rs10893366

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

PKNOX2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0226 (6787/29950,GnomAD)
T=0219 (6396/29118,TOPMED)
T=0285 (1426/5008,1000G)
T=0174 (671/3854,ALSPAC)
T=0181 (671/3708,TWINSUK)

Position: chr11:125308507 (GRCh38.p7) (11q24.2)

Phenotype: AD | ND

Dataset:

GWASdb2 | GWASCatalog

Publications: 8 publication(s)

Genomic View: See rs on genome

Enhancer: 384 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 11	NC_000011.10:g.125308507C>T
GRCh37.p13 chr 11	NC_000011.9:g.125178403C>T

Gene: PKNOX2, PBX/knotted 1 homeobox 2(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PKNOX2 transcript	NM_022062.2:c.	N/A	Intron Variant
PKNOX2 transcript variant X5	XM_005271642.2:c.	N/A	Intron Variant
PKNOX2 transcript variant X12	XM_006718894.2:c.	N/A	Intron Variant
PKNOX2 transcript variant X2	XM_011542944.2:c.	N/A	Intron Variant
PKNOX2 transcript variant X6	XM_011542945.2:c.	N/A	Intron Variant
PKNOX2 transcript variant X11	XM_011542946.1:c.	N/A	Intron Variant
PKNOX2 transcript variant X13	XM_011542947.2:c.	N/A	Intron Variant
PKNOX2 transcript variant X2	XM_017018110.1:c.	N/A	Intron Variant
PKNOX2 transcript variant X14	XM_017018111.1:c.	N/A	Intron Variant
PKNOX2 transcript variant X5	XM_005271643.2:c.	N/A	Genic Upstream Transcript Variant
PKNOX2 transcript variant X10	XM_017018112.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.710	T=0.290
1000Genomes	American	Sub	694	C=0.890	T=0.110
1000Genomes	East Asian	Sub	1008	C=0.481	T=0.519
1000Genomes	Europe	Sub	1006	C=0.830	T=0.170
1000Genomes	Global	Study-wide	5008	C=0.715	T=0.285
1000Genomes	South Asian	Sub	978	C=0.720	T=0.280
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.826	T=0.174
The Genome Aggregation Database	African	Sub	8714	C=0.730	T=0.270
The Genome Aggregation Database	American	Sub	836	C=0.910	T=0.090
The Genome Aggregation Database	East Asian	Sub	1618	C=0.483	T=0.517
The Genome Aggregation Database	Europe	Sub	18480	C=0.811	T=0.188
The Genome Aggregation Database	Global	Study-wide	29950	C=0.773	T=0.226
The Genome Aggregation Database	Other	Sub	302	C=0.850	T=0.150
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.780	T=0.219
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.819	T=0.181

PMID	Title	Author	Journal
26044620	Gene network analysis shows immune-signaling and ERK1/2 as novel genetic markers for multiple addiction phenotypes: alcohol, smoking and opioid addiction.	Reyes-Gibby CC	BMC Syst Biol
22488850	Genome-wide search for replicable risk gene regions in alcohol and nicotine co-dependence.	Zuo L	Am J Med Genet B Neuropsychiatr Genet
21703634	A meta-analysis of two genome-wide association studies identifies 3 new loci for alcohol dependence.	Wang KS	J Psychiatr Res
21956439	Genome-wide association study of alcohol dependence implicates KIAA0040 on chromosome 1q.	Zuo L	Neuropsychopharmacology
25043041	Neuropsychosocial profiles of current and future adolescent alcohol misusers.	Whelan R	Nature
20202923	A genome-wide association study of alcohol dependence.	Bierut LJ	Proc Natl Acad Sci U S A
21298047	The nuclear transcription factor PKNOX2 is a candidate gene for substance dependence in European-origin women.	Chen X	PLoS One
23691092	Associations of prenatal nicotine exposure and the dopamine related genes ANKK1 and DRD2 to verbal language.	Eicher JD	PLoS One

P-Value

SNP ID	p-value	Traits	Study
rs10893366	0.0000042	alcohol and nictotine co-dependence	22488850
rs10893366	0.000008	alcohol dependence	21956439
rs10893366	0.0000161	alcohol dependence	21703634

eQTL of rs10893366 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 rs10893366 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	125131366	125134290	E067	-44113
chr11	125134307	125134447	E067	-43956
chr11	125154137	125154597	E067	-23806
chr11	125154599	125154663	E067	-23740
chr11	125154950	125155095	E067	-23308
chr11	125155397	125155447	E067	-22956
chr11	125155551	125155600	E067	-22803
chr11	125155731	125156060	E067	-22343
chr11	125156284	125156367	E067	-22036
chr11	125156412	125156462	E067	-21941
chr11	125156502	125156739	E067	-21664
chr11	125156835	125156983	E067	-21420
chr11	125157125	125158152	E067	-20251
chr11	125184527	125185677	E067	6124
chr11	125185752	125186058	E067	7349
chr11	125197278	125197400	E067	18875
chr11	125197429	125197808	E067	19026
chr11	125197863	125198089	E067	19460
chr11	125199654	125199716	E067	21251
chr11	125199752	125199894	E067	21349
chr11	125199945	125200053	E067	21542
chr11	125207750	125208342	E067	29347
chr11	125208410	125209748	E067	30007
chr11	125212818	125213118	E067	34415
chr11	125213124	125214119	E067	34721
chr11	125214121	125214171	E067	35718
chr11	125214301	125214364	E067	35898
chr11	125214476	125214537	E067	36073
chr11	125214635	125214865	E067	36232
chr11	125214900	125214954	E067	36497
chr11	125214979	125215209	E067	36576
chr11	125215284	125216692	E067	36881
chr11	125217879	125219083	E067	39476
chr11	125131366	125134290	E068	-44113
chr11	125134307	125134447	E068	-43956
chr11	125140729	125140962	E068	-37441
chr11	125141374	125141814	E068	-36589
chr11	125141882	125142369	E068	-36034
chr11	125142474	125142551	E068	-35852
chr11	125142609	125142707	E068	-35696
chr11	125142726	125142895	E068	-35508
chr11	125142909	125143089	E068	-35314
chr11	125145806	125146168	E068	-32235
chr11	125156502	125156739	E068	-21664
chr11	125156835	125156983	E068	-21420
chr11	125157125	125158152	E068	-20251
chr11	125158209	125158531	E068	-19872
chr11	125158563	125158637	E068	-19766
chr11	125165680	125165741	E068	-12662
chr11	125165798	125166315	E068	-12088
chr11	125184138	125184512	E068	5735
chr11	125184527	125185677	E068	6124
chr11	125197278	125197400	E068	18875
chr11	125197429	125197808	E068	19026
chr11	125200181	125200591	E068	21778
chr11	125200614	125200781	E068	22211
chr11	125212818	125213118	E068	34415
chr11	125213124	125214119	E068	34721
chr11	125214121	125214171	E068	35718
chr11	125214301	125214364	E068	35898
chr11	125214476	125214537	E068	36073
chr11	125214635	125214865	E068	36232
chr11	125214900	125214954	E068	36497
chr11	125214979	125215209	E068	36576
chr11	125217879	125219083	E068	39476
chr11	125219104	125219528	E068	40701
chr11	125131366	125134290	E069	-44113
chr11	125141374	125141814	E069	-36589
chr11	125141882	125142369	E069	-36034
chr11	125159278	125159318	E069	-19085
chr11	125184527	125185677	E069	6124
chr11	125196971	125197021	E069	18568
chr11	125197154	125197198	E069	18751
chr11	125197278	125197400	E069	18875
chr11	125197429	125197808	E069	19026
chr11	125212818	125213118	E069	34415
chr11	125213124	125214119	E069	34721
chr11	125214121	125214171	E069	35718
chr11	125214301	125214364	E069	35898
chr11	125214476	125214537	E069	36073
chr11	125214635	125214865	E069	36232
chr11	125214900	125214954	E069	36497
chr11	125214979	125215209	E069	36576
chr11	125128558	125128627	E070	-49776
chr11	125128634	125128904	E070	-49499
chr11	125129144	125129194	E070	-49209
chr11	125129198	125129238	E070	-49165
chr11	125129567	125129729	E070	-48674
chr11	125131366	125134290	E070	-44113
chr11	125139844	125139930	E070	-38473
chr11	125139967	125140082	E070	-38321
chr11	125140111	125140218	E070	-38185
chr11	125140313	125140435	E070	-37968
chr11	125140493	125140543	E070	-37860
chr11	125140729	125140962	E070	-37441
chr11	125141374	125141814	E070	-36589
chr11	125141882	125142369	E070	-36034
chr11	125142474	125142551	E070	-35852
chr11	125142609	125142707	E070	-35696
chr11	125142726	125142895	E070	-35508
chr11	125142909	125143089	E070	-35314
chr11	125143235	125143299	E070	-35104
chr11	125143305	125143345	E070	-35058
chr11	125146352	125146431	E070	-31972
chr11	125146644	125146738	E070	-31665
chr11	125149513	125149598	E070	-28805
chr11	125149752	125149824	E070	-28579
chr11	125150029	125150118	E070	-28285
chr11	125150133	125150183	E070	-28220
chr11	125150402	125150461	E070	-27942
chr11	125150463	125150564	E070	-27839
chr11	125150698	125150752	E070	-27651
chr11	125150858	125150902	E070	-27501
chr11	125150937	125150994	E070	-27409
chr11	125151060	125151110	E070	-27293
chr11	125151259	125151402	E070	-27001
chr11	125151570	125151647	E070	-26756
chr11	125154137	125154597	E070	-23806
chr11	125154599	125154663	E070	-23740
chr11	125154950	125155095	E070	-23308
chr11	125155397	125155447	E070	-22956
chr11	125155551	125155600	E070	-22803
chr11	125155731	125156060	E070	-22343
chr11	125156284	125156367	E070	-22036
chr11	125156412	125156462	E070	-21941
chr11	125156502	125156739	E070	-21664
chr11	125156835	125156983	E070	-21420
chr11	125157125	125158152	E070	-20251
chr11	125158209	125158531	E070	-19872
chr11	125158563	125158637	E070	-19766
chr11	125158912	125159014	E070	-19389
chr11	125159278	125159318	E070	-19085
chr11	125159472	125159529	E070	-18874
chr11	125159602	125159652	E070	-18751
chr11	125159703	125159789	E070	-18614
chr11	125159903	125159947	E070	-18456
chr11	125159997	125160304	E070	-18099
chr11	125160388	125160543	E070	-17860
chr11	125160575	125160629	E070	-17774
chr11	125161069	125161151	E070	-17252
chr11	125162463	125162552	E070	-15851
chr11	125162738	125162839	E070	-15564
chr11	125162967	125163017	E070	-15386
chr11	125163243	125163339	E070	-15064
chr11	125170592	125171566	E070	-6837
chr11	125173823	125173887	E070	-4516
chr11	125173896	125173950	E070	-4453
chr11	125174019	125174116	E070	-4287
chr11	125174189	125174375	E070	-4028
chr11	125174429	125174517	E070	-3886
chr11	125174547	125174649	E070	-3754
chr11	125183541	125184056	E070	5138
chr11	125184138	125184512	E070	5735
chr11	125184527	125185677	E070	6124
chr11	125185752	125186058	E070	7349
chr11	125203480	125203777	E070	25077
chr11	125203877	125203927	E070	25474
chr11	125204203	125204253	E070	25800
chr11	125204280	125204330	E070	25877
chr11	125211773	125211860	E070	33370
chr11	125212255	125212748	E070	33852
chr11	125212818	125213118	E070	34415
chr11	125213124	125214119	E070	34721
chr11	125214121	125214171	E070	35718
chr11	125214635	125214865	E070	36232
chr11	125214900	125214954	E070	36497
chr11	125214979	125215209	E070	36576
chr11	125215284	125216692	E070	36881
chr11	125216787	125217043	E070	38384
chr11	125217161	125217852	E070	38758
chr11	125217879	125219083	E070	39476
chr11	125220628	125220714	E070	42225
chr11	125220718	125220768	E070	42315
chr11	125220959	125221065	E070	42556
chr11	125134307	125134447	E071	-43956
chr11	125140729	125140962	E071	-37441
chr11	125141374	125141814	E071	-36589
chr11	125141882	125142369	E071	-36034
chr11	125142474	125142551	E071	-35852
chr11	125142609	125142707	E071	-35696
chr11	125142726	125142895	E071	-35508
chr11	125142909	125143089	E071	-35314
chr11	125156412	125156462	E071	-21941
chr11	125156502	125156739	E071	-21664
chr11	125156835	125156983	E071	-21420
chr11	125157125	125158152	E071	-20251
chr11	125158912	125159014	E071	-19389
chr11	125159278	125159318	E071	-19085
chr11	125159472	125159529	E071	-18874
chr11	125159602	125159652	E071	-18751
chr11	125159703	125159789	E071	-18614
chr11	125183541	125184056	E071	5138
chr11	125184138	125184512	E071	5735
chr11	125184527	125185677	E071	6124
chr11	125197278	125197400	E071	18875
chr11	125197429	125197808	E071	19026
chr11	125197863	125198089	E071	19460
chr11	125198161	125198247	E071	19758
chr11	125212818	125213118	E071	34415
chr11	125213124	125214119	E071	34721
chr11	125214121	125214171	E071	35718
chr11	125214301	125214364	E071	35898
chr11	125214476	125214537	E071	36073
chr11	125214635	125214865	E071	36232
chr11	125214900	125214954	E071	36497
chr11	125214979	125215209	E071	36576
chr11	125215284	125216692	E071	36881
chr11	125131366	125134290	E072	-44113
chr11	125134307	125134447	E072	-43956
chr11	125149513	125149598	E072	-28805
chr11	125157125	125158152	E072	-20251
chr11	125165680	125165741	E072	-12662
chr11	125165798	125166315	E072	-12088
chr11	125172344	125172395	E072	-6008
chr11	125183541	125184056	E072	5138
chr11	125184138	125184512	E072	5735
chr11	125184527	125185677	E072	6124
chr11	125185752	125186058	E072	7349
chr11	125194679	125194729	E072	16276
chr11	125197278	125197400	E072	18875
chr11	125197429	125197808	E072	19026
chr11	125197863	125198089	E072	19460
chr11	125198161	125198247	E072	19758
chr11	125199654	125199716	E072	21251
chr11	125199752	125199894	E072	21349
chr11	125199945	125200053	E072	21542
chr11	125212818	125213118	E072	34415
chr11	125213124	125214119	E072	34721
chr11	125214121	125214171	E072	35718
chr11	125214301	125214364	E072	35898
chr11	125214476	125214537	E072	36073
chr11	125214635	125214865	E072	36232
chr11	125214900	125214954	E072	36497
chr11	125214979	125215209	E072	36576
chr11	125215284	125216692	E072	36881
chr11	125227444	125227567	E072	49041
chr11	125131147	125131207	E073	-47196
chr11	125131366	125134290	E073	-44113
chr11	125134307	125134447	E073	-43956
chr11	125140111	125140218	E073	-38185
chr11	125140313	125140435	E073	-37968
chr11	125140493	125140543	E073	-37860
chr11	125140729	125140962	E073	-37441
chr11	125154599	125154663	E073	-23740
chr11	125165680	125165741	E073	-12662
chr11	125165798	125166315	E073	-12088
chr11	125184138	125184512	E073	5735
chr11	125184527	125185677	E073	6124
chr11	125185752	125186058	E073	7349
chr11	125203480	125203777	E073	25077
chr11	125207418	125207472	E073	29015
chr11	125207638	125207692	E073	29235
chr11	125207750	125208342	E073	29347
chr11	125208410	125209748	E073	30007
chr11	125211436	125211573	E073	33033
chr11	125211773	125211860	E073	33370
chr11	125212255	125212748	E073	33852
chr11	125212818	125213118	E073	34415
chr11	125213124	125214119	E073	34721
chr11	125214121	125214171	E073	35718
chr11	125214301	125214364	E073	35898
chr11	125214476	125214537	E073	36073
chr11	125214635	125214865	E073	36232
chr11	125214900	125214954	E073	36497
chr11	125214979	125215209	E073	36576
chr11	125215284	125216692	E073	36881
chr11	125216787	125217043	E073	38384
chr11	125217161	125217852	E073	38758
chr11	125217879	125219083	E073	39476
chr11	125219104	125219528	E073	40701
chr11	125219642	125219919	E073	41239
chr11	125219988	125220051	E073	41585
chr11	125221405	125221630	E073	43002
chr11	125221666	125221758	E073	43263
chr11	125131366	125134290	E074	-44113
chr11	125141374	125141814	E074	-36589
chr11	125141882	125142369	E074	-36034
chr11	125212818	125213118	E074	34415
chr11	125213124	125214119	E074	34721
chr11	125214121	125214171	E074	35718
chr11	125214301	125214364	E074	35898
chr11	125214476	125214537	E074	36073
chr11	125214635	125214865	E074	36232
chr11	125214900	125214954	E074	36497
chr11	125214979	125215209	E074	36576
chr11	125131366	125134290	E081	-44113
chr11	125149513	125149598	E081	-28805
chr11	125149752	125149824	E081	-28579
chr11	125150029	125150118	E081	-28285
chr11	125150133	125150183	E081	-28220
chr11	125150402	125150461	E081	-27942
chr11	125150463	125150564	E081	-27839
chr11	125150698	125150752	E081	-27651
chr11	125150858	125150902	E081	-27501
chr11	125150937	125150994	E081	-27409
chr11	125151060	125151110	E081	-27293
chr11	125151259	125151402	E081	-27001
chr11	125157125	125158152	E081	-20251
chr11	125158209	125158531	E081	-19872
chr11	125158563	125158637	E081	-19766
chr11	125165186	125165250	E081	-13153
chr11	125165300	125165382	E081	-13021
chr11	125165409	125165486	E081	-12917
chr11	125165680	125165741	E081	-12662
chr11	125165798	125166315	E081	-12088
chr11	125170592	125171566	E081	-6837
chr11	125173170	125173361	E081	-5042
chr11	125173572	125173622	E081	-4781
chr11	125173744	125173794	E081	-4609
chr11	125173823	125173887	E081	-4516
chr11	125173896	125173950	E081	-4453
chr11	125174019	125174116	E081	-4287
chr11	125174189	125174375	E081	-4028
chr11	125174429	125174517	E081	-3886
chr11	125174547	125174649	E081	-3754
chr11	125174680	125174773	E081	-3630
chr11	125174992	125175042	E081	-3361
chr11	125184138	125184512	E081	5735
chr11	125184527	125185677	E081	6124
chr11	125185752	125186058	E081	7349
chr11	125200614	125200781	E081	22211
chr11	125200841	125200933	E081	22438
chr11	125203480	125203777	E081	25077
chr11	125208410	125209748	E081	30007
chr11	125209750	125209946	E081	31347
chr11	125211436	125211573	E081	33033
chr11	125211773	125211860	E081	33370
chr11	125212255	125212748	E081	33852
chr11	125212818	125213118	E081	34415
chr11	125213124	125214119	E081	34721
chr11	125214121	125214171	E081	35718
chr11	125214301	125214364	E081	35898
chr11	125214476	125214537	E081	36073
chr11	125214635	125214865	E081	36232
chr11	125214900	125214954	E081	36497
chr11	125214979	125215209	E081	36576
chr11	125215284	125216692	E081	36881
chr11	125216787	125217043	E081	38384
chr11	125217161	125217852	E081	38758
chr11	125217879	125219083	E081	39476
chr11	125219104	125219528	E081	40701
chr11	125219642	125219919	E081	41239
chr11	125219988	125220051	E081	41585
chr11	125220100	125220150	E081	41697
chr11	125220203	125220294	E081	41800
chr11	125220404	125220571	E081	42001
chr11	125220628	125220714	E081	42225
chr11	125220718	125220768	E081	42315
chr11	125220959	125221065	E081	42556
chr11	125221186	125221403	E081	42783
chr11	125128558	125128627	E082	-49776
chr11	125149513	125149598	E082	-28805
chr11	125149752	125149824	E082	-28579
chr11	125150029	125150118	E082	-28285
chr11	125150133	125150183	E082	-28220
chr11	125150402	125150461	E082	-27942
chr11	125150463	125150564	E082	-27839
chr11	125154137	125154597	E082	-23806
chr11	125154599	125154663	E082	-23740
chr11	125154950	125155095	E082	-23308
chr11	125157125	125158152	E082	-20251
chr11	125159472	125159529	E082	-18874
chr11	125173572	125173622	E082	-4781
chr11	125173744	125173794	E082	-4609
chr11	125173823	125173887	E082	-4516
chr11	125173896	125173950	E082	-4453
chr11	125184138	125184512	E082	5735
chr11	125184527	125185677	E082	6124
chr11	125194679	125194729	E082	16276
chr11	125194772	125194850	E082	16369
chr11	125194965	125195005	E082	16562
chr11	125195168	125195570	E082	16765
chr11	125212255	125212748	E082	33852
chr11	125212818	125213118	E082	34415
chr11	125213124	125214119	E082	34721
chr11	125214121	125214171	E082	35718
chr11	125214301	125214364	E082	35898
chr11	125214476	125214537	E082	36073
chr11	125214635	125214865	E082	36232
chr11	125214900	125214954	E082	36497
chr11	125214979	125215209	E082	36576
chr11	125215284	125216692	E082	36881
chr11	125220959	125221065	E082	42556
chr11	125221186	125221403	E082	42783