rs11602925

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

PKNOX2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0237 (7095/29880,GnomAD)
G=0234 (6813/29118,TOPMED)
G=0273 (1367/5008,1000G)
G=0176 (679/3854,ALSPAC)
G=0186 (689/3708,TWINSUK)

Position: chr11:125301535 (GRCh38.p7) (11q24.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 4 publication(s)

Genomic View: See rs on genome

Enhancer: 423 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.125301535A>G
GRCh37.p13 chr 11	NC_000011.9:g.125171431A>G

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	A=0.635	G=0.365
1000Genomes	American	Sub	694	A=0.870	G=0.130
1000Genomes	East Asian	Sub	1008	A=0.607	G=0.393
1000Genomes	Europe	Sub	1006	A=0.823	G=0.177
1000Genomes	Global	Study-wide	5008	A=0.727	G=0.273
1000Genomes	South Asian	Sub	978	A=0.770	G=0.230
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.824	G=0.176
The Genome Aggregation Database	African	Sub	8674	A=0.690	G=0.310
The Genome Aggregation Database	American	Sub	838	A=0.900	G=0.100
The Genome Aggregation Database	East Asian	Sub	1610	A=0.598	G=0.402
The Genome Aggregation Database	Europe	Sub	18456	A=0.802	G=0.197
The Genome Aggregation Database	Global	Study-wide	29880	A=0.762	G=0.237
The Genome Aggregation Database	Other	Sub	302	A=0.890	G=0.110
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.766	G=0.234
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.814	G=0.186

PMID	Title	Author	Journal
21703634	A meta-analysis of two genome-wide association studies identifies 3 new loci for alcohol dependence.	Wang KS	J Psychiatr Res
23691092	Associations of prenatal nicotine exposure and the dopamine related genes ANKK1 and DRD2 to verbal language.	Eicher JD	PLoS One
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
21298047	The nuclear transcription factor PKNOX2 is a candidate gene for substance dependence in European-origin women.	Chen X	PLoS One

P-Value

SNP ID	p-value	Traits	Study
rs11602925	2.31E-05	alcohol dependence	21703634

eQTL of rs11602925 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 rs11602925 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	125124157	125124209	E067	-47222
chr11	125124308	125124396	E067	-47035
chr11	125124482	125124540	E067	-46891
chr11	125124623	125124683	E067	-46748
chr11	125125867	125126013	E067	-45418
chr11	125126082	125126382	E067	-45049
chr11	125126422	125126520	E067	-44911
chr11	125126589	125126840	E067	-44591
chr11	125127025	125127086	E067	-44345
chr11	125127177	125127340	E067	-44091
chr11	125127436	125127637	E067	-43794
chr11	125131366	125134290	E067	-37141
chr11	125134307	125134447	E067	-36984
chr11	125154137	125154597	E067	-16834
chr11	125154599	125154663	E067	-16768
chr11	125154950	125155095	E067	-16336
chr11	125155397	125155447	E067	-15984
chr11	125155551	125155600	E067	-15831
chr11	125155731	125156060	E067	-15371
chr11	125156284	125156367	E067	-15064
chr11	125156412	125156462	E067	-14969
chr11	125156502	125156739	E067	-14692
chr11	125156835	125156983	E067	-14448
chr11	125157125	125158152	E067	-13279
chr11	125184527	125185677	E067	13096
chr11	125185752	125186058	E067	14321
chr11	125197278	125197400	E067	25847
chr11	125197429	125197808	E067	25998
chr11	125197863	125198089	E067	26432
chr11	125199654	125199716	E067	28223
chr11	125199752	125199894	E067	28321
chr11	125199945	125200053	E067	28514
chr11	125207750	125208342	E067	36319
chr11	125208410	125209748	E067	36979
chr11	125212818	125213118	E067	41387
chr11	125213124	125214119	E067	41693
chr11	125214121	125214171	E067	42690
chr11	125214301	125214364	E067	42870
chr11	125214476	125214537	E067	43045
chr11	125214635	125214865	E067	43204
chr11	125214900	125214954	E067	43469
chr11	125214979	125215209	E067	43548
chr11	125215284	125216692	E067	43853
chr11	125217879	125219083	E067	46448
chr11	125123692	125123768	E068	-47663
chr11	125123811	125124019	E068	-47412
chr11	125124062	125124116	E068	-47315
chr11	125124157	125124209	E068	-47222
chr11	125124308	125124396	E068	-47035
chr11	125131366	125134290	E068	-37141
chr11	125134307	125134447	E068	-36984
chr11	125140729	125140962	E068	-30469
chr11	125141374	125141814	E068	-29617
chr11	125141882	125142369	E068	-29062
chr11	125142474	125142551	E068	-28880
chr11	125142609	125142707	E068	-28724
chr11	125142726	125142895	E068	-28536
chr11	125142909	125143089	E068	-28342
chr11	125145806	125146168	E068	-25263
chr11	125156502	125156739	E068	-14692
chr11	125156835	125156983	E068	-14448
chr11	125157125	125158152	E068	-13279
chr11	125158209	125158531	E068	-12900
chr11	125158563	125158637	E068	-12794
chr11	125165680	125165741	E068	-5690
chr11	125165798	125166315	E068	-5116
chr11	125184138	125184512	E068	12707
chr11	125184527	125185677	E068	13096
chr11	125197278	125197400	E068	25847
chr11	125197429	125197808	E068	25998
chr11	125200181	125200591	E068	28750
chr11	125200614	125200781	E068	29183
chr11	125212818	125213118	E068	41387
chr11	125213124	125214119	E068	41693
chr11	125214121	125214171	E068	42690
chr11	125214301	125214364	E068	42870
chr11	125214476	125214537	E068	43045
chr11	125214635	125214865	E068	43204
chr11	125214900	125214954	E068	43469
chr11	125214979	125215209	E068	43548
chr11	125217879	125219083	E068	46448
chr11	125219104	125219528	E068	47673
chr11	125131366	125134290	E069	-37141
chr11	125141374	125141814	E069	-29617
chr11	125141882	125142369	E069	-29062
chr11	125159278	125159318	E069	-12113
chr11	125184527	125185677	E069	13096
chr11	125196971	125197021	E069	25540
chr11	125197154	125197198	E069	25723
chr11	125197278	125197400	E069	25847
chr11	125197429	125197808	E069	25998
chr11	125212818	125213118	E069	41387
chr11	125213124	125214119	E069	41693
chr11	125214121	125214171	E069	42690
chr11	125214301	125214364	E069	42870
chr11	125214476	125214537	E069	43045
chr11	125214635	125214865	E069	43204
chr11	125214900	125214954	E069	43469
chr11	125214979	125215209	E069	43548
chr11	125126422	125126520	E070	-44911
chr11	125126589	125126840	E070	-44591
chr11	125127025	125127086	E070	-44345
chr11	125127177	125127340	E070	-44091
chr11	125127436	125127637	E070	-43794
chr11	125127752	125127839	E070	-43592
chr11	125127924	125128109	E070	-43322
chr11	125128163	125128343	E070	-43088
chr11	125128357	125128457	E070	-42974
chr11	125128558	125128627	E070	-42804
chr11	125128634	125128904	E070	-42527
chr11	125129144	125129194	E070	-42237
chr11	125129198	125129238	E070	-42193
chr11	125129567	125129729	E070	-41702
chr11	125131366	125134290	E070	-37141
chr11	125139844	125139930	E070	-31501
chr11	125139967	125140082	E070	-31349
chr11	125140111	125140218	E070	-31213
chr11	125140313	125140435	E070	-30996
chr11	125140493	125140543	E070	-30888
chr11	125140729	125140962	E070	-30469
chr11	125141374	125141814	E070	-29617
chr11	125141882	125142369	E070	-29062
chr11	125142474	125142551	E070	-28880
chr11	125142609	125142707	E070	-28724
chr11	125142726	125142895	E070	-28536
chr11	125142909	125143089	E070	-28342
chr11	125143235	125143299	E070	-28132
chr11	125143305	125143345	E070	-28086
chr11	125146352	125146431	E070	-25000
chr11	125146644	125146738	E070	-24693
chr11	125149513	125149598	E070	-21833
chr11	125149752	125149824	E070	-21607
chr11	125150029	125150118	E070	-21313
chr11	125150133	125150183	E070	-21248
chr11	125150402	125150461	E070	-20970
chr11	125150463	125150564	E070	-20867
chr11	125150698	125150752	E070	-20679
chr11	125150858	125150902	E070	-20529
chr11	125150937	125150994	E070	-20437
chr11	125151060	125151110	E070	-20321
chr11	125151259	125151402	E070	-20029
chr11	125151570	125151647	E070	-19784
chr11	125154137	125154597	E070	-16834
chr11	125154599	125154663	E070	-16768
chr11	125154950	125155095	E070	-16336
chr11	125155397	125155447	E070	-15984
chr11	125155551	125155600	E070	-15831
chr11	125155731	125156060	E070	-15371
chr11	125156284	125156367	E070	-15064
chr11	125156412	125156462	E070	-14969
chr11	125156502	125156739	E070	-14692
chr11	125156835	125156983	E070	-14448
chr11	125157125	125158152	E070	-13279
chr11	125158209	125158531	E070	-12900
chr11	125158563	125158637	E070	-12794
chr11	125158912	125159014	E070	-12417
chr11	125159278	125159318	E070	-12113
chr11	125159472	125159529	E070	-11902
chr11	125159602	125159652	E070	-11779
chr11	125159703	125159789	E070	-11642
chr11	125159903	125159947	E070	-11484
chr11	125159997	125160304	E070	-11127
chr11	125160388	125160543	E070	-10888
chr11	125160575	125160629	E070	-10802
chr11	125161069	125161151	E070	-10280
chr11	125162463	125162552	E070	-8879
chr11	125162738	125162839	E070	-8592
chr11	125162967	125163017	E070	-8414
chr11	125163243	125163339	E070	-8092
chr11	125170592	125171566	E070	0
chr11	125173823	125173887	E070	2392
chr11	125173896	125173950	E070	2465
chr11	125174019	125174116	E070	2588
chr11	125174189	125174375	E070	2758
chr11	125174429	125174517	E070	2998
chr11	125174547	125174649	E070	3116
chr11	125183541	125184056	E070	12110
chr11	125184138	125184512	E070	12707
chr11	125184527	125185677	E070	13096
chr11	125185752	125186058	E070	14321
chr11	125203480	125203777	E070	32049
chr11	125203877	125203927	E070	32446
chr11	125204203	125204253	E070	32772
chr11	125204280	125204330	E070	32849
chr11	125211773	125211860	E070	40342
chr11	125212255	125212748	E070	40824
chr11	125212818	125213118	E070	41387
chr11	125213124	125214119	E070	41693
chr11	125214121	125214171	E070	42690
chr11	125214635	125214865	E070	43204
chr11	125214900	125214954	E070	43469
chr11	125214979	125215209	E070	43548
chr11	125215284	125216692	E070	43853
chr11	125216787	125217043	E070	45356
chr11	125217161	125217852	E070	45730
chr11	125217879	125219083	E070	46448
chr11	125220628	125220714	E070	49197
chr11	125220718	125220768	E070	49287
chr11	125220959	125221065	E070	49528
chr11	125126422	125126520	E071	-44911
chr11	125126589	125126840	E071	-44591
chr11	125134307	125134447	E071	-36984
chr11	125140729	125140962	E071	-30469
chr11	125141374	125141814	E071	-29617
chr11	125141882	125142369	E071	-29062
chr11	125142474	125142551	E071	-28880
chr11	125142609	125142707	E071	-28724
chr11	125142726	125142895	E071	-28536
chr11	125142909	125143089	E071	-28342
chr11	125156412	125156462	E071	-14969
chr11	125156502	125156739	E071	-14692
chr11	125156835	125156983	E071	-14448
chr11	125157125	125158152	E071	-13279
chr11	125158912	125159014	E071	-12417
chr11	125159278	125159318	E071	-12113
chr11	125159472	125159529	E071	-11902
chr11	125159602	125159652	E071	-11779
chr11	125159703	125159789	E071	-11642
chr11	125183541	125184056	E071	12110
chr11	125184138	125184512	E071	12707
chr11	125184527	125185677	E071	13096
chr11	125197278	125197400	E071	25847
chr11	125197429	125197808	E071	25998
chr11	125197863	125198089	E071	26432
chr11	125198161	125198247	E071	26730
chr11	125212818	125213118	E071	41387
chr11	125213124	125214119	E071	41693
chr11	125214121	125214171	E071	42690
chr11	125214301	125214364	E071	42870
chr11	125214476	125214537	E071	43045
chr11	125214635	125214865	E071	43204
chr11	125214900	125214954	E071	43469
chr11	125214979	125215209	E071	43548
chr11	125215284	125216692	E071	43853
chr11	125124157	125124209	E072	-47222
chr11	125124308	125124396	E072	-47035
chr11	125124482	125124540	E072	-46891
chr11	125125867	125126013	E072	-45418
chr11	125126082	125126382	E072	-45049
chr11	125126422	125126520	E072	-44911
chr11	125131366	125134290	E072	-37141
chr11	125134307	125134447	E072	-36984
chr11	125149513	125149598	E072	-21833
chr11	125157125	125158152	E072	-13279
chr11	125165680	125165741	E072	-5690
chr11	125165798	125166315	E072	-5116
chr11	125172344	125172395	E072	913
chr11	125183541	125184056	E072	12110
chr11	125184138	125184512	E072	12707
chr11	125184527	125185677	E072	13096
chr11	125185752	125186058	E072	14321
chr11	125194679	125194729	E072	23248
chr11	125197278	125197400	E072	25847
chr11	125197429	125197808	E072	25998
chr11	125197863	125198089	E072	26432
chr11	125198161	125198247	E072	26730
chr11	125199654	125199716	E072	28223
chr11	125199752	125199894	E072	28321
chr11	125199945	125200053	E072	28514
chr11	125212818	125213118	E072	41387
chr11	125213124	125214119	E072	41693
chr11	125214121	125214171	E072	42690
chr11	125214301	125214364	E072	42870
chr11	125214476	125214537	E072	43045
chr11	125214635	125214865	E072	43204
chr11	125214900	125214954	E072	43469
chr11	125214979	125215209	E072	43548
chr11	125215284	125216692	E072	43853
chr11	125124062	125124116	E073	-47315
chr11	125124157	125124209	E073	-47222
chr11	125124308	125124396	E073	-47035
chr11	125124482	125124540	E073	-46891
chr11	125126082	125126382	E073	-45049
chr11	125126422	125126520	E073	-44911
chr11	125126589	125126840	E073	-44591
chr11	125127025	125127086	E073	-44345
chr11	125127177	125127340	E073	-44091
chr11	125131147	125131207	E073	-40224
chr11	125131366	125134290	E073	-37141
chr11	125134307	125134447	E073	-36984
chr11	125140111	125140218	E073	-31213
chr11	125140313	125140435	E073	-30996
chr11	125140493	125140543	E073	-30888
chr11	125140729	125140962	E073	-30469
chr11	125154599	125154663	E073	-16768
chr11	125165680	125165741	E073	-5690
chr11	125165798	125166315	E073	-5116
chr11	125184138	125184512	E073	12707
chr11	125184527	125185677	E073	13096
chr11	125185752	125186058	E073	14321
chr11	125203480	125203777	E073	32049
chr11	125207418	125207472	E073	35987
chr11	125207638	125207692	E073	36207
chr11	125207750	125208342	E073	36319
chr11	125208410	125209748	E073	36979
chr11	125211436	125211573	E073	40005
chr11	125211773	125211860	E073	40342
chr11	125212255	125212748	E073	40824
chr11	125212818	125213118	E073	41387
chr11	125213124	125214119	E073	41693
chr11	125214121	125214171	E073	42690
chr11	125214301	125214364	E073	42870
chr11	125214476	125214537	E073	43045
chr11	125214635	125214865	E073	43204
chr11	125214900	125214954	E073	43469
chr11	125214979	125215209	E073	43548
chr11	125215284	125216692	E073	43853
chr11	125216787	125217043	E073	45356
chr11	125217161	125217852	E073	45730
chr11	125217879	125219083	E073	46448
chr11	125219104	125219528	E073	47673
chr11	125219642	125219919	E073	48211
chr11	125219988	125220051	E073	48557
chr11	125131366	125134290	E074	-37141
chr11	125141374	125141814	E074	-29617
chr11	125141882	125142369	E074	-29062
chr11	125212818	125213118	E074	41387
chr11	125213124	125214119	E074	41693
chr11	125214121	125214171	E074	42690
chr11	125214301	125214364	E074	42870
chr11	125214476	125214537	E074	43045
chr11	125214635	125214865	E074	43204
chr11	125214900	125214954	E074	43469
chr11	125214979	125215209	E074	43548
chr11	125131366	125134290	E081	-37141
chr11	125149513	125149598	E081	-21833
chr11	125149752	125149824	E081	-21607
chr11	125150029	125150118	E081	-21313
chr11	125150133	125150183	E081	-21248
chr11	125150402	125150461	E081	-20970
chr11	125150463	125150564	E081	-20867
chr11	125150698	125150752	E081	-20679
chr11	125150858	125150902	E081	-20529
chr11	125150937	125150994	E081	-20437
chr11	125151060	125151110	E081	-20321
chr11	125151259	125151402	E081	-20029
chr11	125157125	125158152	E081	-13279
chr11	125158209	125158531	E081	-12900
chr11	125158563	125158637	E081	-12794
chr11	125165186	125165250	E081	-6181
chr11	125165300	125165382	E081	-6049
chr11	125165409	125165486	E081	-5945
chr11	125165680	125165741	E081	-5690
chr11	125165798	125166315	E081	-5116
chr11	125170592	125171566	E081	0
chr11	125173170	125173361	E081	1739
chr11	125173572	125173622	E081	2141
chr11	125173744	125173794	E081	2313
chr11	125173823	125173887	E081	2392
chr11	125173896	125173950	E081	2465
chr11	125174019	125174116	E081	2588
chr11	125174189	125174375	E081	2758
chr11	125174429	125174517	E081	2998
chr11	125174547	125174649	E081	3116
chr11	125174680	125174773	E081	3249
chr11	125174992	125175042	E081	3561
chr11	125184138	125184512	E081	12707
chr11	125184527	125185677	E081	13096
chr11	125185752	125186058	E081	14321
chr11	125200614	125200781	E081	29183
chr11	125200841	125200933	E081	29410
chr11	125203480	125203777	E081	32049
chr11	125208410	125209748	E081	36979
chr11	125209750	125209946	E081	38319
chr11	125211436	125211573	E081	40005
chr11	125211773	125211860	E081	40342
chr11	125212255	125212748	E081	40824
chr11	125212818	125213118	E081	41387
chr11	125213124	125214119	E081	41693
chr11	125214121	125214171	E081	42690
chr11	125214301	125214364	E081	42870
chr11	125214476	125214537	E081	43045
chr11	125214635	125214865	E081	43204
chr11	125214900	125214954	E081	43469
chr11	125214979	125215209	E081	43548
chr11	125215284	125216692	E081	43853
chr11	125216787	125217043	E081	45356
chr11	125217161	125217852	E081	45730
chr11	125217879	125219083	E081	46448
chr11	125219104	125219528	E081	47673
chr11	125219642	125219919	E081	48211
chr11	125219988	125220051	E081	48557
chr11	125220100	125220150	E081	48669
chr11	125220203	125220294	E081	48772
chr11	125220404	125220571	E081	48973
chr11	125220628	125220714	E081	49197
chr11	125220718	125220768	E081	49287
chr11	125220959	125221065	E081	49528
chr11	125221186	125221403	E081	49755
chr11	125128558	125128627	E082	-42804
chr11	125149513	125149598	E082	-21833
chr11	125149752	125149824	E082	-21607
chr11	125150029	125150118	E082	-21313
chr11	125150133	125150183	E082	-21248
chr11	125150402	125150461	E082	-20970
chr11	125150463	125150564	E082	-20867
chr11	125154137	125154597	E082	-16834
chr11	125154599	125154663	E082	-16768
chr11	125154950	125155095	E082	-16336
chr11	125157125	125158152	E082	-13279
chr11	125159472	125159529	E082	-11902
chr11	125173572	125173622	E082	2141
chr11	125173744	125173794	E082	2313
chr11	125173823	125173887	E082	2392
chr11	125173896	125173950	E082	2465
chr11	125184138	125184512	E082	12707
chr11	125184527	125185677	E082	13096
chr11	125194679	125194729	E082	23248
chr11	125194772	125194850	E082	23341
chr11	125194965	125195005	E082	23534
chr11	125195168	125195570	E082	23737
chr11	125212255	125212748	E082	40824
chr11	125212818	125213118	E082	41387
chr11	125213124	125214119	E082	41693
chr11	125214121	125214171	E082	42690
chr11	125214301	125214364	E082	42870
chr11	125214476	125214537	E082	43045
chr11	125214635	125214865	E082	43204
chr11	125214900	125214954	E082	43469
chr11	125214979	125215209	E082	43548
chr11	125215284	125216692	E082	43853
chr11	125220959	125221065	E082	49528
chr11	125221186	125221403	E082	49755