rs10893365

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

PKNOX2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0271 (8129/29982,GnomAD)
C=0290 (8461/29118,TOPMED)
C=0335 (1676/5008,1000G)
C=0174 (671/3854,ALSPAC)
C=0182 (674/3708,TWINSUK)

Position: chr11:125306541 (GRCh38.p7) (11q24.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 6 publication(s)

Genomic View: See rs on genome

Enhancer: 399 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.125306541T>C
GRCh37.p13 chr 11	NC_000011.9:g.125176437T>C

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	T=0.540	C=0.460
1000Genomes	American	Sub	694	T=0.880	C=0.120
1000Genomes	East Asian	Sub	1008	T=0.462	C=0.538
1000Genomes	Europe	Sub	1006	T=0.826	C=0.174
1000Genomes	Global	Study-wide	5008	T=0.665	C=0.335
1000Genomes	South Asian	Sub	978	T=0.720	C=0.280
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.826	C=0.174
The Genome Aggregation Database	African	Sub	8722	T=0.583	C=0.417
The Genome Aggregation Database	American	Sub	838	T=0.910	C=0.090
The Genome Aggregation Database	East Asian	Sub	1620	T=0.467	C=0.533
The Genome Aggregation Database	Europe	Sub	18500	T=0.810	C=0.189
The Genome Aggregation Database	Global	Study-wide	29982	T=0.728	C=0.271
The Genome Aggregation Database	Other	Sub	302	T=0.830	C=0.170
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.709	C=0.290
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.818	C=0.182

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
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
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
rs10893365	0.00000955	alcohol dependence	21703634
rs10893365	0.000036	alcohol dependence	21956439

eQTL of rs10893365 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 rs10893365 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	125126589	125126840	E067	-49597
chr11	125127025	125127086	E067	-49351
chr11	125127177	125127340	E067	-49097
chr11	125127436	125127637	E067	-48800
chr11	125131366	125134290	E067	-42147
chr11	125134307	125134447	E067	-41990
chr11	125154137	125154597	E067	-21840
chr11	125154599	125154663	E067	-21774
chr11	125154950	125155095	E067	-21342
chr11	125155397	125155447	E067	-20990
chr11	125155551	125155600	E067	-20837
chr11	125155731	125156060	E067	-20377
chr11	125156284	125156367	E067	-20070
chr11	125156412	125156462	E067	-19975
chr11	125156502	125156739	E067	-19698
chr11	125156835	125156983	E067	-19454
chr11	125157125	125158152	E067	-18285
chr11	125184527	125185677	E067	8090
chr11	125185752	125186058	E067	9315
chr11	125197278	125197400	E067	20841
chr11	125197429	125197808	E067	20992
chr11	125197863	125198089	E067	21426
chr11	125199654	125199716	E067	23217
chr11	125199752	125199894	E067	23315
chr11	125199945	125200053	E067	23508
chr11	125207750	125208342	E067	31313
chr11	125208410	125209748	E067	31973
chr11	125212818	125213118	E067	36381
chr11	125213124	125214119	E067	36687
chr11	125214121	125214171	E067	37684
chr11	125214301	125214364	E067	37864
chr11	125214476	125214537	E067	38039
chr11	125214635	125214865	E067	38198
chr11	125214900	125214954	E067	38463
chr11	125214979	125215209	E067	38542
chr11	125215284	125216692	E067	38847
chr11	125217879	125219083	E067	41442
chr11	125131366	125134290	E068	-42147
chr11	125134307	125134447	E068	-41990
chr11	125140729	125140962	E068	-35475
chr11	125141374	125141814	E068	-34623
chr11	125141882	125142369	E068	-34068
chr11	125142474	125142551	E068	-33886
chr11	125142609	125142707	E068	-33730
chr11	125142726	125142895	E068	-33542
chr11	125142909	125143089	E068	-33348
chr11	125145806	125146168	E068	-30269
chr11	125156502	125156739	E068	-19698
chr11	125156835	125156983	E068	-19454
chr11	125157125	125158152	E068	-18285
chr11	125158209	125158531	E068	-17906
chr11	125158563	125158637	E068	-17800
chr11	125165680	125165741	E068	-10696
chr11	125165798	125166315	E068	-10122
chr11	125184138	125184512	E068	7701
chr11	125184527	125185677	E068	8090
chr11	125197278	125197400	E068	20841
chr11	125197429	125197808	E068	20992
chr11	125200181	125200591	E068	23744
chr11	125200614	125200781	E068	24177
chr11	125212818	125213118	E068	36381
chr11	125213124	125214119	E068	36687
chr11	125214121	125214171	E068	37684
chr11	125214301	125214364	E068	37864
chr11	125214476	125214537	E068	38039
chr11	125214635	125214865	E068	38198
chr11	125214900	125214954	E068	38463
chr11	125214979	125215209	E068	38542
chr11	125217879	125219083	E068	41442
chr11	125219104	125219528	E068	42667
chr11	125131366	125134290	E069	-42147
chr11	125141374	125141814	E069	-34623
chr11	125141882	125142369	E069	-34068
chr11	125159278	125159318	E069	-17119
chr11	125184527	125185677	E069	8090
chr11	125196971	125197021	E069	20534
chr11	125197154	125197198	E069	20717
chr11	125197278	125197400	E069	20841
chr11	125197429	125197808	E069	20992
chr11	125212818	125213118	E069	36381
chr11	125213124	125214119	E069	36687
chr11	125214121	125214171	E069	37684
chr11	125214301	125214364	E069	37864
chr11	125214476	125214537	E069	38039
chr11	125214635	125214865	E069	38198
chr11	125214900	125214954	E069	38463
chr11	125214979	125215209	E069	38542
chr11	125126589	125126840	E070	-49597
chr11	125127025	125127086	E070	-49351
chr11	125127177	125127340	E070	-49097
chr11	125127436	125127637	E070	-48800
chr11	125127752	125127839	E070	-48598
chr11	125127924	125128109	E070	-48328
chr11	125128163	125128343	E070	-48094
chr11	125128357	125128457	E070	-47980
chr11	125128558	125128627	E070	-47810
chr11	125128634	125128904	E070	-47533
chr11	125129144	125129194	E070	-47243
chr11	125129198	125129238	E070	-47199
chr11	125129567	125129729	E070	-46708
chr11	125131366	125134290	E070	-42147
chr11	125139844	125139930	E070	-36507
chr11	125139967	125140082	E070	-36355
chr11	125140111	125140218	E070	-36219
chr11	125140313	125140435	E070	-36002
chr11	125140493	125140543	E070	-35894
chr11	125140729	125140962	E070	-35475
chr11	125141374	125141814	E070	-34623
chr11	125141882	125142369	E070	-34068
chr11	125142474	125142551	E070	-33886
chr11	125142609	125142707	E070	-33730
chr11	125142726	125142895	E070	-33542
chr11	125142909	125143089	E070	-33348
chr11	125143235	125143299	E070	-33138
chr11	125143305	125143345	E070	-33092
chr11	125146352	125146431	E070	-30006
chr11	125146644	125146738	E070	-29699
chr11	125149513	125149598	E070	-26839
chr11	125149752	125149824	E070	-26613
chr11	125150029	125150118	E070	-26319
chr11	125150133	125150183	E070	-26254
chr11	125150402	125150461	E070	-25976
chr11	125150463	125150564	E070	-25873
chr11	125150698	125150752	E070	-25685
chr11	125150858	125150902	E070	-25535
chr11	125150937	125150994	E070	-25443
chr11	125151060	125151110	E070	-25327
chr11	125151259	125151402	E070	-25035
chr11	125151570	125151647	E070	-24790
chr11	125154137	125154597	E070	-21840
chr11	125154599	125154663	E070	-21774
chr11	125154950	125155095	E070	-21342
chr11	125155397	125155447	E070	-20990
chr11	125155551	125155600	E070	-20837
chr11	125155731	125156060	E070	-20377
chr11	125156284	125156367	E070	-20070
chr11	125156412	125156462	E070	-19975
chr11	125156502	125156739	E070	-19698
chr11	125156835	125156983	E070	-19454
chr11	125157125	125158152	E070	-18285
chr11	125158209	125158531	E070	-17906
chr11	125158563	125158637	E070	-17800
chr11	125158912	125159014	E070	-17423
chr11	125159278	125159318	E070	-17119
chr11	125159472	125159529	E070	-16908
chr11	125159602	125159652	E070	-16785
chr11	125159703	125159789	E070	-16648
chr11	125159903	125159947	E070	-16490
chr11	125159997	125160304	E070	-16133
chr11	125160388	125160543	E070	-15894
chr11	125160575	125160629	E070	-15808
chr11	125161069	125161151	E070	-15286
chr11	125162463	125162552	E070	-13885
chr11	125162738	125162839	E070	-13598
chr11	125162967	125163017	E070	-13420
chr11	125163243	125163339	E070	-13098
chr11	125170592	125171566	E070	-4871
chr11	125173823	125173887	E070	-2550
chr11	125173896	125173950	E070	-2487
chr11	125174019	125174116	E070	-2321
chr11	125174189	125174375	E070	-2062
chr11	125174429	125174517	E070	-1920
chr11	125174547	125174649	E070	-1788
chr11	125183541	125184056	E070	7104
chr11	125184138	125184512	E070	7701
chr11	125184527	125185677	E070	8090
chr11	125185752	125186058	E070	9315
chr11	125203480	125203777	E070	27043
chr11	125203877	125203927	E070	27440
chr11	125204203	125204253	E070	27766
chr11	125204280	125204330	E070	27843
chr11	125211773	125211860	E070	35336
chr11	125212255	125212748	E070	35818
chr11	125212818	125213118	E070	36381
chr11	125213124	125214119	E070	36687
chr11	125214121	125214171	E070	37684
chr11	125214635	125214865	E070	38198
chr11	125214900	125214954	E070	38463
chr11	125214979	125215209	E070	38542
chr11	125215284	125216692	E070	38847
chr11	125216787	125217043	E070	40350
chr11	125217161	125217852	E070	40724
chr11	125217879	125219083	E070	41442
chr11	125220628	125220714	E070	44191
chr11	125220718	125220768	E070	44281
chr11	125220959	125221065	E070	44522
chr11	125126589	125126840	E071	-49597
chr11	125134307	125134447	E071	-41990
chr11	125140729	125140962	E071	-35475
chr11	125141374	125141814	E071	-34623
chr11	125141882	125142369	E071	-34068
chr11	125142474	125142551	E071	-33886
chr11	125142609	125142707	E071	-33730
chr11	125142726	125142895	E071	-33542
chr11	125142909	125143089	E071	-33348
chr11	125156412	125156462	E071	-19975
chr11	125156502	125156739	E071	-19698
chr11	125156835	125156983	E071	-19454
chr11	125157125	125158152	E071	-18285
chr11	125158912	125159014	E071	-17423
chr11	125159278	125159318	E071	-17119
chr11	125159472	125159529	E071	-16908
chr11	125159602	125159652	E071	-16785
chr11	125159703	125159789	E071	-16648
chr11	125183541	125184056	E071	7104
chr11	125184138	125184512	E071	7701
chr11	125184527	125185677	E071	8090
chr11	125197278	125197400	E071	20841
chr11	125197429	125197808	E071	20992
chr11	125197863	125198089	E071	21426
chr11	125198161	125198247	E071	21724
chr11	125212818	125213118	E071	36381
chr11	125213124	125214119	E071	36687
chr11	125214121	125214171	E071	37684
chr11	125214301	125214364	E071	37864
chr11	125214476	125214537	E071	38039
chr11	125214635	125214865	E071	38198
chr11	125214900	125214954	E071	38463
chr11	125214979	125215209	E071	38542
chr11	125215284	125216692	E071	38847
chr11	125131366	125134290	E072	-42147
chr11	125134307	125134447	E072	-41990
chr11	125149513	125149598	E072	-26839
chr11	125157125	125158152	E072	-18285
chr11	125165680	125165741	E072	-10696
chr11	125165798	125166315	E072	-10122
chr11	125172344	125172395	E072	-4042
chr11	125183541	125184056	E072	7104
chr11	125184138	125184512	E072	7701
chr11	125184527	125185677	E072	8090
chr11	125185752	125186058	E072	9315
chr11	125194679	125194729	E072	18242
chr11	125197278	125197400	E072	20841
chr11	125197429	125197808	E072	20992
chr11	125197863	125198089	E072	21426
chr11	125198161	125198247	E072	21724
chr11	125199654	125199716	E072	23217
chr11	125199752	125199894	E072	23315
chr11	125199945	125200053	E072	23508
chr11	125212818	125213118	E072	36381
chr11	125213124	125214119	E072	36687
chr11	125214121	125214171	E072	37684
chr11	125214301	125214364	E072	37864
chr11	125214476	125214537	E072	38039
chr11	125214635	125214865	E072	38198
chr11	125214900	125214954	E072	38463
chr11	125214979	125215209	E072	38542
chr11	125215284	125216692	E072	38847
chr11	125126589	125126840	E073	-49597
chr11	125127025	125127086	E073	-49351
chr11	125127177	125127340	E073	-49097
chr11	125131147	125131207	E073	-45230
chr11	125131366	125134290	E073	-42147
chr11	125134307	125134447	E073	-41990
chr11	125140111	125140218	E073	-36219
chr11	125140313	125140435	E073	-36002
chr11	125140493	125140543	E073	-35894
chr11	125140729	125140962	E073	-35475
chr11	125154599	125154663	E073	-21774
chr11	125165680	125165741	E073	-10696
chr11	125165798	125166315	E073	-10122
chr11	125184138	125184512	E073	7701
chr11	125184527	125185677	E073	8090
chr11	125185752	125186058	E073	9315
chr11	125203480	125203777	E073	27043
chr11	125207418	125207472	E073	30981
chr11	125207638	125207692	E073	31201
chr11	125207750	125208342	E073	31313
chr11	125208410	125209748	E073	31973
chr11	125211436	125211573	E073	34999
chr11	125211773	125211860	E073	35336
chr11	125212255	125212748	E073	35818
chr11	125212818	125213118	E073	36381
chr11	125213124	125214119	E073	36687
chr11	125214121	125214171	E073	37684
chr11	125214301	125214364	E073	37864
chr11	125214476	125214537	E073	38039
chr11	125214635	125214865	E073	38198
chr11	125214900	125214954	E073	38463
chr11	125214979	125215209	E073	38542
chr11	125215284	125216692	E073	38847
chr11	125216787	125217043	E073	40350
chr11	125217161	125217852	E073	40724
chr11	125217879	125219083	E073	41442
chr11	125219104	125219528	E073	42667
chr11	125219642	125219919	E073	43205
chr11	125219988	125220051	E073	43551
chr11	125221405	125221630	E073	44968
chr11	125221666	125221758	E073	45229
chr11	125131366	125134290	E074	-42147
chr11	125141374	125141814	E074	-34623
chr11	125141882	125142369	E074	-34068
chr11	125212818	125213118	E074	36381
chr11	125213124	125214119	E074	36687
chr11	125214121	125214171	E074	37684
chr11	125214301	125214364	E074	37864
chr11	125214476	125214537	E074	38039
chr11	125214635	125214865	E074	38198
chr11	125214900	125214954	E074	38463
chr11	125214979	125215209	E074	38542
chr11	125131366	125134290	E081	-42147
chr11	125149513	125149598	E081	-26839
chr11	125149752	125149824	E081	-26613
chr11	125150029	125150118	E081	-26319
chr11	125150133	125150183	E081	-26254
chr11	125150402	125150461	E081	-25976
chr11	125150463	125150564	E081	-25873
chr11	125150698	125150752	E081	-25685
chr11	125150858	125150902	E081	-25535
chr11	125150937	125150994	E081	-25443
chr11	125151060	125151110	E081	-25327
chr11	125151259	125151402	E081	-25035
chr11	125157125	125158152	E081	-18285
chr11	125158209	125158531	E081	-17906
chr11	125158563	125158637	E081	-17800
chr11	125165186	125165250	E081	-11187
chr11	125165300	125165382	E081	-11055
chr11	125165409	125165486	E081	-10951
chr11	125165680	125165741	E081	-10696
chr11	125165798	125166315	E081	-10122
chr11	125170592	125171566	E081	-4871
chr11	125173170	125173361	E081	-3076
chr11	125173572	125173622	E081	-2815
chr11	125173744	125173794	E081	-2643
chr11	125173823	125173887	E081	-2550
chr11	125173896	125173950	E081	-2487
chr11	125174019	125174116	E081	-2321
chr11	125174189	125174375	E081	-2062
chr11	125174429	125174517	E081	-1920
chr11	125174547	125174649	E081	-1788
chr11	125174680	125174773	E081	-1664
chr11	125174992	125175042	E081	-1395
chr11	125184138	125184512	E081	7701
chr11	125184527	125185677	E081	8090
chr11	125185752	125186058	E081	9315
chr11	125200614	125200781	E081	24177
chr11	125200841	125200933	E081	24404
chr11	125203480	125203777	E081	27043
chr11	125208410	125209748	E081	31973
chr11	125209750	125209946	E081	33313
chr11	125211436	125211573	E081	34999
chr11	125211773	125211860	E081	35336
chr11	125212255	125212748	E081	35818
chr11	125212818	125213118	E081	36381
chr11	125213124	125214119	E081	36687
chr11	125214121	125214171	E081	37684
chr11	125214301	125214364	E081	37864
chr11	125214476	125214537	E081	38039
chr11	125214635	125214865	E081	38198
chr11	125214900	125214954	E081	38463
chr11	125214979	125215209	E081	38542
chr11	125215284	125216692	E081	38847
chr11	125216787	125217043	E081	40350
chr11	125217161	125217852	E081	40724
chr11	125217879	125219083	E081	41442
chr11	125219104	125219528	E081	42667
chr11	125219642	125219919	E081	43205
chr11	125219988	125220051	E081	43551
chr11	125220100	125220150	E081	43663
chr11	125220203	125220294	E081	43766
chr11	125220404	125220571	E081	43967
chr11	125220628	125220714	E081	44191
chr11	125220718	125220768	E081	44281
chr11	125220959	125221065	E081	44522
chr11	125221186	125221403	E081	44749
chr11	125128558	125128627	E082	-47810
chr11	125149513	125149598	E082	-26839
chr11	125149752	125149824	E082	-26613
chr11	125150029	125150118	E082	-26319
chr11	125150133	125150183	E082	-26254
chr11	125150402	125150461	E082	-25976
chr11	125150463	125150564	E082	-25873
chr11	125154137	125154597	E082	-21840
chr11	125154599	125154663	E082	-21774
chr11	125154950	125155095	E082	-21342
chr11	125157125	125158152	E082	-18285
chr11	125159472	125159529	E082	-16908
chr11	125173572	125173622	E082	-2815
chr11	125173744	125173794	E082	-2643
chr11	125173823	125173887	E082	-2550
chr11	125173896	125173950	E082	-2487
chr11	125184138	125184512	E082	7701
chr11	125184527	125185677	E082	8090
chr11	125194679	125194729	E082	18242
chr11	125194772	125194850	E082	18335
chr11	125194965	125195005	E082	18528
chr11	125195168	125195570	E082	18731
chr11	125212255	125212748	E082	35818
chr11	125212818	125213118	E082	36381
chr11	125213124	125214119	E082	36687
chr11	125214121	125214171	E082	37684
chr11	125214301	125214364	E082	37864
chr11	125214476	125214537	E082	38039
chr11	125214635	125214865	E082	38198
chr11	125214900	125214954	E082	38463
chr11	125214979	125215209	E082	38542
chr11	125215284	125216692	E082	38847
chr11	125220959	125221065	E082	44522
chr11	125221186	125221403	E082	44749