rs890622

Organism: Homo sapiens

Alleles: G>C

Gene : Feature

TANC1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0088 (2663/29960,GnomAD)
C=0098 (2868/29118,TOPMED)
C=0092 (462/5008,1000G)
C=0064 (246/3854,ALSPAC)
C=0058 (216/3708,TWINSUK)

Position: chr2:159108877 (GRCh38.p7) (2q24.2)

Phenotype: ND

Dataset:

GWASCatalog

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 386 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.159108877G>C
GRCh37.p13 chr 2	NC_000002.11:g.159965389G>C

Gene: TANC1, tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TANC1 transcript variant 2	NM_001145909.1:c.	N/A	Intron Variant
TANC1 transcript variant 1	NM_033394.2:c.	N/A	Intron Variant
TANC1 transcript variant X10	XM_005246918.4:c.	N/A	Intron Variant
TANC1 transcript variant X11	XM_006712810.3:c.	N/A	Intron Variant
TANC1 transcript variant X15	XM_006712812.3:c.	N/A	Intron Variant
TANC1 transcript variant X25	XM_006712814.3:c.	N/A	Intron Variant
TANC1 transcript variant X2	XM_011512048.2:c.	N/A	Intron Variant
TANC1 transcript variant X6	XM_011512051.2:c.	N/A	Intron Variant
TANC1 transcript variant X8	XM_011512053.2:c.	N/A	Intron Variant
TANC1 transcript variant X13	XM_011512055.2:c.	N/A	Intron Variant
TANC1 transcript variant X21	XM_011512058.2:c.	N/A	Intron Variant
TANC1 transcript variant X1	XM_017005141.1:c.	N/A	Intron Variant
TANC1 transcript variant X3	XM_017005142.1:c.	N/A	Intron Variant
TANC1 transcript variant X4	XM_017005143.1:c.	N/A	Intron Variant
TANC1 transcript variant X5	XM_017005144.1:c.	N/A	Intron Variant
TANC1 transcript variant X7	XM_017005145.1:c.	N/A	Intron Variant
TANC1 transcript variant X9	XM_017005146.1:c.	N/A	Intron Variant
TANC1 transcript variant X12	XM_017005147.1:c.	N/A	Intron Variant
TANC1 transcript variant X13	XM_017005148.1:c.	N/A	Intron Variant
TANC1 transcript variant X12	XM_017005149.1:c.	N/A	Intron Variant
TANC1 transcript variant X14	XM_017005150.1:c.	N/A	Intron Variant
TANC1 transcript variant X16	XM_017005151.1:c.	N/A	Intron Variant
TANC1 transcript variant X17	XM_017005152.1:c.	N/A	Intron Variant
TANC1 transcript variant X18	XM_017005153.1:c.	N/A	Intron Variant
TANC1 transcript variant X19	XM_017005154.1:c.	N/A	Intron Variant
TANC1 transcript variant X23	XM_017005155.1:c.	N/A	Intron Variant
TANC1 transcript variant X23	XM_017005156.1:c.	N/A	Intron Variant
TANC1 transcript variant X27	XM_017005157.1:c.	N/A	Intron Variant
TANC1 transcript variant X29	XM_017005158.1:c.	N/A	Intron Variant
TANC1 transcript variant X22	XM_011512059.2:c.	N/A	Genic Upstream Transcript Variant
TANC1 transcript variant X26	XM_011512062.2:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.852	C=0.148
1000Genomes	American	Sub	694	G=0.760	C=0.240
1000Genomes	East Asian	Sub	1008	G=0.985	C=0.015
1000Genomes	Europe	Sub	1006	G=0.942	C=0.058
1000Genomes	Global	Study-wide	5008	G=0.908	C=0.092
1000Genomes	South Asian	Sub	978	G=0.970	C=0.030
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.936	C=0.064
The Genome Aggregation Database	African	Sub	8710	G=0.871	C=0.129
The Genome Aggregation Database	American	Sub	838	G=0.790	C=0.210
The Genome Aggregation Database	East Asian	Sub	1620	G=0.994	C=0.006
The Genome Aggregation Database	Europe	Sub	18490	G=0.927	C=0.072
The Genome Aggregation Database	Global	Study-wide	29960	G=0.911	C=0.088
The Genome Aggregation Database	Other	Sub	302	G=0.970	C=0.030
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.901	C=0.098
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.942	C=0.058

PMID	Title	Author	Journal
28440896	Genome-wide meta-analysis identifies a novel susceptibility signal at CACNA2D3 for nicotine dependence.	Yin X	Am J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID	p-value	Traits	Study
rs890622	2E-06	nicotine dependence	28440896

eQTL of rs890622 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 rs890622 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	159920305	159920418	E067	-44971
chr2	159920482	159920560	E067	-44829
chr2	159920702	159920936	E067	-44453
chr2	159920988	159921937	E067	-43452
chr2	159922033	159922129	E067	-43260
chr2	159922147	159922211	E067	-43178
chr2	159928108	159928373	E067	-37016
chr2	159929335	159930113	E067	-35276
chr2	159930621	159930701	E067	-34688
chr2	159942928	159943955	E067	-21434
chr2	159945551	159945757	E067	-19632
chr2	159945758	159945905	E067	-19484
chr2	159946104	159946424	E067	-18965
chr2	159946498	159946692	E067	-18697
chr2	159946883	159946963	E067	-18426
chr2	159947020	159947797	E067	-17592
chr2	159949987	159950406	E067	-14983
chr2	159950611	159951321	E067	-14068
chr2	159967979	159968102	E067	2590
chr2	159968166	159968280	E067	2777
chr2	159974738	159975517	E067	9349
chr2	159985925	159986087	E067	20536
chr2	159986269	159986458	E067	20880
chr2	159986481	159986664	E067	21092
chr2	159986709	159986773	E067	21320
chr2	159986896	159987183	E067	21507
chr2	159987355	159987417	E067	21966
chr2	159991765	159993209	E067	26376
chr2	159993408	159993539	E067	28019
chr2	159994036	159994239	E067	28647
chr2	159994305	159994457	E067	28916
chr2	160003497	160004644	E067	38108
chr2	160004726	160004783	E067	39337
chr2	160005457	160005728	E067	40068
chr2	160006308	160006615	E067	40919
chr2	160006707	160006764	E067	41318
chr2	160006808	160007035	E067	41419
chr2	160007053	160007223	E067	41664
chr2	159920988	159921937	E068	-43452
chr2	159922033	159922129	E068	-43260
chr2	159922147	159922211	E068	-43178
chr2	159922275	159922360	E068	-43029
chr2	159928108	159928373	E068	-37016
chr2	159929335	159930113	E068	-35276
chr2	159930621	159930701	E068	-34688
chr2	159932801	159933104	E068	-32285
chr2	159941017	159941374	E068	-24015
chr2	159941443	159941534	E068	-23855
chr2	159941589	159941850	E068	-23539
chr2	159942042	159942092	E068	-23297
chr2	159942127	159942182	E068	-23207
chr2	159942315	159942552	E068	-22837
chr2	159942928	159943955	E068	-21434
chr2	159945551	159945757	E068	-19632
chr2	159945758	159945905	E068	-19484
chr2	159946104	159946424	E068	-18965
chr2	159946498	159946692	E068	-18697
chr2	159946883	159946963	E068	-18426
chr2	159947020	159947797	E068	-17592
chr2	159947947	159948428	E068	-16961
chr2	159948536	159948825	E068	-16564
chr2	159949467	159949525	E068	-15864
chr2	159949546	159949650	E068	-15739
chr2	159949987	159950406	E068	-14983
chr2	159950611	159951321	E068	-14068
chr2	159967322	159967611	E068	1933
chr2	159967717	159967777	E068	2328
chr2	159967814	159967941	E068	2425
chr2	159967979	159968102	E068	2590
chr2	159968166	159968280	E068	2777
chr2	159974738	159975517	E068	9349
chr2	159975537	159975917	E068	10148
chr2	159980842	159982052	E068	15453
chr2	159985925	159986087	E068	20536
chr2	159986896	159987183	E068	21507
chr2	159987355	159987417	E068	21966
chr2	159991625	159991690	E068	26236
chr2	159991765	159993209	E068	26376
chr2	159993408	159993539	E068	28019
chr2	159994036	159994239	E068	28647
chr2	159994305	159994457	E068	28916
chr2	159994507	159994705	E068	29118
chr2	159994922	159995101	E068	29533
chr2	160003497	160004644	E068	38108
chr2	160006308	160006615	E068	40919
chr2	160006707	160006764	E068	41318
chr2	160006808	160007035	E068	41419
chr2	160007053	160007223	E068	41664
chr2	160007381	160007425	E068	41992
chr2	160009735	160009978	E068	44346
chr2	160010032	160010428	E068	44643
chr2	160010599	160010698	E068	45210
chr2	159920702	159920936	E069	-44453
chr2	159920988	159921937	E069	-43452
chr2	159922033	159922129	E069	-43260
chr2	159922147	159922211	E069	-43178
chr2	159928108	159928373	E069	-37016
chr2	159929335	159930113	E069	-35276
chr2	159930621	159930701	E069	-34688
chr2	159941017	159941374	E069	-24015
chr2	159941443	159941534	E069	-23855
chr2	159941589	159941850	E069	-23539
chr2	159942042	159942092	E069	-23297
chr2	159942127	159942182	E069	-23207
chr2	159942315	159942552	E069	-22837
chr2	159945551	159945757	E069	-19632
chr2	159945758	159945905	E069	-19484
chr2	159946104	159946424	E069	-18965
chr2	159946498	159946692	E069	-18697
chr2	159946883	159946963	E069	-18426
chr2	159947020	159947797	E069	-17592
chr2	159947947	159948428	E069	-16961
chr2	159948536	159948825	E069	-16564
chr2	159949467	159949525	E069	-15864
chr2	159949546	159949650	E069	-15739
chr2	159949987	159950406	E069	-14983
chr2	159950611	159951321	E069	-14068
chr2	159958370	159958504	E069	-6885
chr2	159958519	159958569	E069	-6820
chr2	159963995	159964185	E069	-1204
chr2	159964236	159964489	E069	-900
chr2	159964801	159964984	E069	-405
chr2	159965130	159965300	E069	-89
chr2	159967322	159967611	E069	1933
chr2	159967717	159967777	E069	2328
chr2	159967814	159967941	E069	2425
chr2	159967979	159968102	E069	2590
chr2	159968166	159968280	E069	2777
chr2	159974738	159975517	E069	9349
chr2	159975537	159975917	E069	10148
chr2	159980842	159982052	E069	15453
chr2	159985925	159986087	E069	20536
chr2	159986269	159986458	E069	20880
chr2	159991625	159991690	E069	26236
chr2	159991765	159993209	E069	26376
chr2	159994507	159994705	E069	29118
chr2	159994922	159995101	E069	29533
chr2	160003497	160004644	E069	38108
chr2	160004726	160004783	E069	39337
chr2	160005457	160005728	E069	40068
chr2	160006308	160006615	E069	40919
chr2	160006707	160006764	E069	41318
chr2	160006808	160007035	E069	41419
chr2	160010599	160010698	E069	45210
chr2	159985925	159986087	E070	20536
chr2	159986269	159986458	E070	20880
chr2	159986481	159986664	E070	21092
chr2	159986709	159986773	E070	21320
chr2	159986896	159987183	E070	21507
chr2	159991765	159993209	E070	26376
chr2	160003497	160004644	E070	38108
chr2	159920702	159920936	E071	-44453
chr2	159920988	159921937	E071	-43452
chr2	159922033	159922129	E071	-43260
chr2	159922147	159922211	E071	-43178
chr2	159922275	159922360	E071	-43029
chr2	159927313	159927474	E071	-37915
chr2	159928108	159928373	E071	-37016
chr2	159929335	159930113	E071	-35276
chr2	159930621	159930701	E071	-34688
chr2	159932373	159932502	E071	-32887
chr2	159932801	159933104	E071	-32285
chr2	159941017	159941374	E071	-24015
chr2	159941443	159941534	E071	-23855
chr2	159941589	159941850	E071	-23539
chr2	159942042	159942092	E071	-23297
chr2	159942127	159942182	E071	-23207
chr2	159942315	159942552	E071	-22837
chr2	159942928	159943955	E071	-21434
chr2	159945551	159945757	E071	-19632
chr2	159945758	159945905	E071	-19484
chr2	159946104	159946424	E071	-18965
chr2	159946498	159946692	E071	-18697
chr2	159946883	159946963	E071	-18426
chr2	159947020	159947797	E071	-17592
chr2	159947947	159948428	E071	-16961
chr2	159948536	159948825	E071	-16564
chr2	159949467	159949525	E071	-15864
chr2	159949546	159949650	E071	-15739
chr2	159949987	159950406	E071	-14983
chr2	159950611	159951321	E071	-14068
chr2	159963995	159964185	E071	-1204
chr2	159964236	159964489	E071	-900
chr2	159964801	159964984	E071	-405
chr2	159965130	159965300	E071	-89
chr2	159965676	159965776	E071	287
chr2	159966077	159966285	E071	688
chr2	159967322	159967611	E071	1933
chr2	159967717	159967777	E071	2328
chr2	159967814	159967941	E071	2425
chr2	159974738	159975517	E071	9349
chr2	159975537	159975917	E071	10148
chr2	159980842	159982052	E071	15453
chr2	159982532	159982592	E071	17143
chr2	159982800	159982860	E071	17411
chr2	159984857	159985053	E071	19468
chr2	159985925	159986087	E071	20536
chr2	159986269	159986458	E071	20880
chr2	159986481	159986664	E071	21092
chr2	159986709	159986773	E071	21320
chr2	159986896	159987183	E071	21507
chr2	159987355	159987417	E071	21966
chr2	159991625	159991690	E071	26236
chr2	159991765	159993209	E071	26376
chr2	159993408	159993539	E071	28019
chr2	159994036	159994239	E071	28647
chr2	159994305	159994457	E071	28916
chr2	159994507	159994705	E071	29118
chr2	159994922	159995101	E071	29533
chr2	159995221	159995668	E071	29832
chr2	160003497	160004644	E071	38108
chr2	160004726	160004783	E071	39337
chr2	160006308	160006615	E071	40919
chr2	160006707	160006764	E071	41318
chr2	160006808	160007035	E071	41419
chr2	160009735	160009978	E071	44346
chr2	160010032	160010428	E071	44643
chr2	159920702	159920936	E072	-44453
chr2	159920988	159921937	E072	-43452
chr2	159928108	159928373	E072	-37016
chr2	159929335	159930113	E072	-35276
chr2	159930621	159930701	E072	-34688
chr2	159932373	159932502	E072	-32887
chr2	159932801	159933104	E072	-32285
chr2	159941443	159941534	E072	-23855
chr2	159941589	159941850	E072	-23539
chr2	159942042	159942092	E072	-23297
chr2	159942127	159942182	E072	-23207
chr2	159942315	159942552	E072	-22837
chr2	159942928	159943955	E072	-21434
chr2	159945551	159945757	E072	-19632
chr2	159945758	159945905	E072	-19484
chr2	159946104	159946424	E072	-18965
chr2	159946498	159946692	E072	-18697
chr2	159946883	159946963	E072	-18426
chr2	159947020	159947797	E072	-17592
chr2	159947947	159948428	E072	-16961
chr2	159948536	159948825	E072	-16564
chr2	159949987	159950406	E072	-14983
chr2	159950611	159951321	E072	-14068
chr2	159958370	159958504	E072	-6885
chr2	159958519	159958569	E072	-6820
chr2	159964236	159964489	E072	-900
chr2	159974581	159974678	E072	9192
chr2	159974738	159975517	E072	9349
chr2	159980842	159982052	E072	15453
chr2	159984857	159985053	E072	19468
chr2	159985925	159986087	E072	20536
chr2	159987355	159987417	E072	21966
chr2	159988087	159988855	E072	22698
chr2	159991625	159991690	E072	26236
chr2	159991765	159993209	E072	26376
chr2	159993408	159993539	E072	28019
chr2	159994036	159994239	E072	28647
chr2	159994305	159994457	E072	28916
chr2	159994507	159994705	E072	29118
chr2	160003497	160004644	E072	38108
chr2	160004726	160004783	E072	39337
chr2	160005457	160005728	E072	40068
chr2	160006308	160006615	E072	40919
chr2	160006707	160006764	E072	41318
chr2	160006808	160007035	E072	41419
chr2	160007053	160007223	E072	41664
chr2	159920988	159921937	E073	-43452
chr2	159942928	159943955	E073	-21434
chr2	159945551	159945757	E073	-19632
chr2	159945758	159945905	E073	-19484
chr2	159946104	159946424	E073	-18965
chr2	159946498	159946692	E073	-18697
chr2	159946883	159946963	E073	-18426
chr2	159947020	159947797	E073	-17592
chr2	159947947	159948428	E073	-16961
chr2	159948536	159948825	E073	-16564
chr2	159949467	159949525	E073	-15864
chr2	159949546	159949650	E073	-15739
chr2	159950611	159951321	E073	-14068
chr2	159958519	159958569	E073	-6820
chr2	159974581	159974678	E073	9192
chr2	159974738	159975517	E073	9349
chr2	159975537	159975917	E073	10148
chr2	159986269	159986458	E073	20880
chr2	159986481	159986664	E073	21092
chr2	159986709	159986773	E073	21320
chr2	159986896	159987183	E073	21507
chr2	159991765	159993209	E073	26376
chr2	159993408	159993539	E073	28019
chr2	159994036	159994239	E073	28647
chr2	160003497	160004644	E073	38108
chr2	160004726	160004783	E073	39337
chr2	160006308	160006615	E073	40919
chr2	160006707	160006764	E073	41318
chr2	160006808	160007035	E073	41419
chr2	160007053	160007223	E073	41664
chr2	160010032	160010428	E073	44643
chr2	160010599	160010698	E073	45210
chr2	160010939	160010979	E073	45550
chr2	159920702	159920936	E074	-44453
chr2	159920988	159921937	E074	-43452
chr2	159922033	159922129	E074	-43260
chr2	159922147	159922211	E074	-43178
chr2	159922275	159922360	E074	-43029
chr2	159922418	159922632	E074	-42757
chr2	159923164	159923270	E074	-42119
chr2	159923275	159923593	E074	-41796
chr2	159925861	159926041	E074	-39348
chr2	159926430	159926512	E074	-38877
chr2	159928108	159928373	E074	-37016
chr2	159929335	159930113	E074	-35276
chr2	159930621	159930701	E074	-34688
chr2	159932801	159933104	E074	-32285
chr2	159941017	159941374	E074	-24015
chr2	159941443	159941534	E074	-23855
chr2	159941589	159941850	E074	-23539
chr2	159942042	159942092	E074	-23297
chr2	159942127	159942182	E074	-23207
chr2	159942315	159942552	E074	-22837
chr2	159942928	159943955	E074	-21434
chr2	159945551	159945757	E074	-19632
chr2	159945758	159945905	E074	-19484
chr2	159946104	159946424	E074	-18965
chr2	159946498	159946692	E074	-18697
chr2	159946883	159946963	E074	-18426
chr2	159947020	159947797	E074	-17592
chr2	159947947	159948428	E074	-16961
chr2	159948536	159948825	E074	-16564
chr2	159949467	159949525	E074	-15864
chr2	159949546	159949650	E074	-15739
chr2	159949987	159950406	E074	-14983
chr2	159950611	159951321	E074	-14068
chr2	159963995	159964185	E074	-1204
chr2	159964236	159964489	E074	-900
chr2	159964801	159964984	E074	-405
chr2	159965130	159965300	E074	-89
chr2	159965676	159965776	E074	287
chr2	159966077	159966285	E074	688
chr2	159967172	159967252	E074	1783
chr2	159967322	159967611	E074	1933
chr2	159967717	159967777	E074	2328
chr2	159967814	159967941	E074	2425
chr2	159967979	159968102	E074	2590
chr2	159968166	159968280	E074	2777
chr2	159976124	159976770	E074	10735
chr2	159980842	159982052	E074	15453
chr2	159984857	159985053	E074	19468
chr2	159985925	159986087	E074	20536
chr2	159986896	159987183	E074	21507
chr2	159990004	159990062	E074	24615
chr2	159990076	159990126	E074	24687
chr2	159990395	159990627	E074	25006
chr2	159991625	159991690	E074	26236
chr2	159991765	159993209	E074	26376
chr2	159993408	159993539	E074	28019
chr2	159994036	159994239	E074	28647
chr2	159994305	159994457	E074	28916
chr2	159994507	159994705	E074	29118
chr2	159994922	159995101	E074	29533
chr2	160003497	160004644	E074	38108
chr2	160004726	160004783	E074	39337
chr2	160006308	160006615	E074	40919
chr2	160006707	160006764	E074	41318
chr2	160006808	160007035	E074	41419
chr2	160007053	160007223	E074	41664
chr2	160007381	160007425	E074	41992
chr2	160007454	160007504	E074	42065
chr2	159920702	159920936	E081	-44453
chr2	159964236	159964489	E081	-900
chr2	159964801	159964984	E081	-405
chr2	159965130	159965300	E081	-89
chr2	159965676	159965776	E081	287
chr2	159986269	159986458	E081	20880
chr2	159986481	159986664	E081	21092
chr2	159986709	159986773	E081	21320
chr2	159991765	159993209	E081	26376
chr2	160001758	160002433	E081	36369
chr2	160002480	160002734	E081	37091
chr2	160003497	160004644	E081	38108
chr2	160004726	160004783	E081	39337
chr2	160005457	160005728	E081	40068
chr2	159964236	159964489	E082	-900
chr2	159964801	159964984	E082	-405
chr2	159965130	159965300	E082	-89
chr2	160003497	160004644	E082	38108
chr2	160006308	160006615	E082	40919
chr2	160006707	160006764	E082	41318
chr2	160006808	160007035	E082	41419
chr2	160007053	160007223	E082	41664