rs6709476

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

TCF7L1 : Intron Variant
LOC102724579 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0243 (7283/29926,GnomAD)
A=0337 (9832/29116,TOPMED)
A=0282 (1412/5008,1000G)
A=0086 (331/3854,ALSPAC)
A=0089 (331/3708,TWINSUK)

Position: chr2:85216801 (GRCh38.p7) (2p11.2)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 272 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.85216801G>A
GRCh37.p13 chr 2	NC_000002.11:g.85443924G>A

Gene: TCF7L1, transcription factor 7 like 1(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TCF7L1 transcript	NM_031283.2:c.	N/A	Intron Variant
TCF7L1 transcript variant X1	XM_006712109.2:c.	N/A	Intron Variant

Gene: LOC102724579, uncharacterized LOC102724579(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC102724579 transcript	NR_136323.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.278	A=0.722
1000Genomes	American	Sub	694	G=0.740	A=0.260
1000Genomes	East Asian	Sub	1008	G=0.918	A=0.082
1000Genomes	Europe	Sub	1006	G=0.912	A=0.088
1000Genomes	Global	Study-wide	5008	G=0.718	A=0.282
1000Genomes	South Asian	Sub	978	G=0.890	A=0.110
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.914	A=0.086
The Genome Aggregation Database	African	Sub	8684	G=0.368	A=0.632
The Genome Aggregation Database	American	Sub	836	G=0.810	A=0.190
The Genome Aggregation Database	East Asian	Sub	1616	G=0.925	A=0.075
The Genome Aggregation Database	Europe	Sub	18488	G=0.920	A=0.079
The Genome Aggregation Database	Global	Study-wide	29926	G=0.756	A=0.243
The Genome Aggregation Database	Other	Sub	302	G=0.880	A=0.120
Trans-Omics for Precision Medicine	Global	Study-wide	29116	G=0.662	A=0.337
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.911	A=0.089

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
rs6709476	5.57E-05	nicotine smoking	19268276

eQTL of rs6709476 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 rs6709476 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 )
chr2	85441555	85441776	E067	-2148
chr2	85442016	85442203	E067	-1721
chr2	85442269	85443582	E067	-342
chr2	85443710	85443843	E067	-81
chr2	85443902	85443952	E067	0
chr2	85444113	85444414	E067	189
chr2	85458836	85459209	E067	14912
chr2	85462118	85462341	E067	18194
chr2	85462492	85462636	E067	18568
chr2	85462762	85462812	E067	18838
chr2	85467382	85467532	E067	23458
chr2	85467945	85468036	E067	24021
chr2	85468124	85468478	E067	24200
chr2	85470345	85470896	E067	26421
chr2	85470898	85471080	E067	26974
chr2	85473458	85473682	E067	29534
chr2	85473691	85473877	E067	29767
chr2	85473906	85474134	E067	29982
chr2	85475807	85476540	E067	31883
chr2	85476587	85476663	E067	32663
chr2	85476833	85476900	E067	32909
chr2	85477255	85477421	E067	33331
chr2	85493184	85493331	E067	49260
chr2	85493365	85493858	E067	49441
chr2	85402457	85402507	E068	-41417
chr2	85402520	85403121	E068	-40803
chr2	85403180	85403356	E068	-40568
chr2	85406638	85406956	E068	-36968
chr2	85406979	85407079	E068	-36845
chr2	85407165	85407240	E068	-36684
chr2	85407690	85407900	E068	-36024
chr2	85422045	85422116	E068	-21808
chr2	85423203	85423402	E068	-20522
chr2	85423964	85424207	E068	-19717
chr2	85440626	85440842	E068	-3082
chr2	85440918	85440968	E068	-2956
chr2	85440988	85441076	E068	-2848
chr2	85441116	85441548	E068	-2376
chr2	85441555	85441776	E068	-2148
chr2	85443710	85443843	E068	-81
chr2	85443902	85443952	E068	0
chr2	85444113	85444414	E068	189
chr2	85458836	85459209	E068	14912
chr2	85459219	85459386	E068	15295
chr2	85462118	85462341	E068	18194
chr2	85462492	85462636	E068	18568
chr2	85462762	85462812	E068	18838
chr2	85467382	85467532	E068	23458
chr2	85467945	85468036	E068	24021
chr2	85468124	85468478	E068	24200
chr2	85473196	85473366	E068	29272
chr2	85473458	85473682	E068	29534
chr2	85473691	85473877	E068	29767
chr2	85473906	85474134	E068	29982
chr2	85474529	85474626	E068	30605
chr2	85474715	85475031	E068	30791
chr2	85475067	85475187	E068	31143
chr2	85475365	85475579	E068	31441
chr2	85475807	85476540	E068	31883
chr2	85476587	85476663	E068	32663
chr2	85476833	85476900	E068	32909
chr2	85477255	85477421	E068	33331
chr2	85481585	85481663	E068	37661
chr2	85481777	85481956	E068	37853
chr2	85482035	85483887	E068	38111
chr2	85484160	85484250	E068	40236
chr2	85484269	85484340	E068	40345
chr2	85484460	85484823	E068	40536
chr2	85484890	85485089	E068	40966
chr2	85485169	85485308	E068	41245
chr2	85485442	85485502	E068	41518
chr2	85485537	85485667	E068	41613
chr2	85493365	85493858	E068	49441
chr2	85415955	85416005	E069	-27919
chr2	85416126	85417492	E069	-26432
chr2	85442016	85442203	E069	-1721
chr2	85442269	85443582	E069	-342
chr2	85443710	85443843	E069	-81
chr2	85443902	85443952	E069	0
chr2	85444113	85444414	E069	189
chr2	85462118	85462341	E069	18194
chr2	85462492	85462636	E069	18568
chr2	85462762	85462812	E069	18838
chr2	85467382	85467532	E069	23458
chr2	85467945	85468036	E069	24021
chr2	85470345	85470896	E069	26421
chr2	85470898	85471080	E069	26974
chr2	85472474	85472524	E069	28550
chr2	85473196	85473366	E069	29272
chr2	85473458	85473682	E069	29534
chr2	85474715	85475031	E069	30791
chr2	85475067	85475187	E069	31143
chr2	85475365	85475579	E069	31441
chr2	85476587	85476663	E069	32663
chr2	85476833	85476900	E069	32909
chr2	85481585	85481663	E069	37661
chr2	85481777	85481956	E069	37853
chr2	85482035	85483887	E069	38111
chr2	85493184	85493331	E069	49260
chr2	85493365	85493858	E069	49441
chr2	85415955	85416005	E070	-27919
chr2	85416126	85417492	E070	-26432
chr2	85442016	85442203	E070	-1721
chr2	85443902	85443952	E070	0
chr2	85444113	85444414	E070	189
chr2	85462118	85462341	E070	18194
chr2	85472046	85472109	E070	28122
chr2	85472163	85472236	E070	28239
chr2	85472353	85472403	E070	28429
chr2	85472474	85472524	E070	28550
chr2	85473196	85473366	E070	29272
chr2	85473458	85473682	E070	29534
chr2	85473691	85473877	E070	29767
chr2	85473906	85474134	E070	29982
chr2	85474529	85474626	E070	30605
chr2	85474715	85475031	E070	30791
chr2	85475067	85475187	E070	31143
chr2	85475365	85475579	E070	31441
chr2	85480916	85481050	E070	36992
chr2	85481150	85481346	E070	37226
chr2	85481393	85481444	E070	37469
chr2	85481585	85481663	E070	37661
chr2	85481777	85481956	E070	37853
chr2	85482035	85483887	E070	38111
chr2	85402457	85402507	E071	-41417
chr2	85402520	85403121	E071	-40803
chr2	85403180	85403356	E071	-40568
chr2	85406310	85406592	E071	-37332
chr2	85406638	85406956	E071	-36968
chr2	85406979	85407079	E071	-36845
chr2	85407165	85407240	E071	-36684
chr2	85442016	85442203	E071	-1721
chr2	85443710	85443843	E071	-81
chr2	85443902	85443952	E071	0
chr2	85444113	85444414	E071	189
chr2	85444814	85444964	E071	890
chr2	85462118	85462341	E071	18194
chr2	85462492	85462636	E071	18568
chr2	85462762	85462812	E071	18838
chr2	85467382	85467532	E071	23458
chr2	85467945	85468036	E071	24021
chr2	85468124	85468478	E071	24200
chr2	85470345	85470896	E071	26421
chr2	85470898	85471080	E071	26974
chr2	85475365	85475579	E071	31441
chr2	85475807	85476540	E071	31883
chr2	85476587	85476663	E071	32663
chr2	85476833	85476900	E071	32909
chr2	85477255	85477421	E071	33331
chr2	85480916	85481050	E071	36992
chr2	85481150	85481346	E071	37226
chr2	85481393	85481444	E071	37469
chr2	85481585	85481663	E071	37661
chr2	85481777	85481956	E071	37853
chr2	85482035	85483887	E071	38111
chr2	85484890	85485089	E071	40966
chr2	85485442	85485502	E071	41518
chr2	85492950	85493042	E071	49026
chr2	85493184	85493331	E071	49260
chr2	85493365	85493858	E071	49441
chr2	85415955	85416005	E072	-27919
chr2	85416126	85417492	E072	-26432
chr2	85442016	85442203	E072	-1721
chr2	85443710	85443843	E072	-81
chr2	85443902	85443952	E072	0
chr2	85444113	85444414	E072	189
chr2	85448180	85448230	E072	4256
chr2	85448525	85448676	E072	4601
chr2	85458836	85459209	E072	14912
chr2	85459219	85459386	E072	15295
chr2	85462118	85462341	E072	18194
chr2	85462492	85462636	E072	18568
chr2	85462762	85462812	E072	18838
chr2	85467382	85467532	E072	23458
chr2	85470345	85470896	E072	26421
chr2	85470898	85471080	E072	26974
chr2	85472046	85472109	E072	28122
chr2	85473458	85473682	E072	29534
chr2	85473691	85473877	E072	29767
chr2	85473906	85474134	E072	29982
chr2	85475365	85475579	E072	31441
chr2	85475807	85476540	E072	31883
chr2	85476587	85476663	E072	32663
chr2	85482035	85483887	E072	38111
chr2	85442016	85442203	E073	-1721
chr2	85442269	85443582	E073	-342
chr2	85443710	85443843	E073	-81
chr2	85443902	85443952	E073	0
chr2	85444113	85444414	E073	189
chr2	85462118	85462341	E073	18194
chr2	85462492	85462636	E073	18568
chr2	85462762	85462812	E073	18838
chr2	85463985	85464308	E073	20061
chr2	85467382	85467532	E073	23458
chr2	85467945	85468036	E073	24021
chr2	85470345	85470896	E073	26421
chr2	85470898	85471080	E073	26974
chr2	85472046	85472109	E073	28122
chr2	85472163	85472236	E073	28239
chr2	85472353	85472403	E073	28429
chr2	85472474	85472524	E073	28550
chr2	85473196	85473366	E073	29272
chr2	85473458	85473682	E073	29534
chr2	85473691	85473877	E073	29767
chr2	85473906	85474134	E073	29982
chr2	85474529	85474626	E073	30605
chr2	85474715	85475031	E073	30791
chr2	85475067	85475187	E073	31143
chr2	85475365	85475579	E073	31441
chr2	85475807	85476540	E073	31883
chr2	85476587	85476663	E073	32663
chr2	85476833	85476900	E073	32909
chr2	85481585	85481663	E073	37661
chr2	85481777	85481956	E073	37853
chr2	85482035	85483887	E073	38111
chr2	85484460	85484823	E073	40536
chr2	85484890	85485089	E073	40966
chr2	85485169	85485308	E073	41245
chr2	85485442	85485502	E073	41518
chr2	85485537	85485667	E073	41613
chr2	85485850	85485890	E073	41926
chr2	85485899	85485943	E073	41975
chr2	85485976	85486085	E073	42052
chr2	85400029	85400118	E074	-43806
chr2	85402134	85402453	E074	-41471
chr2	85402457	85402507	E074	-41417
chr2	85402520	85403121	E074	-40803
chr2	85405952	85406183	E074	-37741
chr2	85406310	85406592	E074	-37332
chr2	85440626	85440842	E074	-3082
chr2	85440918	85440968	E074	-2956
chr2	85440988	85441076	E074	-2848
chr2	85441116	85441548	E074	-2376
chr2	85441555	85441776	E074	-2148
chr2	85443710	85443843	E074	-81
chr2	85443902	85443952	E074	0
chr2	85444113	85444414	E074	189
chr2	85458836	85459209	E074	14912
chr2	85459219	85459386	E074	15295
chr2	85459561	85459620	E074	15637
chr2	85459737	85459844	E074	15813
chr2	85462118	85462341	E074	18194
chr2	85462492	85462636	E074	18568
chr2	85462762	85462812	E074	18838
chr2	85467382	85467532	E074	23458
chr2	85470345	85470896	E074	26421
chr2	85470898	85471080	E074	26974
chr2	85473458	85473682	E074	29534
chr2	85473691	85473877	E074	29767
chr2	85473906	85474134	E074	29982
chr2	85481585	85481663	E074	37661
chr2	85481777	85481956	E074	37853
chr2	85482035	85483887	E074	38111
chr2	85484890	85485089	E074	40966
chr2	85485169	85485308	E074	41245
chr2	85493365	85493858	E074	49441
chr2	85442016	85442203	E081	-1721
chr2	85442269	85443582	E081	-342
chr2	85443710	85443843	E081	-81
chr2	85443902	85443952	E081	0
chr2	85444113	85444414	E081	189
chr2	85473458	85473682	E081	29534
chr2	85473691	85473877	E081	29767
chr2	85473906	85474134	E081	29982
chr2	85482035	85483887	E081	38111
chr2	85443710	85443843	E082	-81
chr2	85473196	85473366	E082	29272
chr2	85473458	85473682	E082	29534
chr2	85473691	85473877	E082	29767
chr2	85473906	85474134	E082	29982
chr2	85485976	85486085	E082	42052
chr2	85486123	85487039	E082	42199