rs2857845

Organism: Homo sapiens

Alleles: A>T

Gene : Feature

GRK4 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0096 (2882/29968,GnomAD)
T=0096 (2816/29118,TOPMED)
T=0073 (368/5008,1000G)
T=0168 (649/3854,ALSPAC)
T=0165 (610/3708,TWINSUK)

Position: chr4:3026386 (GRCh38.p7) (4p16.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 25 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.3026386A>T
GRCh37.p13 chr 4	NC_000004.11:g.3028113A>T
GRK4 RefSeqGene	NG_029102.1:g.67771A>T

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	A=0.992	T=0.008
1000Genomes	American	Sub	694	A=0.900	T=0.100
1000Genomes	East Asian	Sub	1008	A=0.999	T=0.001
1000Genomes	Europe	Sub	1006	A=0.824	T=0.176
1000Genomes	Global	Study-wide	5008	A=0.927	T=0.073
1000Genomes	South Asian	Sub	978	A=0.890	T=0.110
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.832	T=0.168
The Genome Aggregation Database	African	Sub	8722	A=0.965	T=0.035
The Genome Aggregation Database	American	Sub	838	A=0.910	T=0.090
The Genome Aggregation Database	East Asian	Sub	1622	A=0.999	T=0.001
The Genome Aggregation Database	Europe	Sub	18484	A=0.867	T=0.132
The Genome Aggregation Database	Global	Study-wide	29968	A=0.903	T=0.096
The Genome Aggregation Database	Other	Sub	302	A=0.810	T=0.190
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.903	T=0.096
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.835	T=0.165

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs2857845	0.00036	alcohol dependence	21314694

eQTL of rs2857845 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 rs2857845 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	3044526	3044726	E068	16413
chr4	2978913	2979167	E069	-48946
chr4	3038942	3039374	E069	10829
chr4	3044394	3044491	E069	16281
chr4	3020999	3021079	E070	-7034
chr4	3044526	3044726	E070	16413
chr4	2978913	2979167	E071	-48946
chr4	2979320	2979482	E071	-48631
chr4	2979520	2979734	E071	-48379
chr4	2980195	2980538	E071	-47575
chr4	3040490	3040532	E071	12377
chr4	2978913	2979167	E072	-48946
chr4	3039580	3039659	E072	11467
chr4	3044394	3044491	E072	16281
chr4	3047041	3047732	E072	18928
chr4	2978913	2979167	E073	-48946
chr4	2979320	2979482	E073	-48631
chr4	2979520	2979734	E073	-48379
chr4	3044394	3044491	E073	16281
chr4	3044526	3044726	E073	16413
chr4	2979520	2979734	E074	-48379
chr4	3044394	3044491	E074	16281
chr4	3044526	3044726	E074	16413
chr4	2978913	2979167	E081	-48946
chr4	3044394	3044491	E081	16281

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr4	3043020	3043912	E067	14907
chr4	3044039	3044139	E067	15926
chr4	3074688	3076747	E067	46575
chr4	3076797	3077632	E067	48684
chr4	3043020	3043912	E068	14907
chr4	3044039	3044139	E068	15926
chr4	3074688	3076747	E068	46575
chr4	3076797	3077632	E068	48684
chr4	3043020	3043912	E069	14907
chr4	3044039	3044139	E069	15926
chr4	3074688	3076747	E069	46575
chr4	3076797	3077632	E069	48684
chr4	3043020	3043912	E070	14907
chr4	3044039	3044139	E070	15926
chr4	3074688	3076747	E070	46575
chr4	3076797	3077632	E070	48684
chr4	3043020	3043912	E071	14907
chr4	3044039	3044139	E071	15926
chr4	3074688	3076747	E071	46575
chr4	3076797	3077632	E071	48684
chr4	3043020	3043912	E072	14907
chr4	3044039	3044139	E072	15926
chr4	3074688	3076747	E072	46575
chr4	3076797	3077632	E072	48684
chr4	3043020	3043912	E073	14907
chr4	3044039	3044139	E073	15926
chr4	3074688	3076747	E073	46575
chr4	3076797	3077632	E073	48684
chr4	3043020	3043912	E074	14907
chr4	3044039	3044139	E074	15926
chr4	3074688	3076747	E074	46575
chr4	3076797	3077632	E074	48684
chr4	3074688	3076747	E081	46575
chr4	3076797	3077632	E081	48684
chr4	3043020	3043912	E082	14907
chr4	3044039	3044139	E082	15926
chr4	3074688	3076747	E082	46575
chr4	3076797	3077632	E082	48684