rs8179953

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

EPHB1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0271 (8118/29940,GnomAD)
A=0270 (7869/29118,TOPMED)
A=0254 (1271/5008,1000G)
A=0290 (1118/3854,ALSPAC)
A=0306 (1133/3708,TWINSUK)

Position: chr3:135235483 (GRCh38.p7) (3q22.2)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 60 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 3	NC_000003.12:g.135235483G>A
GRCh37.p13 chr 3	NC_000003.11:g.134954325G>A

Gene: EPHB1, EPH receptor B1(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
EPHB1 transcript	NM_004441.4:c.	N/A	Intron Variant
EPHB1 transcript variant X4	XM_011512542.1:c.	N/A	Intron Variant
EPHB1 transcript variant X1	XM_017005866.1:c.	N/A	Intron Variant
EPHB1 transcript variant X2	XM_017005867.1:c.	N/A	Intron Variant
EPHB1 transcript variant X3	XM_017005868.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.764	A=0.236
1000Genomes	American	Sub	694	G=0.730	A=0.270
1000Genomes	East Asian	Sub	1008	G=0.761	A=0.239
1000Genomes	Europe	Sub	1006	G=0.697	A=0.303
1000Genomes	Global	Study-wide	5008	G=0.746	A=0.254
1000Genomes	South Asian	Sub	978	G=0.770	A=0.230
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.710	A=0.290
The Genome Aggregation Database	African	Sub	8724	G=0.747	A=0.253
The Genome Aggregation Database	American	Sub	838	G=0.760	A=0.240
The Genome Aggregation Database	East Asian	Sub	1622	G=0.774	A=0.226
The Genome Aggregation Database	Europe	Sub	18454	G=0.716	A=0.283
The Genome Aggregation Database	Global	Study-wide	29940	G=0.728	A=0.271
The Genome Aggregation Database	Other	Sub	302	G=0.600	A=0.400
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.729	A=0.270
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.694	A=0.306

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
rs8179953	0.000929	nicotine smoking	19268276

eQTL of rs8179953 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 rs8179953 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 )
chr3	134911896	134912046	E067	-42279
chr3	134947768	134947856	E068	-6469
chr3	134947910	134948328	E068	-5997
chr3	134956300	134956509	E068	1975
chr3	134911896	134912046	E069	-42279
chr3	134947061	134947417	E069	-6908
chr3	134947547	134947606	E069	-6719
chr3	134947768	134947856	E069	-6469
chr3	134947910	134948328	E069	-5997
chr3	134959676	134959733	E069	5351
chr3	134935612	134935835	E070	-18490
chr3	134947061	134947417	E070	-6908
chr3	134947547	134947606	E070	-6719
chr3	134947768	134947856	E070	-6469
chr3	134947910	134948328	E070	-5997
chr3	134950590	134951078	E070	-3247
chr3	134951180	134951325	E070	-3000
chr3	134957036	134957691	E070	2711
chr3	134957790	134958400	E070	3465
chr3	134958470	134958681	E070	4145
chr3	134987863	134987983	E070	33538
chr3	134988100	134988300	E070	33775
chr3	134990193	134990318	E070	35868
chr3	134990517	134990695	E070	36192
chr3	134990897	134991013	E070	36572
chr3	134991153	134991223	E070	36828
chr3	134911896	134912046	E071	-42279
chr3	134947547	134947606	E071	-6719
chr3	134947768	134947856	E071	-6469
chr3	134947910	134948328	E071	-5997
chr3	134957790	134958400	E071	3465
chr3	134958470	134958681	E071	4145
chr3	134959376	134959527	E071	5051
chr3	134911896	134912046	E072	-42279
chr3	134947910	134948328	E072	-5997
chr3	134911896	134912046	E073	-42279
chr3	134947768	134947856	E073	-6469
chr3	134947910	134948328	E073	-5997
chr3	134911896	134912046	E074	-42279
chr3	134947768	134947856	E081	-6469
chr3	134956300	134956509	E081	1975
chr3	134957036	134957691	E081	2711
chr3	134957790	134958400	E081	3465
chr3	134958470	134958681	E081	4145
chr3	134990193	134990318	E081	35868
chr3	134990517	134990695	E081	36192
chr3	134990897	134991013	E081	36572
chr3	134991153	134991223	E081	36828
chr3	134945034	134945256	E082	-9069
chr3	134945733	134945832	E082	-8493
chr3	134956300	134956509	E082	1975
chr3	134957036	134957691	E082	2711
chr3	134957790	134958400	E082	3465
chr3	134958470	134958681	E082	4145
chr3	134959376	134959527	E082	5051
chr3	134959676	134959733	E082	5351
chr3	134990193	134990318	E082	35868
chr3	134990517	134990695	E082	36192
chr3	134990897	134991013	E082	36572
chr3	134991153	134991223	E082	36828