rs11900784

Organism: Homo sapiens

Alleles: A>T

Gene : Feature

ANTXR1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0338 (10119/29928,GnomAD)
T=0430 (12530/29116,TOPMED)
A==0485 (2431/5008,1000G)
T=0133 (512/3854,ALSPAC)
T=0127 (471/3708,TWINSUK)

Position: chr2:69045364 (GRCh38.p7) (2p13.3)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 125 Enhancers around

Promoter: 10 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.69045364A>T
GRCh37.p13 chr 2	NC_000002.11:g.69272496A>T
ANTXR1 RefSeqGene	NG_012649.1:g.37221A>T

Gene: ANTXR1, anthrax toxin receptor 1(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ANTXR1 transcript variant 3	NM_018153.3:c.	N/A	Intron Variant
ANTXR1 transcript variant 1	NM_032208.2:c.	N/A	Intron Variant
ANTXR1 transcript variant 2	NM_053034.2:c.	N/A	Intron Variant
ANTXR1 transcript variant X1	XM_017005075.1:c.	N/A	Intron Variant
ANTXR1 transcript variant X2	XM_017005076.1:c.	N/A	Intron Variant
ANTXR1 transcript variant X3	XM_017005077.1:c.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.197	T=0.803
1000Genomes	American	Sub	694	A=0.530	T=0.470
1000Genomes	East Asian	Sub	1008	A=0.292	T=0.708
1000Genomes	Europe	Sub	1006	A=0.853	T=0.147
1000Genomes	Global	Study-wide	5008	A=0.485	T=0.515
1000Genomes	South Asian	Sub	978	A=0.660	T=0.340
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.867	T=0.133
The Genome Aggregation Database	African	Sub	8700	A=0.300	T=0.700
The Genome Aggregation Database	American	Sub	834	A=0.560	T=0.440
The Genome Aggregation Database	East Asian	Sub	1606	A=0.319	T=0.681
The Genome Aggregation Database	Europe	Sub	18486	A=0.865	T=0.135
The Genome Aggregation Database	Global	Study-wide	29928	A=0.661	T=0.338
The Genome Aggregation Database	Other	Sub	302	A=0.760	T=0.240
Trans-Omics for Precision Medicine	Global	Study-wide	29116	A=0.569	T=0.430
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.873	T=0.127

PMID	Title	Author	Journal
23542338	A genomewide association study of smoking relapse in four European population-based samples.	Tozzi F	Psychiatr Genet

SNP ID	p-value	Traits	Study
rs11900784	3.09E-06	nicotine dependence (smoking)	23542338

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

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 )
chr2	69258684	69258783	E067	-13713
chr2	69258784	69258846	E067	-13650
chr2	69304289	69304410	E067	31793
chr2	69304491	69304623	E067	31995
chr2	69304874	69304924	E067	32378
chr2	69309437	69310358	E067	36941
chr2	69310402	69310589	E067	37906
chr2	69310632	69310787	E067	38136
chr2	69310838	69310960	E067	38342
chr2	69244328	69244586	E068	-27910
chr2	69244803	69244899	E068	-27597
chr2	69244971	69245391	E068	-27105
chr2	69247633	69248104	E068	-24392
chr2	69248153	69248213	E068	-24283
chr2	69248273	69248410	E068	-24086
chr2	69268366	69268544	E068	-3952
chr2	69294027	69294071	E068	21531
chr2	69294181	69294231	E068	21685
chr2	69294333	69294441	E068	21837
chr2	69294473	69294572	E068	21977
chr2	69294730	69294793	E068	22234
chr2	69294831	69294894	E068	22335
chr2	69304289	69304410	E068	31793
chr2	69304491	69304623	E068	31995
chr2	69304874	69304924	E068	32378
chr2	69309437	69310358	E068	36941
chr2	69310402	69310589	E068	37906
chr2	69310632	69310787	E068	38136
chr2	69310838	69310960	E068	38342
chr2	69311346	69311398	E068	38850
chr2	69244328	69244586	E069	-27910
chr2	69257740	69258416	E069	-14080
chr2	69258684	69258783	E069	-13713
chr2	69258784	69258846	E069	-13650
chr2	69294181	69294231	E069	21685
chr2	69294333	69294441	E069	21837
chr2	69294473	69294572	E069	21977
chr2	69294730	69294793	E069	22234
chr2	69294831	69294894	E069	22335
chr2	69309437	69310358	E069	36941
chr2	69310402	69310589	E069	37906
chr2	69310632	69310787	E069	38136
chr2	69244803	69244899	E070	-27597
chr2	69247633	69248104	E070	-24392
chr2	69248153	69248213	E070	-24283
chr2	69248273	69248410	E070	-24086
chr2	69248832	69248886	E070	-23610
chr2	69249708	69250003	E070	-22493
chr2	69257740	69258416	E070	-14080
chr2	69258684	69258783	E070	-13713
chr2	69258784	69258846	E070	-13650
chr2	69258977	69259069	E070	-13427
chr2	69260747	69261113	E070	-11383
chr2	69304289	69304410	E070	31793
chr2	69304491	69304623	E070	31995
chr2	69304874	69304924	E070	32378
chr2	69310632	69310787	E070	38136
chr2	69310838	69310960	E070	38342
chr2	69243855	69244220	E071	-28276
chr2	69244328	69244586	E071	-27910
chr2	69244803	69244899	E071	-27597
chr2	69244971	69245391	E071	-27105
chr2	69247633	69248104	E071	-24392
chr2	69248153	69248213	E071	-24283
chr2	69248273	69248410	E071	-24086
chr2	69257740	69258416	E071	-14080
chr2	69258684	69258783	E071	-13713
chr2	69258784	69258846	E071	-13650
chr2	69258977	69259069	E071	-13427
chr2	69259559	69259657	E071	-12839
chr2	69268366	69268544	E071	-3952
chr2	69288635	69288889	E071	16139
chr2	69289181	69289240	E071	16685
chr2	69289306	69289368	E071	16810
chr2	69289474	69289645	E071	16978
chr2	69289780	69289955	E071	17284
chr2	69304289	69304410	E071	31793
chr2	69304491	69304623	E071	31995
chr2	69309129	69309376	E071	36633
chr2	69309437	69310358	E071	36941
chr2	69310402	69310589	E071	37906
chr2	69310632	69310787	E071	38136
chr2	69310838	69310960	E071	38342
chr2	69311346	69311398	E071	38850
chr2	69304289	69304410	E072	31793
chr2	69304491	69304623	E072	31995
chr2	69304874	69304924	E072	32378
chr2	69309437	69310358	E072	36941
chr2	69310402	69310589	E072	37906
chr2	69262131	69262237	E073	-10259
chr2	69294181	69294231	E073	21685
chr2	69294333	69294441	E073	21837
chr2	69294473	69294572	E073	21977
chr2	69294730	69294793	E073	22234
chr2	69294831	69294894	E073	22335
chr2	69309129	69309376	E073	36633
chr2	69309437	69310358	E073	36941
chr2	69310402	69310589	E073	37906
chr2	69310632	69310787	E073	38136
chr2	69310838	69310960	E073	38342
chr2	69311346	69311398	E073	38850
chr2	69244328	69244586	E074	-27910
chr2	69244971	69245391	E074	-27105
chr2	69247633	69248104	E074	-24392
chr2	69248153	69248213	E074	-24283
chr2	69258684	69258783	E074	-13713
chr2	69258784	69258846	E074	-13650
chr2	69258977	69259069	E074	-13427
chr2	69304289	69304410	E074	31793
chr2	69304491	69304623	E074	31995
chr2	69304874	69304924	E074	32378
chr2	69308436	69308547	E074	35940
chr2	69309129	69309376	E074	36633
chr2	69309437	69310358	E074	36941
chr2	69310402	69310589	E074	37906
chr2	69310632	69310787	E074	38136
chr2	69310838	69310960	E074	38342
chr2	69311346	69311398	E074	38850
chr2	69316437	69316816	E074	43941
chr2	69247633	69248104	E081	-24392
chr2	69244803	69244899	E082	-27597
chr2	69244971	69245391	E082	-27105
chr2	69247633	69248104	E082	-24392
chr2	69248153	69248213	E082	-24283
chr2	69248273	69248410	E082	-24086

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	69239556	69242187	E067	-30309
chr2	69239556	69242187	E068	-30309
chr2	69239556	69242187	E069	-30309
chr2	69239556	69242187	E070	-30309
chr2	69239556	69242187	E071	-30309
chr2	69239556	69242187	E072	-30309
chr2	69239556	69242187	E073	-30309
chr2	69239556	69242187	E074	-30309
chr2	69239556	69242187	E081	-30309
chr2	69239556	69242187	E082	-30309

rs11900784

Genomic Coordinates

Gene: ANTXR1, anthrax toxin receptor 1(plus strand)

Population Frequency

P-Value

eQTL of rs11900784 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs11900784 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Promoter Annotation (GRCh37.p13)