rs7103228

Organism: Homo sapiens

Alleles: G>A / G>T

Gene : Feature

GRIK4 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0249 (7430/29842,GnomAD)
A=0310 (9027/29118,TOPMED)
A=0306 (1534/5008,1000G)

Position: chr11:120710058 (GRCh38.p7) (11q23.3)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 54 Enhancers around

Promoter: 9 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 11	NC_000011.10:g.120710058G>A
GRCh38.p7 chr 11	NC_000011.10:g.120710058G>T
GRCh37.p13 chr 11	NC_000011.9:g.120580767G>A
GRCh37.p13 chr 11	NC_000011.9:g.120580767G>T
GRIK4 RefSeqGene	LRG_1012
GRIK4 RefSeqGene	LRG_1012

Gene: GRIK4, glutamate ionotropic receptor kainate type subunit 4(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
GRIK4 transcript variant 1	NM_001282470.2:c.	N/A	Intron Variant
GRIK4 transcript variant 3	NM_001282473.2:c.	N/A	Intron Variant
GRIK4 transcript variant 2	NM_014619.4:c.	N/A	Intron Variant
GRIK4 transcript variant X1	XM_011542784.1:c.	N/A	Intron Variant
GRIK4 transcript variant X2	XM_017017621.1:c.	N/A	Intron Variant
GRIK4 transcript variant X3	XM_017017622.1:c.	N/A	Intron Variant
GRIK4 transcript variant X4	XM_011542786.2:c.	N/A	Genic Upstream Transcript Variant
GRIK4 transcript variant X5	XM_011542787.2:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.449	A=0.551
1000Genomes	American	Sub	694	G=0.850	A=0.150
1000Genomes	East Asian	Sub	1008	G=0.752	A=0.248
1000Genomes	Europe	Sub	1006	G=0.849	A=0.151
1000Genomes	Global	Study-wide	5008	G=0.694	A=0.306
1000Genomes	South Asian	Sub	978	G=0.690	A=0.310
The Genome Aggregation Database	African	Sub	8692	G=0.520	A=0.480
The Genome Aggregation Database	American	Sub	838	G=0.870	A=0.130
The Genome Aggregation Database	East Asian	Sub	1612	G=0.733	A=0.267
The Genome Aggregation Database	Europe	Sub	18400	G=0.854	A=0.145
The Genome Aggregation Database	Global	Study-wide	29842	G=0.751	A=0.249
The Genome Aggregation Database	Other	Sub	300	G=0.850	A=0.150
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.690	A=0.310

PMID	Title	Author	Journal
19268276	Genome-wide association study of smoking initiation and current smoking.	Vink JM	Am J Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs7103228	0.000775	nicotine smoking	19268276

eQTL of rs7103228 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 rs7103228 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 )
chr11	78728786	78729924	E067	35554
chr11	78730042	78730114	E067	36810
chr11	78730126	78730300	E067	36894
chr11	78730624	78730684	E067	37392
chr11	78730859	78730946	E067	37627
chr11	78738517	78738699	E067	45285
chr11	78738728	78738793	E067	45496
chr11	78651417	78652477	E068	-40755
chr11	78673878	78673986	E068	-19246
chr11	78736372	78737245	E068	43140
chr11	78737281	78737617	E068	44049
chr11	78672147	78672686	E070	-20546
chr11	78673878	78673986	E071	-19246
chr11	78730042	78730114	E071	36810
chr11	78730126	78730300	E071	36894
chr11	78730624	78730684	E071	37392
chr11	78730859	78730946	E071	37627
chr11	78731147	78731214	E071	37915
chr11	78731954	78732071	E071	38722
chr11	78733444	78733511	E071	40212
chr11	78730042	78730114	E072	36810
chr11	78730126	78730300	E072	36894
chr11	78730624	78730684	E072	37392
chr11	78730859	78730946	E072	37627
chr11	78731147	78731214	E072	37915
chr11	78673878	78673986	E073	-19246
chr11	78730126	78730300	E074	36894
chr11	78730624	78730684	E074	37392
chr11	78730859	78730946	E074	37627
chr11	78731954	78732071	E074	38722
chr11	78644588	78644773	E081	-48459
chr11	78644865	78644962	E081	-48270
chr11	78673878	78673986	E081	-19246
chr11	78674257	78674452	E081	-18780
chr11	78730859	78730946	E081	37627
chr11	78731147	78731214	E081	37915
chr11	78649745	78649835	E082	-43397
chr11	78649863	78649928	E082	-43304
chr11	78649956	78650028	E082	-43204
chr11	78650064	78650339	E082	-42893
chr11	78650359	78650466	E082	-42766
chr11	78665260	78665820	E082	-27412
chr11	78665868	78665958	E082	-27274
chr11	78665962	78666052	E082	-27180
chr11	78680232	78680291	E082	-12941
chr11	78680398	78680565	E082	-12667
chr11	78702090	78702140	E082	8858
chr11	78702441	78702481	E082	9209
chr11	78702636	78702684	E082	9404
chr11	78741409	78741459	E082	48177
chr11	78741476	78741899	E082	48244
chr11	78742062	78742188	E082	48830
chr11	78742246	78742324	E082	49014
chr11	78742376	78742469	E082	49144

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr11	78672701	78673809	E067	-19423
chr11	78672701	78673809	E068	-19423
chr11	78672701	78673809	E069	-19423
chr11	78672701	78673809	E070	-19423
chr11	78672701	78673809	E071	-19423
chr11	78672701	78673809	E072	-19423
chr11	78672701	78673809	E073	-19423
chr11	78672701	78673809	E074	-19423
chr11	78672701	78673809	E082	-19423