rs11220015

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

PKNOX2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0238 (7116/29882,GnomAD)
A=0235 (6842/29118,TOPMED)
A=0274 (1370/5008,1000G)
A=0178 (685/3854,ALSPAC)
A=0188 (696/3708,TWINSUK)

Position: chr11:125301478 (GRCh38.p7) (11q24.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 4 publication(s)

Genomic View: See rs on genome

Enhancer: 421 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.125301478G>A
GRCh37.p13 chr 11	NC_000011.9:g.125171374G>A

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	G=0.635	A=0.365
1000Genomes	American	Sub	694	G=0.870	A=0.130
1000Genomes	East Asian	Sub	1008	G=0.607	A=0.393
1000Genomes	Europe	Sub	1006	G=0.819	A=0.181
1000Genomes	Global	Study-wide	5008	G=0.726	A=0.274
1000Genomes	South Asian	Sub	978	G=0.770	A=0.230
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.822	A=0.178
The Genome Aggregation Database	African	Sub	8674	G=0.689	A=0.311
The Genome Aggregation Database	American	Sub	838	G=0.900	A=0.100
The Genome Aggregation Database	East Asian	Sub	1610	G=0.599	A=0.401
The Genome Aggregation Database	Europe	Sub	18458	G=0.802	A=0.197
The Genome Aggregation Database	Global	Study-wide	29882	G=0.761	A=0.238
The Genome Aggregation Database	Other	Sub	302	G=0.890	A=0.110
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.765	A=0.235
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.812	A=0.188

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
rs11220015	3.66E-05	alcohol dependence	21703634

eQTL of rs11220015 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 rs11220015 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	-47165
chr11	125124308	125124396	E067	-46978
chr11	125124482	125124540	E067	-46834
chr11	125124623	125124683	E067	-46691
chr11	125125867	125126013	E067	-45361
chr11	125126082	125126382	E067	-44992
chr11	125126422	125126520	E067	-44854
chr11	125126589	125126840	E067	-44534
chr11	125127025	125127086	E067	-44288
chr11	125127177	125127340	E067	-44034
chr11	125127436	125127637	E067	-43737
chr11	125131366	125134290	E067	-37084
chr11	125134307	125134447	E067	-36927
chr11	125154137	125154597	E067	-16777
chr11	125154599	125154663	E067	-16711
chr11	125154950	125155095	E067	-16279
chr11	125155397	125155447	E067	-15927
chr11	125155551	125155600	E067	-15774
chr11	125155731	125156060	E067	-15314
chr11	125156284	125156367	E067	-15007
chr11	125156412	125156462	E067	-14912
chr11	125156502	125156739	E067	-14635
chr11	125156835	125156983	E067	-14391
chr11	125157125	125158152	E067	-13222
chr11	125184527	125185677	E067	13153
chr11	125185752	125186058	E067	14378
chr11	125197278	125197400	E067	25904
chr11	125197429	125197808	E067	26055
chr11	125197863	125198089	E067	26489
chr11	125199654	125199716	E067	28280
chr11	125199752	125199894	E067	28378
chr11	125199945	125200053	E067	28571
chr11	125207750	125208342	E067	36376
chr11	125208410	125209748	E067	37036
chr11	125212818	125213118	E067	41444
chr11	125213124	125214119	E067	41750
chr11	125214121	125214171	E067	42747
chr11	125214301	125214364	E067	42927
chr11	125214476	125214537	E067	43102
chr11	125214635	125214865	E067	43261
chr11	125214900	125214954	E067	43526
chr11	125214979	125215209	E067	43605
chr11	125215284	125216692	E067	43910
chr11	125217879	125219083	E067	46505
chr11	125123692	125123768	E068	-47606
chr11	125123811	125124019	E068	-47355
chr11	125124062	125124116	E068	-47258
chr11	125124157	125124209	E068	-47165
chr11	125124308	125124396	E068	-46978
chr11	125131366	125134290	E068	-37084
chr11	125134307	125134447	E068	-36927
chr11	125140729	125140962	E068	-30412
chr11	125141374	125141814	E068	-29560
chr11	125141882	125142369	E068	-29005
chr11	125142474	125142551	E068	-28823
chr11	125142609	125142707	E068	-28667
chr11	125142726	125142895	E068	-28479
chr11	125142909	125143089	E068	-28285
chr11	125145806	125146168	E068	-25206
chr11	125156502	125156739	E068	-14635
chr11	125156835	125156983	E068	-14391
chr11	125157125	125158152	E068	-13222
chr11	125158209	125158531	E068	-12843
chr11	125158563	125158637	E068	-12737
chr11	125165680	125165741	E068	-5633
chr11	125165798	125166315	E068	-5059
chr11	125184138	125184512	E068	12764
chr11	125184527	125185677	E068	13153
chr11	125197278	125197400	E068	25904
chr11	125197429	125197808	E068	26055
chr11	125200181	125200591	E068	28807
chr11	125200614	125200781	E068	29240
chr11	125212818	125213118	E068	41444
chr11	125213124	125214119	E068	41750
chr11	125214121	125214171	E068	42747
chr11	125214301	125214364	E068	42927
chr11	125214476	125214537	E068	43102
chr11	125214635	125214865	E068	43261
chr11	125214900	125214954	E068	43526
chr11	125214979	125215209	E068	43605
chr11	125217879	125219083	E068	46505
chr11	125219104	125219528	E068	47730
chr11	125131366	125134290	E069	-37084
chr11	125141374	125141814	E069	-29560
chr11	125141882	125142369	E069	-29005
chr11	125159278	125159318	E069	-12056
chr11	125184527	125185677	E069	13153
chr11	125196971	125197021	E069	25597
chr11	125197154	125197198	E069	25780
chr11	125197278	125197400	E069	25904
chr11	125197429	125197808	E069	26055
chr11	125212818	125213118	E069	41444
chr11	125213124	125214119	E069	41750
chr11	125214121	125214171	E069	42747
chr11	125214301	125214364	E069	42927
chr11	125214476	125214537	E069	43102
chr11	125214635	125214865	E069	43261
chr11	125214900	125214954	E069	43526
chr11	125214979	125215209	E069	43605
chr11	125126422	125126520	E070	-44854
chr11	125126589	125126840	E070	-44534
chr11	125127025	125127086	E070	-44288
chr11	125127177	125127340	E070	-44034
chr11	125127436	125127637	E070	-43737
chr11	125127752	125127839	E070	-43535
chr11	125127924	125128109	E070	-43265
chr11	125128163	125128343	E070	-43031
chr11	125128357	125128457	E070	-42917
chr11	125128558	125128627	E070	-42747
chr11	125128634	125128904	E070	-42470
chr11	125129144	125129194	E070	-42180
chr11	125129198	125129238	E070	-42136
chr11	125129567	125129729	E070	-41645
chr11	125131366	125134290	E070	-37084
chr11	125139844	125139930	E070	-31444
chr11	125139967	125140082	E070	-31292
chr11	125140111	125140218	E070	-31156
chr11	125140313	125140435	E070	-30939
chr11	125140493	125140543	E070	-30831
chr11	125140729	125140962	E070	-30412
chr11	125141374	125141814	E070	-29560
chr11	125141882	125142369	E070	-29005
chr11	125142474	125142551	E070	-28823
chr11	125142609	125142707	E070	-28667
chr11	125142726	125142895	E070	-28479
chr11	125142909	125143089	E070	-28285
chr11	125143235	125143299	E070	-28075
chr11	125143305	125143345	E070	-28029
chr11	125146352	125146431	E070	-24943
chr11	125146644	125146738	E070	-24636
chr11	125149513	125149598	E070	-21776
chr11	125149752	125149824	E070	-21550
chr11	125150029	125150118	E070	-21256
chr11	125150133	125150183	E070	-21191
chr11	125150402	125150461	E070	-20913
chr11	125150463	125150564	E070	-20810
chr11	125150698	125150752	E070	-20622
chr11	125150858	125150902	E070	-20472
chr11	125150937	125150994	E070	-20380
chr11	125151060	125151110	E070	-20264
chr11	125151259	125151402	E070	-19972
chr11	125151570	125151647	E070	-19727
chr11	125154137	125154597	E070	-16777
chr11	125154599	125154663	E070	-16711
chr11	125154950	125155095	E070	-16279
chr11	125155397	125155447	E070	-15927
chr11	125155551	125155600	E070	-15774
chr11	125155731	125156060	E070	-15314
chr11	125156284	125156367	E070	-15007
chr11	125156412	125156462	E070	-14912
chr11	125156502	125156739	E070	-14635
chr11	125156835	125156983	E070	-14391
chr11	125157125	125158152	E070	-13222
chr11	125158209	125158531	E070	-12843
chr11	125158563	125158637	E070	-12737
chr11	125158912	125159014	E070	-12360
chr11	125159278	125159318	E070	-12056
chr11	125159472	125159529	E070	-11845
chr11	125159602	125159652	E070	-11722
chr11	125159703	125159789	E070	-11585
chr11	125159903	125159947	E070	-11427
chr11	125159997	125160304	E070	-11070
chr11	125160388	125160543	E070	-10831
chr11	125160575	125160629	E070	-10745
chr11	125161069	125161151	E070	-10223
chr11	125162463	125162552	E070	-8822
chr11	125162738	125162839	E070	-8535
chr11	125162967	125163017	E070	-8357
chr11	125163243	125163339	E070	-8035
chr11	125170592	125171566	E070	0
chr11	125173823	125173887	E070	2449
chr11	125173896	125173950	E070	2522
chr11	125174019	125174116	E070	2645
chr11	125174189	125174375	E070	2815
chr11	125174429	125174517	E070	3055
chr11	125174547	125174649	E070	3173
chr11	125183541	125184056	E070	12167
chr11	125184138	125184512	E070	12764
chr11	125184527	125185677	E070	13153
chr11	125185752	125186058	E070	14378
chr11	125203480	125203777	E070	32106
chr11	125203877	125203927	E070	32503
chr11	125204203	125204253	E070	32829
chr11	125204280	125204330	E070	32906
chr11	125211773	125211860	E070	40399
chr11	125212255	125212748	E070	40881
chr11	125212818	125213118	E070	41444
chr11	125213124	125214119	E070	41750
chr11	125214121	125214171	E070	42747
chr11	125214635	125214865	E070	43261
chr11	125214900	125214954	E070	43526
chr11	125214979	125215209	E070	43605
chr11	125215284	125216692	E070	43910
chr11	125216787	125217043	E070	45413
chr11	125217161	125217852	E070	45787
chr11	125217879	125219083	E070	46505
chr11	125220628	125220714	E070	49254
chr11	125220718	125220768	E070	49344
chr11	125220959	125221065	E070	49585
chr11	125126422	125126520	E071	-44854
chr11	125126589	125126840	E071	-44534
chr11	125134307	125134447	E071	-36927
chr11	125140729	125140962	E071	-30412
chr11	125141374	125141814	E071	-29560
chr11	125141882	125142369	E071	-29005
chr11	125142474	125142551	E071	-28823
chr11	125142609	125142707	E071	-28667
chr11	125142726	125142895	E071	-28479
chr11	125142909	125143089	E071	-28285
chr11	125156412	125156462	E071	-14912
chr11	125156502	125156739	E071	-14635
chr11	125156835	125156983	E071	-14391
chr11	125157125	125158152	E071	-13222
chr11	125158912	125159014	E071	-12360
chr11	125159278	125159318	E071	-12056
chr11	125159472	125159529	E071	-11845
chr11	125159602	125159652	E071	-11722
chr11	125159703	125159789	E071	-11585
chr11	125183541	125184056	E071	12167
chr11	125184138	125184512	E071	12764
chr11	125184527	125185677	E071	13153
chr11	125197278	125197400	E071	25904
chr11	125197429	125197808	E071	26055
chr11	125197863	125198089	E071	26489
chr11	125198161	125198247	E071	26787
chr11	125212818	125213118	E071	41444
chr11	125213124	125214119	E071	41750
chr11	125214121	125214171	E071	42747
chr11	125214301	125214364	E071	42927
chr11	125214476	125214537	E071	43102
chr11	125214635	125214865	E071	43261
chr11	125214900	125214954	E071	43526
chr11	125214979	125215209	E071	43605
chr11	125215284	125216692	E071	43910
chr11	125124157	125124209	E072	-47165
chr11	125124308	125124396	E072	-46978
chr11	125124482	125124540	E072	-46834
chr11	125125867	125126013	E072	-45361
chr11	125126082	125126382	E072	-44992
chr11	125126422	125126520	E072	-44854
chr11	125131366	125134290	E072	-37084
chr11	125134307	125134447	E072	-36927
chr11	125149513	125149598	E072	-21776
chr11	125157125	125158152	E072	-13222
chr11	125165680	125165741	E072	-5633
chr11	125165798	125166315	E072	-5059
chr11	125172344	125172395	E072	970
chr11	125183541	125184056	E072	12167
chr11	125184138	125184512	E072	12764
chr11	125184527	125185677	E072	13153
chr11	125185752	125186058	E072	14378
chr11	125194679	125194729	E072	23305
chr11	125197278	125197400	E072	25904
chr11	125197429	125197808	E072	26055
chr11	125197863	125198089	E072	26489
chr11	125198161	125198247	E072	26787
chr11	125199654	125199716	E072	28280
chr11	125199752	125199894	E072	28378
chr11	125199945	125200053	E072	28571
chr11	125212818	125213118	E072	41444
chr11	125213124	125214119	E072	41750
chr11	125214121	125214171	E072	42747
chr11	125214301	125214364	E072	42927
chr11	125214476	125214537	E072	43102
chr11	125214635	125214865	E072	43261
chr11	125214900	125214954	E072	43526
chr11	125214979	125215209	E072	43605
chr11	125215284	125216692	E072	43910
chr11	125124062	125124116	E073	-47258
chr11	125124157	125124209	E073	-47165
chr11	125124308	125124396	E073	-46978
chr11	125124482	125124540	E073	-46834
chr11	125126082	125126382	E073	-44992
chr11	125126422	125126520	E073	-44854
chr11	125126589	125126840	E073	-44534
chr11	125127025	125127086	E073	-44288
chr11	125127177	125127340	E073	-44034
chr11	125131147	125131207	E073	-40167
chr11	125131366	125134290	E073	-37084
chr11	125134307	125134447	E073	-36927
chr11	125140111	125140218	E073	-31156
chr11	125140313	125140435	E073	-30939
chr11	125140493	125140543	E073	-30831
chr11	125140729	125140962	E073	-30412
chr11	125154599	125154663	E073	-16711
chr11	125165680	125165741	E073	-5633
chr11	125165798	125166315	E073	-5059
chr11	125184138	125184512	E073	12764
chr11	125184527	125185677	E073	13153
chr11	125185752	125186058	E073	14378
chr11	125203480	125203777	E073	32106
chr11	125207418	125207472	E073	36044
chr11	125207638	125207692	E073	36264
chr11	125207750	125208342	E073	36376
chr11	125208410	125209748	E073	37036
chr11	125211436	125211573	E073	40062
chr11	125211773	125211860	E073	40399
chr11	125212255	125212748	E073	40881
chr11	125212818	125213118	E073	41444
chr11	125213124	125214119	E073	41750
chr11	125214121	125214171	E073	42747
chr11	125214301	125214364	E073	42927
chr11	125214476	125214537	E073	43102
chr11	125214635	125214865	E073	43261
chr11	125214900	125214954	E073	43526
chr11	125214979	125215209	E073	43605
chr11	125215284	125216692	E073	43910
chr11	125216787	125217043	E073	45413
chr11	125217161	125217852	E073	45787
chr11	125217879	125219083	E073	46505
chr11	125219104	125219528	E073	47730
chr11	125219642	125219919	E073	48268
chr11	125219988	125220051	E073	48614
chr11	125131366	125134290	E074	-37084
chr11	125141374	125141814	E074	-29560
chr11	125141882	125142369	E074	-29005
chr11	125212818	125213118	E074	41444
chr11	125213124	125214119	E074	41750
chr11	125214121	125214171	E074	42747
chr11	125214301	125214364	E074	42927
chr11	125214476	125214537	E074	43102
chr11	125214635	125214865	E074	43261
chr11	125214900	125214954	E074	43526
chr11	125214979	125215209	E074	43605
chr11	125131366	125134290	E081	-37084
chr11	125149513	125149598	E081	-21776
chr11	125149752	125149824	E081	-21550
chr11	125150029	125150118	E081	-21256
chr11	125150133	125150183	E081	-21191
chr11	125150402	125150461	E081	-20913
chr11	125150463	125150564	E081	-20810
chr11	125150698	125150752	E081	-20622
chr11	125150858	125150902	E081	-20472
chr11	125150937	125150994	E081	-20380
chr11	125151060	125151110	E081	-20264
chr11	125151259	125151402	E081	-19972
chr11	125157125	125158152	E081	-13222
chr11	125158209	125158531	E081	-12843
chr11	125158563	125158637	E081	-12737
chr11	125165186	125165250	E081	-6124
chr11	125165300	125165382	E081	-5992
chr11	125165409	125165486	E081	-5888
chr11	125165680	125165741	E081	-5633
chr11	125165798	125166315	E081	-5059
chr11	125170592	125171566	E081	0
chr11	125173170	125173361	E081	1796
chr11	125173572	125173622	E081	2198
chr11	125173744	125173794	E081	2370
chr11	125173823	125173887	E081	2449
chr11	125173896	125173950	E081	2522
chr11	125174019	125174116	E081	2645
chr11	125174189	125174375	E081	2815
chr11	125174429	125174517	E081	3055
chr11	125174547	125174649	E081	3173
chr11	125174680	125174773	E081	3306
chr11	125174992	125175042	E081	3618
chr11	125184138	125184512	E081	12764
chr11	125184527	125185677	E081	13153
chr11	125185752	125186058	E081	14378
chr11	125200614	125200781	E081	29240
chr11	125200841	125200933	E081	29467
chr11	125203480	125203777	E081	32106
chr11	125208410	125209748	E081	37036
chr11	125209750	125209946	E081	38376
chr11	125211436	125211573	E081	40062
chr11	125211773	125211860	E081	40399
chr11	125212255	125212748	E081	40881
chr11	125212818	125213118	E081	41444
chr11	125213124	125214119	E081	41750
chr11	125214121	125214171	E081	42747
chr11	125214301	125214364	E081	42927
chr11	125214476	125214537	E081	43102
chr11	125214635	125214865	E081	43261
chr11	125214900	125214954	E081	43526
chr11	125214979	125215209	E081	43605
chr11	125215284	125216692	E081	43910
chr11	125216787	125217043	E081	45413
chr11	125217161	125217852	E081	45787
chr11	125217879	125219083	E081	46505
chr11	125219104	125219528	E081	47730
chr11	125219642	125219919	E081	48268
chr11	125219988	125220051	E081	48614
chr11	125220100	125220150	E081	48726
chr11	125220203	125220294	E081	48829
chr11	125220404	125220571	E081	49030
chr11	125220628	125220714	E081	49254
chr11	125220718	125220768	E081	49344
chr11	125220959	125221065	E081	49585
chr11	125128558	125128627	E082	-42747
chr11	125149513	125149598	E082	-21776
chr11	125149752	125149824	E082	-21550
chr11	125150029	125150118	E082	-21256
chr11	125150133	125150183	E082	-21191
chr11	125150402	125150461	E082	-20913
chr11	125150463	125150564	E082	-20810
chr11	125154137	125154597	E082	-16777
chr11	125154599	125154663	E082	-16711
chr11	125154950	125155095	E082	-16279
chr11	125157125	125158152	E082	-13222
chr11	125159472	125159529	E082	-11845
chr11	125173572	125173622	E082	2198
chr11	125173744	125173794	E082	2370
chr11	125173823	125173887	E082	2449
chr11	125173896	125173950	E082	2522
chr11	125184138	125184512	E082	12764
chr11	125184527	125185677	E082	13153
chr11	125194679	125194729	E082	23305
chr11	125194772	125194850	E082	23398
chr11	125194965	125195005	E082	23591
chr11	125195168	125195570	E082	23794
chr11	125212255	125212748	E082	40881
chr11	125212818	125213118	E082	41444
chr11	125213124	125214119	E082	41750
chr11	125214121	125214171	E082	42747
chr11	125214301	125214364	E082	42927
chr11	125214476	125214537	E082	43102
chr11	125214635	125214865	E082	43261
chr11	125214900	125214954	E082	43526
chr11	125214979	125215209	E082	43605
chr11	125215284	125216692	E082	43910
chr11	125220959	125221065	E082	49585