:c.	N/A	Intron Variant
GRK4 transcript variant X23	XM_005247962.3:c.	N/A	Intron Variant
GRK4 transcript variant X24	XM_006713880.3:c.	N/A	Intron Variant
GRK4 transcript variant X1	XM_011513447.2:c.	N/A	Intron Variant
GRK4 transcript variant X2	XM_011513448.2:c.	N/A	Intron Variant
GRK4 transcript variant X5	XM_011513449.2:c.	N/A	Intron Variant
GRK4 transcript variant X6	XM_011513450.2:c.	N/A	Intron Variant
GRK4 transcript variant X7	XM_011513451.2:c.	N/A	Intron Variant
GRK4 transcript variant X8	XM_011513452.2:c.	N/A	Intron Variant
GRK4 transcript variant X9	XM_011513453.2:c.	N/A	Intron Variant
GRK4 transcript variant X10	XM_011513454.2:c.	N/A	Intron Variant
GRK4 transcript variant X13	XM_011513455.2:c.	N/A	Intron Variant
GRK4 transcript variant X16	XM_011513456.2:c.	N/A	Intron Variant
GRK4 transcript variant X3	XM_017008052.1:c.	N/A	Intron Variant
GRK4 transcript variant X4	XM_017008053.1:c.	N/A	Intron Variant
GRK4 transcript variant X12	XM_017008054.1:c.	N/A	Intron Variant
GRK4 transcript variant X14	XM_017008055.1:c.	N/A	Intron Variant
GRK4 transcript variant X15	XM_017008056.1:c.	N/A	Intron Variant
GRK4 transcript variant X20	XM_017008057.1:c.	N/A	Intron Variant
GRK4 transcript variant X21	XM_017008058.1:c.	N/A	Intron Variant
GRK4 transcript variant X20	XM_017008059.1:c.	N/A	Intron Variant
GRK4 transcript variant X21	XM_017008060.1:c.	N/A	Intron Variant
GRK4 transcript variant X22	XM_017008061.1:c.	N/A	Intron Variant
GRK4 transcript variant X22	XM_017008062.1:c.	N/A	Intron Variant
GRK4 transcript variant X25	XM_017008063.1:c.	N/A	Intron Variant
GRK4 transcript variant X26	XM_017008064.1:c.	N/A	Intron Variant
GRK4 transcript variant X30	XM_017008065.1:c.	N/A	Intron Variant
GRK4 transcript variant X31	XM_017008066.1:c.	N/A	Intron Variant
GRK4 transcript variant X27	XM_011513457.2:c.	N/A	Genic Downstream Transcript Variant
GRK4 transcript variant X28	XR_001741211.1:n.	N/A	Intron Variant
GRK4 transcript variant X11	XR_924941.2:n.	N/A	Intron Variant
GRK4 transcript variant X29	XR_924943.2:n.	N/A	Intron Variant
GRK4 transcript variant X17	XR_001741210.1:n.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.166	C=0.834
1000Genomes	American	Sub	694	T=0.360	C=0.640
1000Genomes	East Asian	Sub	1008	T=0.469	C=0.531
1000Genomes	Europe	Sub	1006	T=0.428	C=0.572
1000Genomes	Global	Study-wide	5008	T=0.328	C=0.672
1000Genomes	South Asian	Sub	978	T=0.270	C=0.730
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.424	C=0.576
The Genome Aggregation Database	African	Sub	8700	T=0.220	C=0.780
The Genome Aggregation Database	American	Sub	836	T=0.360	C=0.640
The Genome Aggregation Database	East Asian	Sub	1618	T=0.502	C=0.498
The Genome Aggregation Database	Europe	Sub	18462	T=0.417	C=0.582
The Genome Aggregation Database	Global	Study-wide	29918	T=0.362	C=0.637
The Genome Aggregation Database	Other	Sub	302	T=0.350	C=0.650
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.327	C=0.672
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.413	C=0.587

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res
23691058	Dosage transmission disequilibrium test (dTDT) for linkage and association detection.	Zhang Z	PLoS One

P-Value

SNP ID	p-value	Traits	Study
rs2857839	0.0000066	alcohol dependence	23691058
rs2857839	0.00025	alcohol dependence	20201924

eQTL of rs2857839 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr4:3036630	HTT-AS	ENSG00000251075.1	T>C	5.3115e-6	-39611	Cerebellum
Chr4:3036630	HTT-AS	ENSG00000251075.1	T>C	2.6858e-7	-39611	Cerebellar_Hemisphere

meQTL of rs2857839 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg02754929	chr4:3295736		-0.0546368870238406	7.9349e-12

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	3079605	3079913	E067	42975
chr4	3044526	3044726	E068	7896
chr4	3078331	3078523	E068	41701
chr4	3038942	3039374	E069	2312
chr4	3044394	3044491	E069	7764
chr4	3078331	3078523	E069	41701
chr4	3079605	3079913	E069	42975
chr4	3020999	3021079	E070	-15551
chr4	3044526	3044726	E070	7896
chr4	3078331	3078523	E070	41701
chr4	3079605	3079913	E070	42975
chr4	3040490	3040532	E071	3860
chr4	3039580	3039659	E072	2950
chr4	3044394	3044491	E072	7764
chr4	3047041	3047732	E072	10411
chr4	3044394	3044491	E073	7764
chr4	3044526	3044726	E073	7896
chr4	3044394	3044491	E074	7764
chr4	3044526	3044726	E074	7896
chr4	3044394	3044491	E081	7764
chr4	3078331	3078523	E081	41701
chr4	3079605	3079913	E081	42975
chr4	3078331	3078523	E082	41701

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr4	3043020	3043912	E067	6390
chr4	3044039	3044139	E067	7409
chr4	3074688	3076747	E067	38058
chr4	3076797	3077632	E067	40167
chr4	3043020	3043912	E068	6390
chr4	3044039	3044139	E068	7409
chr4	3074688	3076747	E068	38058
chr4	3076797	3077632	E068	40167
chr4	3043020	3043912	E069	6390
chr4	3044039	3044139	E069	7409
chr4	3074688	3076747	E069	38058
chr4	3076797	3077632	E069	40167
chr4	3043020	3043912	E070	6390
chr4	3044039	3044139	E070	7409
chr4	3074688	3076747	E070	38058
chr4	3076797	3077632	E070	40167
chr4	3043020	3043912	E071	6390
chr4	3044039	3044139	E071	7409
chr4	3074688	3076747	E071	38058
chr4	3076797	3077632	E071	40167
chr4	3043020	3043912	E072	6390
chr4	3044039	3044139	E072	7409
chr4	3074688	3076747	E072	38058
chr4	3076797	3077632	E072	40167
chr4	3043020	3043912	E073	6390
chr4	3044039	3044139	E073	7409
chr4	3074688	3076747	E073	38058
chr4	3076797	3077632	E073	40167
chr4	3043020	3043912	E074	6390
chr4	3044039	3044139	E074	7409
chr4	3074688	3076747	E074	38058
chr4	3076797	3077632	E074	40167
chr4	3074688	3076747	E081	38058
chr4	3076797	3077632	E081	40167
chr4	3043020	3043912	E082	6390
chr4	3044039	3044139	E082	7409
chr4	3074688	3076747	E082	38058
chr4	3076797	3077632	E082	40167