rs1406095

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

TUB : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T==0490 (14640/29880,GnomAD)
C=0489 (14255/29118,TOPMED)
C=0496 (2484/5008,1000G)
T==0479 (1845/3854,ALSPAC)
T==0483 (1791/3708,TWINSUK)

Position: chr11:8073135 (GRCh38.p7) (11p15.4)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 456 Enhancers around

Promoter: 10 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 11	NC_000011.10:g.8073135T>C
GRCh37.p13 chr 11	NC_000011.9:g.8094682T>C
TUB RefSeqGene	NG_029912.1:g.39503T>C

Gene: TUB, tubby bipartite transcription factor(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TUB transcript variant 1	NM_003320.4:c.	N/A	Intron Variant
TUB transcript variant 2	NM_177972.2:c.	N/A	Genic Upstream Transcript Variant
TUB transcript variant X1	XM_005253109.3:c.	N/A	Intron Variant
TUB transcript variant X2	XM_011520344.2:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.504	C=0.496
1000Genomes	American	Sub	694	T=0.470	C=0.530
1000Genomes	East Asian	Sub	1008	T=0.558	C=0.442
1000Genomes	Europe	Sub	1006	T=0.518	C=0.482
1000Genomes	Global	Study-wide	5008	T=0.504	C=0.496
1000Genomes	South Asian	Sub	978	T=0.460	C=0.540
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.479	C=0.521
The Genome Aggregation Database	African	Sub	8688	T=0.515	C=0.485
The Genome Aggregation Database	American	Sub	838	T=0.440	C=0.560
The Genome Aggregation Database	East Asian	Sub	1618	T=0.515	C=0.485
The Genome Aggregation Database	Europe	Sub	18436	T=0.475	C=0.524
The Genome Aggregation Database	Global	Study-wide	29880	T=0.490	C=0.510
The Genome Aggregation Database	Other	Sub	300	T=0.660	C=0.340
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.510	C=0.489
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.483	C=0.517

PMID	Title	Author	Journal
22488850	Genome-wide search for replicable risk gene regions in alcohol and nicotine co-dependence.	Zuo L	Am J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID	p-value	Traits	Study
rs1406095	8E-06	alcohol and nictotine co-dependence	22488850

eQTL of rs1406095 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 rs1406095 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	8054252	8054474	E067	-40208
chr11	8054479	8055256	E067	-39426
chr11	8060735	8060785	E067	-33897
chr11	8060856	8060900	E067	-33782
chr11	8076506	8076596	E067	-18086
chr11	8077405	8077449	E067	-17233
chr11	8077536	8077765	E067	-16917
chr11	8077848	8078014	E067	-16668
chr11	8078035	8078091	E067	-16591
chr11	8078204	8078264	E067	-16418
chr11	8078328	8078584	E067	-16098
chr11	8078634	8078970	E067	-15712
chr11	8081654	8081748	E067	-12934
chr11	8081780	8081835	E067	-12847
chr11	8082068	8082192	E067	-12490
chr11	8082296	8082578	E067	-12104
chr11	8082697	8082777	E067	-11905
chr11	8093611	8093788	E067	-894
chr11	8093913	8094142	E067	-540
chr11	8105444	8105748	E067	10762
chr11	8106246	8106296	E067	11564
chr11	8106485	8106535	E067	11803
chr11	8106544	8106722	E067	11862
chr11	8106724	8106984	E067	12042
chr11	8107532	8108160	E067	12850
chr11	8108234	8108352	E067	13552
chr11	8108442	8108545	E067	13760
chr11	8108640	8109232	E067	13958
chr11	8109235	8109300	E067	14553
chr11	8109350	8109400	E067	14668
chr11	8109469	8109568	E067	14787
chr11	8113322	8113386	E067	18640
chr11	8114097	8114220	E067	19415
chr11	8114234	8114498	E067	19552
chr11	8114564	8114627	E067	19882
chr11	8114700	8114763	E067	20018
chr11	8115282	8115372	E067	20600
chr11	8132843	8133765	E067	38161
chr11	8054479	8055256	E068	-39426
chr11	8055299	8055396	E068	-39286
chr11	8055492	8055536	E068	-39146
chr11	8055633	8055691	E068	-38991
chr11	8055757	8055847	E068	-38835
chr11	8055937	8056063	E068	-38619
chr11	8056125	8056175	E068	-38507
chr11	8056203	8056306	E068	-38376
chr11	8056342	8056728	E068	-37954
chr11	8059304	8059394	E068	-35288
chr11	8077536	8077765	E068	-16917
chr11	8077848	8078014	E068	-16668
chr11	8078035	8078091	E068	-16591
chr11	8080925	8081061	E068	-13621
chr11	8081167	8081584	E068	-13098
chr11	8081654	8081748	E068	-12934
chr11	8081780	8081835	E068	-12847
chr11	8089608	8090896	E068	-3786
chr11	8091031	8091140	E068	-3542
chr11	8093611	8093788	E068	-894
chr11	8093913	8094142	E068	-540
chr11	8094471	8094592	E068	-90
chr11	8094624	8094769	E068	0
chr11	8094843	8094912	E068	161
chr11	8095008	8095398	E068	326
chr11	8105013	8105123	E068	10331
chr11	8105187	8105370	E068	10505
chr11	8105444	8105748	E068	10762
chr11	8106246	8106296	E068	11564
chr11	8106485	8106535	E068	11803
chr11	8106544	8106722	E068	11862
chr11	8106724	8106984	E068	12042
chr11	8107532	8108160	E068	12850
chr11	8108234	8108352	E068	13552
chr11	8108442	8108545	E068	13760
chr11	8108640	8109232	E068	13958
chr11	8109235	8109300	E068	14553
chr11	8109350	8109400	E068	14668
chr11	8109469	8109568	E068	14787
chr11	8114097	8114220	E068	19415
chr11	8114234	8114498	E068	19552
chr11	8114564	8114627	E068	19882
chr11	8114700	8114763	E068	20018
chr11	8114832	8114882	E068	20150
chr11	8114921	8114983	E068	20239
chr11	8115030	8115090	E068	20348
chr11	8115188	8115262	E068	20506
chr11	8115282	8115372	E068	20600
chr11	8054479	8055256	E069	-39426
chr11	8055299	8055396	E069	-39286
chr11	8076326	8076426	E069	-18256
chr11	8076506	8076596	E069	-18086
chr11	8076610	8077072	E069	-17610
chr11	8077173	8077233	E069	-17449
chr11	8077275	8077315	E069	-17367
chr11	8077405	8077449	E069	-17233
chr11	8077536	8077765	E069	-16917
chr11	8077848	8078014	E069	-16668
chr11	8078035	8078091	E069	-16591
chr11	8078204	8078264	E069	-16418
chr11	8078328	8078584	E069	-16098
chr11	8080728	8080843	E069	-13839
chr11	8080925	8081061	E069	-13621
chr11	8081167	8081584	E069	-13098
chr11	8081654	8081748	E069	-12934
chr11	8081780	8081835	E069	-12847
chr11	8082068	8082192	E069	-12490
chr11	8082296	8082578	E069	-12104
chr11	8082697	8082777	E069	-11905
chr11	8084266	8084357	E069	-10325
chr11	8084510	8084639	E069	-10043
chr11	8084708	8085405	E069	-9277
chr11	8091031	8091140	E069	-3542
chr11	8093913	8094142	E069	-540
chr11	8094471	8094592	E069	-90
chr11	8095008	8095398	E069	326
chr11	8095462	8095626	E069	780
chr11	8104401	8104677	E069	9719
chr11	8104701	8104751	E069	10019
chr11	8104773	8104813	E069	10091
chr11	8104856	8104939	E069	10174
chr11	8105444	8105748	E069	10762
chr11	8106246	8106296	E069	11564
chr11	8106485	8106535	E069	11803
chr11	8106544	8106722	E069	11862
chr11	8106724	8106984	E069	12042
chr11	8107532	8108160	E069	12850
chr11	8108234	8108352	E069	13552
chr11	8108442	8108545	E069	13760
chr11	8108640	8109232	E069	13958
chr11	8109235	8109300	E069	14553
chr11	8109350	8109400	E069	14668
chr11	8109469	8109568	E069	14787
chr11	8114097	8114220	E069	19415
chr11	8114234	8114498	E069	19552
chr11	8114564	8114627	E069	19882
chr11	8114700	8114763	E069	20018
chr11	8114832	8114882	E069	20150
chr11	8114921	8114983	E069	20239
chr11	8115030	8115090	E069	20348
chr11	8115188	8115262	E069	20506
chr11	8115282	8115372	E069	20600
chr11	8115443	8115521	E069	20761
chr11	8115557	8115839	E069	20875
chr11	8115853	8116015	E069	21171
chr11	8116079	8116129	E069	21397
chr11	8116508	8116568	E069	21826
chr11	8116792	8116850	E069	22110
chr11	8117013	8117192	E069	22331
chr11	8117353	8117558	E069	22671
chr11	8117673	8117797	E069	22991
chr11	8054252	8054474	E070	-40208
chr11	8054479	8055256	E070	-39426
chr11	8055299	8055396	E070	-39286
chr11	8055492	8055536	E070	-39146
chr11	8055633	8055691	E070	-38991
chr11	8055757	8055847	E070	-38835
chr11	8055937	8056063	E070	-38619
chr11	8056125	8056175	E070	-38507
chr11	8056203	8056306	E070	-38376
chr11	8056342	8056728	E070	-37954
chr11	8056804	8057004	E070	-37678
chr11	8059304	8059394	E070	-35288
chr11	8060735	8060785	E070	-33897
chr11	8060856	8060900	E070	-33782
chr11	8089608	8090896	E070	-3786
chr11	8091031	8091140	E070	-3542
chr11	8091661	8091739	E070	-2943
chr11	8093611	8093788	E070	-894
chr11	8093913	8094142	E070	-540
chr11	8106246	8106296	E070	11564
chr11	8106485	8106535	E070	11803
chr11	8106544	8106722	E070	11862
chr11	8106724	8106984	E070	12042
chr11	8107532	8108160	E070	12850
chr11	8108234	8108352	E070	13552
chr11	8108442	8108545	E070	13760
chr11	8132843	8133765	E070	38161
chr11	8054252	8054474	E071	-40208
chr11	8054479	8055256	E071	-39426
chr11	8055299	8055396	E071	-39286
chr11	8078204	8078264	E071	-16418
chr11	8078328	8078584	E071	-16098
chr11	8081654	8081748	E071	-12934
chr11	8081780	8081835	E071	-12847
chr11	8082068	8082192	E071	-12490
chr11	8089608	8090896	E071	-3786
chr11	8091031	8091140	E071	-3542
chr11	8091661	8091739	E071	-2943
chr11	8092084	8092290	E071	-2392
chr11	8093494	8093544	E071	-1138
chr11	8093611	8093788	E071	-894
chr11	8093913	8094142	E071	-540
chr11	8105444	8105748	E071	10762
chr11	8106246	8106296	E071	11564
chr11	8106485	8106535	E071	11803
chr11	8106544	8106722	E071	11862
chr11	8106724	8106984	E071	12042
chr11	8107532	8108160	E071	12850
chr11	8108234	8108352	E071	13552
chr11	8108442	8108545	E071	13760
chr11	8108640	8109232	E071	13958
chr11	8109235	8109300	E071	14553
chr11	8109350	8109400	E071	14668
chr11	8109469	8109568	E071	14787
chr11	8110047	8110097	E071	15365
chr11	8114097	8114220	E071	19415
chr11	8114234	8114498	E071	19552
chr11	8114564	8114627	E071	19882
chr11	8114700	8114763	E071	20018
chr11	8114832	8114882	E071	20150
chr11	8114921	8114983	E071	20239
chr11	8132126	8132211	E071	37444
chr11	8132474	8132518	E071	37792
chr11	8132711	8132765	E071	38029
chr11	8132843	8133765	E071	38161
chr11	8135067	8135117	E071	40385
chr11	8054252	8054474	E072	-40208
chr11	8054479	8055256	E072	-39426
chr11	8055299	8055396	E072	-39286
chr11	8060735	8060785	E072	-33897
chr11	8060856	8060900	E072	-33782
chr11	8076087	8076288	E072	-18394
chr11	8076326	8076426	E072	-18256
chr11	8076506	8076596	E072	-18086
chr11	8076610	8077072	E072	-17610
chr11	8077173	8077233	E072	-17449
chr11	8077275	8077315	E072	-17367
chr11	8077405	8077449	E072	-17233
chr11	8077536	8077765	E072	-16917
chr11	8077848	8078014	E072	-16668
chr11	8078035	8078091	E072	-16591
chr11	8078204	8078264	E072	-16418
chr11	8078328	8078584	E072	-16098
chr11	8078634	8078970	E072	-15712
chr11	8080925	8081061	E072	-13621
chr11	8081167	8081584	E072	-13098
chr11	8081654	8081748	E072	-12934
chr11	8081780	8081835	E072	-12847
chr11	8082697	8082777	E072	-11905
chr11	8083137	8083215	E072	-11467
chr11	8083598	8083708	E072	-10974
chr11	8083755	8083878	E072	-10804
chr11	8083894	8083968	E072	-10714
chr11	8083976	8084192	E072	-10490
chr11	8084266	8084357	E072	-10325
chr11	8084510	8084639	E072	-10043
chr11	8084708	8085405	E072	-9277
chr11	8085486	8085732	E072	-8950
chr11	8085745	8085795	E072	-8887
chr11	8101815	8101872	E072	7133
chr11	8105187	8105370	E072	10505
chr11	8105444	8105748	E072	10762
chr11	8106544	8106722	E072	11862
chr11	8106724	8106984	E072	12042
chr11	8107532	8108160	E072	12850
chr11	8108234	8108352	E072	13552
chr11	8108442	8108545	E072	13760
chr11	8108640	8109232	E072	13958
chr11	8109235	8109300	E072	14553
chr11	8109350	8109400	E072	14668
chr11	8109469	8109568	E072	14787
chr11	8114097	8114220	E072	19415
chr11	8114234	8114498	E072	19552
chr11	8114564	8114627	E072	19882
chr11	8114700	8114763	E072	20018
chr11	8114832	8114882	E072	20150
chr11	8114921	8114983	E072	20239
chr11	8115030	8115090	E072	20348
chr11	8115188	8115262	E072	20506
chr11	8115282	8115372	E072	20600
chr11	8115443	8115521	E072	20761
chr11	8115557	8115839	E072	20875
chr11	8115853	8116015	E072	21171
chr11	8116079	8116129	E072	21397
chr11	8132843	8133765	E072	38161
chr11	8047466	8047665	E073	-47017
chr11	8054479	8055256	E073	-39426
chr11	8055299	8055396	E073	-39286
chr11	8055492	8055536	E073	-39146
chr11	8055633	8055691	E073	-38991
chr11	8055757	8055847	E073	-38835
chr11	8060735	8060785	E073	-33897
chr11	8060856	8060900	E073	-33782
chr11	8076087	8076288	E073	-18394
chr11	8076326	8076426	E073	-18256
chr11	8076506	8076596	E073	-18086
chr11	8076610	8077072	E073	-17610
chr11	8077173	8077233	E073	-17449
chr11	8077275	8077315	E073	-17367
chr11	8077405	8077449	E073	-17233
chr11	8077536	8077765	E073	-16917
chr11	8077848	8078014	E073	-16668
chr11	8078035	8078091	E073	-16591
chr11	8078204	8078264	E073	-16418
chr11	8078328	8078584	E073	-16098
chr11	8078634	8078970	E073	-15712
chr11	8080925	8081061	E073	-13621
chr11	8081167	8081584	E073	-13098
chr11	8081654	8081748	E073	-12934
chr11	8081780	8081835	E073	-12847
chr11	8082068	8082192	E073	-12490
chr11	8082697	8082777	E073	-11905
chr11	8083137	8083215	E073	-11467
chr11	8083598	8083708	E073	-10974
chr11	8083755	8083878	E073	-10804
chr11	8083894	8083968	E073	-10714
chr11	8083976	8084192	E073	-10490
chr11	8084266	8084357	E073	-10325
chr11	8084510	8084639	E073	-10043
chr11	8084708	8085405	E073	-9277
chr11	8089608	8090896	E073	-3786
chr11	8091031	8091140	E073	-3542
chr11	8093611	8093788	E073	-894
chr11	8093913	8094142	E073	-540
chr11	8094471	8094592	E073	-90
chr11	8094624	8094769	E073	0
chr11	8105444	8105748	E073	10762
chr11	8106246	8106296	E073	11564
chr11	8106485	8106535	E073	11803
chr11	8106544	8106722	E073	11862
chr11	8106724	8106984	E073	12042
chr11	8108442	8108545	E073	13760
chr11	8108640	8109232	E073	13958
chr11	8109235	8109300	E073	14553
chr11	8109350	8109400	E073	14668
chr11	8109469	8109568	E073	14787
chr11	8110047	8110097	E073	15365
chr11	8110396	8110440	E073	15714
chr11	8110541	8110630	E073	15859
chr11	8114234	8114498	E073	19552
chr11	8114564	8114627	E073	19882
chr11	8114700	8114763	E073	20018
chr11	8114832	8114882	E073	20150
chr11	8114921	8114983	E073	20239
chr11	8115030	8115090	E073	20348
chr11	8115188	8115262	E073	20506
chr11	8115282	8115372	E073	20600
chr11	8115443	8115521	E073	20761
chr11	8115557	8115839	E073	20875
chr11	8115853	8116015	E073	21171
chr11	8117353	8117558	E073	22671
chr11	8117673	8117797	E073	22991
chr11	8118062	8118182	E073	23380
chr11	8118198	8118368	E073	23516
chr11	8132003	8132097	E073	37321
chr11	8132126	8132211	E073	37444
chr11	8132474	8132518	E073	37792
chr11	8132711	8132765	E073	38029
chr11	8132843	8133765	E073	38161
chr11	8054252	8054474	E074	-40208
chr11	8054479	8055256	E074	-39426
chr11	8055299	8055396	E074	-39286
chr11	8076087	8076288	E074	-18394
chr11	8076326	8076426	E074	-18256
chr11	8083755	8083878	E074	-10804
chr11	8083894	8083968	E074	-10714
chr11	8083976	8084192	E074	-10490
chr11	8084266	8084357	E074	-10325
chr11	8084510	8084639	E074	-10043
chr11	8084708	8085405	E074	-9277
chr11	8089608	8090896	E074	-3786
chr11	8091031	8091140	E074	-3542
chr11	8103937	8104380	E074	9255
chr11	8104401	8104677	E074	9719
chr11	8104701	8104751	E074	10019
chr11	8104773	8104813	E074	10091
chr11	8104856	8104939	E074	10174
chr11	8105013	8105123	E074	10331
chr11	8105187	8105370	E074	10505
chr11	8105444	8105748	E074	10762
chr11	8106246	8106296	E074	11564
chr11	8106485	8106535	E074	11803
chr11	8106544	8106722	E074	11862
chr11	8106724	8106984	E074	12042
chr11	8107532	8108160	E074	12850
chr11	8108234	8108352	E074	13552
chr11	8108442	8108545	E074	13760
chr11	8108640	8109232	E074	13958
chr11	8109235	8109300	E074	14553
chr11	8109350	8109400	E074	14668
chr11	8109469	8109568	E074	14787
chr11	8114097	8114220	E074	19415
chr11	8114234	8114498	E074	19552
chr11	8114564	8114627	E074	19882
chr11	8132843	8133765	E074	38161
chr11	8054479	8055256	E081	-39426
chr11	8055299	8055396	E081	-39286
chr11	8055492	8055536	E081	-39146
chr11	8055633	8055691	E081	-38991
chr11	8055757	8055847	E081	-38835
chr11	8055937	8056063	E081	-38619
chr11	8056125	8056175	E081	-38507
chr11	8056203	8056306	E081	-38376
chr11	8056342	8056728	E081	-37954
chr11	8056804	8057004	E081	-37678
chr11	8057148	8057488	E081	-37194
chr11	8060735	8060785	E081	-33897
chr11	8060856	8060900	E081	-33782
chr11	8076326	8076426	E081	-18256
chr11	8076506	8076596	E081	-18086
chr11	8076610	8077072	E081	-17610
chr11	8077173	8077233	E081	-17449
chr11	8077275	8077315	E081	-17367
chr11	8077405	8077449	E081	-17233
chr11	8077536	8077765	E081	-16917
chr11	8077848	8078014	E081	-16668
chr11	8078035	8078091	E081	-16591
chr11	8089608	8090896	E081	-3786
chr11	8091031	8091140	E081	-3542
chr11	8091661	8091739	E081	-2943
chr11	8092690	8092787	E081	-1895
chr11	8093611	8093788	E081	-894
chr11	8100534	8100720	E081	5852
chr11	8101815	8101872	E081	7133
chr11	8103937	8104380	E081	9255
chr11	8104701	8104751	E081	10019
chr11	8104773	8104813	E081	10091
chr11	8104856	8104939	E081	10174
chr11	8105013	8105123	E081	10331
chr11	8105187	8105370	E081	10505
chr11	8105444	8105748	E081	10762
chr11	8106246	8106296	E081	11564
chr11	8106485	8106535	E081	11803
chr11	8106544	8106722	E081	11862
chr11	8106724	8106984	E081	12042
chr11	8107532	8108160	E081	12850
chr11	8108442	8108545	E081	13760
chr11	8116508	8116568	E081	21826
chr11	8116792	8116850	E081	22110
chr11	8117013	8117192	E081	22331
chr11	8117353	8117558	E081	22671
chr11	8117673	8117797	E081	22991
chr11	8132474	8132518	E081	37792
chr11	8132711	8132765	E081	38029
chr11	8132843	8133765	E081	38161
chr11	8054479	8055256	E082	-39426
chr11	8055299	8055396	E082	-39286
chr11	8055492	8055536	E082	-39146
chr11	8055633	8055691	E082	-38991
chr11	8055757	8055847	E082	-38835
chr11	8055937	8056063	E082	-38619
chr11	8056125	8056175	E082	-38507
chr11	8056203	8056306	E082	-38376
chr11	8056342	8056728	E082	-37954
chr11	8056804	8057004	E082	-37678
chr11	8060735	8060785	E082	-33897
chr11	8089608	8090896	E082	-3786
chr11	8091031	8091140	E082	-3542
chr11	8092690	8092787	E082	-1895
chr11	8106246	8106296	E082	11564
chr11	8106485	8106535	E082	11803
chr11	8106544	8106722	E082	11862
chr11	8106724	8106984	E082	12042
chr11	8107532	8108160	E082	12850
chr11	8132126	8132211	E082	37444
chr11	8132474	8132518	E082	37792
chr11	8132711	8132765	E082	38029

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr11	8102036	8103891	E067	7354
chr11	8102036	8103891	E068	7354
chr11	8102036	8103891	E069	7354
chr11	8102036	8103891	E070	7354
chr11	8102036	8103891	E071	7354
chr11	8102036	8103891	E072	7354
chr11	8102036	8103891	E073	7354
chr11	8102036	8103891	E074	7354
chr11	8102036	8103891	E081	7354
chr11	8102036	8103891	E082	7354