rs2642003

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

KANK1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T==0283 (8465/29826,GnomAD)
T==0350 (1755/5008,1000G)
T==0208 (802/3854,ALSPAC)
T==0205 (760/3708,TWINSUK)

Position: chr9:592229 (GRCh38.p7) (9p24.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 382 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 9	NC_000009.12:g.592229T>C
GRCh37.p13 chr 9	NC_000009.11:g.592229T>C
KANK1 RefSeqGene	NG_016331.2:g.126936T>C

Gene: KANK1, KN motif and ankyrin repeat domains 1(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
KANK1 transcript variant 3	NM_001256876.1:c.	N/A	Intron Variant
KANK1 transcript variant 4	NM_001256877.1:c.	N/A	Intron Variant
KANK1 transcript variant 1	NM_015158.3:c.	N/A	Intron Variant
KANK1 transcript variant 2	NM_153186.4:c.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X2	XM_005251411.2:c.	N/A	Intron Variant
KANK1 transcript variant X5	XM_011517819.1:c.	N/A	Intron Variant
KANK1 transcript variant X6	XM_011517820.1:c.	N/A	Intron Variant
KANK1 transcript variant X1	XM_017014511.1:c.	N/A	Intron Variant
KANK1 transcript variant X4	XM_017014513.1:c.	N/A	Intron Variant
KANK1 transcript variant X10	XM_017014515.1:c.	N/A	Intron Variant
KANK1 transcript variant X13	XM_017014518.1:c.	N/A	Intron Variant
KANK1 transcript variant X15	XM_017014520.1:c.	N/A	Intron Variant
KANK1 transcript variant X17	XM_017014522.1:c.	N/A	Intron Variant
KANK1 transcript variant X18	XM_017014523.1:c.	N/A	Intron Variant
KANK1 transcript variant X29	XM_017014528.1:c.	N/A	Intron Variant
KANK1 transcript variant X24	XM_005251414.3:c.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X22	XM_005251415.2:c.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X26	XM_005251416.2:c.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X23	XM_005251417.3:c.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X25	XM_005251418.2:c.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X27	XM_005251419.2:c.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X8	XM_006716743.2:c.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X7	XM_011517821.1:c.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X3	XM_017014512.1:c.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X9	XM_017014514.1:c.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X11	XM_017014516.1:c.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X12	XM_017014517.1:c.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X14	XM_017014519.1:c.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X16	XM_017014521.1:c.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X19	XM_017014524.1:c.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X20	XM_017014525.1:c.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X21	XM_017014526.1:c.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X28	XM_017014527.1:c.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X30	XM_017014529.1:c.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X31	XM_017014530.1:c.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X32	XM_017014531.1:c.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X33	XM_017014532.1:c.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X34	XM_017014533.1:c.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X35	XM_017014534.1:c.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X36	XM_017014535.1:c.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X37	XM_017014536.1:c.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X38	XM_017014537.1:c.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X39	XM_017014538.1:c.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X41	XM_017014539.1:c.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X42	XM_017014540.1:c.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X43	XM_017014541.1:c.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X44	XM_017014542.1:c.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X40	XR_001746257.1:n.	N/A	Genic Upstream Transcript Variant
KANK1 transcript variant X45	XR_001746258.1:n.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.402	C=0.598
1000Genomes	American	Sub	694	T=0.330	C=0.670
1000Genomes	East Asian	Sub	1008	T=0.542	C=0.458
1000Genomes	Europe	Sub	1006	T=0.225	C=0.775
1000Genomes	Global	Study-wide	5008	T=0.350	C=0.650
1000Genomes	South Asian	Sub	978	T=0.230	C=0.770
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.208	C=0.792
The Genome Aggregation Database	African	Sub	8604	T=0.353	C=0.647
The Genome Aggregation Database	American	Sub	836	T=0.290	C=0.710
The Genome Aggregation Database	East Asian	Sub	1610	T=0.598	C=0.402
The Genome Aggregation Database	Europe	Sub	18474	T=0.222	C=0.777
The Genome Aggregation Database	Global	Study-wide	29826	T=0.283	C=0.716
The Genome Aggregation Database	Other	Sub	302	T=0.370	C=0.630
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.205	C=0.795

PMID	Title	Author	Journal
23743675	A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.	Kapoor M	Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs2642003	7.04E-05	alcohol consumption	23743675

eQTL of rs2642003 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 rs2642003 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 )
chr9	544406	544559	E067	-47670
chr9	544637	544773	E067	-47456
chr9	544890	545079	E067	-47150
chr9	545245	545352	E067	-46877
chr9	545536	545720	E067	-46509
chr9	545724	545829	E067	-46400
chr9	546262	547628	E067	-44601
chr9	547741	547856	E067	-44373
chr9	547891	548104	E067	-44125
chr9	548193	548243	E067	-43986
chr9	549261	549344	E067	-42885
chr9	558445	558593	E067	-33636
chr9	560046	560243	E067	-31986
chr9	560348	560446	E067	-31783
chr9	560500	560550	E067	-31679
chr9	560701	560789	E067	-31440
chr9	560845	561205	E067	-31024
chr9	561468	561924	E067	-30305
chr9	562439	562642	E067	-29587
chr9	562912	563844	E067	-28385
chr9	563874	564064	E067	-28165
chr9	569032	570658	E067	-21571
chr9	570713	570786	E067	-21443
chr9	570925	570999	E067	-21230
chr9	571096	571215	E067	-21014
chr9	571221	571532	E067	-20697
chr9	571582	572115	E067	-20114
chr9	572958	573162	E067	-19067
chr9	573583	574603	E067	-17626
chr9	589168	589389	E067	-2840
chr9	589520	589584	E067	-2645
chr9	589600	590159	E067	-2070
chr9	590160	590507	E067	-1722
chr9	591279	591734	E067	-495
chr9	591999	592597	E067	0
chr9	596434	596484	E067	4205
chr9	611236	611286	E067	19007
chr9	611471	611521	E067	19242
chr9	613610	614810	E067	21381
chr9	614921	614971	E067	22692
chr9	614997	615051	E067	22768
chr9	625970	626215	E067	33741
chr9	626378	626418	E067	34149
chr9	626554	626692	E067	34325
chr9	626731	626962	E067	34502
chr9	627032	627454	E067	34803
chr9	544239	544289	E068	-47940
chr9	544406	544559	E068	-47670
chr9	544637	544773	E068	-47456
chr9	544890	545079	E068	-47150
chr9	545245	545352	E068	-46877
chr9	545536	545720	E068	-46509
chr9	545724	545829	E068	-46400
chr9	547891	548104	E068	-44125
chr9	548193	548243	E068	-43986
chr9	548384	548463	E068	-43766
chr9	552035	552935	E068	-39294
chr9	560845	561205	E068	-31024
chr9	561468	561924	E068	-30305
chr9	562439	562642	E068	-29587
chr9	564319	564395	E068	-27834
chr9	564787	564837	E068	-27392
chr9	570713	570786	E068	-21443
chr9	570925	570999	E068	-21230
chr9	571096	571215	E068	-21014
chr9	571221	571532	E068	-20697
chr9	571582	572115	E068	-20114
chr9	573583	574603	E068	-17626
chr9	574613	574653	E068	-17576
chr9	574754	574818	E068	-17411
chr9	579663	579718	E068	-12511
chr9	589168	589389	E068	-2840
chr9	589520	589584	E068	-2645
chr9	589600	590159	E068	-2070
chr9	590160	590507	E068	-1722
chr9	590828	590904	E068	-1325
chr9	590966	591151	E068	-1078
chr9	591279	591734	E068	-495
chr9	591999	592597	E068	0
chr9	608530	608829	E068	16301
chr9	608920	609108	E068	16691
chr9	611236	611286	E068	19007
chr9	611471	611521	E068	19242
chr9	615882	615993	E068	23653
chr9	616662	617026	E068	24433
chr9	617361	617943	E068	25132
chr9	619108	619185	E068	26879
chr9	619431	619591	E068	27202
chr9	621214	621897	E068	28985
chr9	624987	625545	E068	32758
chr9	625570	625630	E068	33341
chr9	625687	625737	E068	33458
chr9	625760	625951	E068	33531
chr9	625970	626215	E068	33741
chr9	626378	626418	E068	34149
chr9	627032	627454	E068	34803
chr9	627620	627910	E068	35391
chr9	628077	628139	E068	35848
chr9	628176	628272	E068	35947
chr9	628389	628472	E068	36160
chr9	628480	628617	E068	36251
chr9	628640	628731	E068	36411
chr9	629215	629404	E068	36986
chr9	629442	629570	E068	37213
chr9	638055	638151	E068	45826
chr9	638197	638452	E068	45968
chr9	639026	639122	E068	46797
chr9	639186	639236	E068	46957
chr9	641365	641539	E068	49136
chr9	641793	641883	E068	49564
chr9	544239	544289	E069	-47940
chr9	544406	544559	E069	-47670
chr9	544637	544773	E069	-47456
chr9	544890	545079	E069	-47150
chr9	545245	545352	E069	-46877
chr9	545536	545720	E069	-46509
chr9	545724	545829	E069	-46400
chr9	546262	547628	E069	-44601
chr9	547741	547856	E069	-44373
chr9	547891	548104	E069	-44125
chr9	548193	548243	E069	-43986
chr9	549261	549344	E069	-42885
chr9	549370	550149	E069	-42080
chr9	552035	552935	E069	-39294
chr9	560348	560446	E069	-31783
chr9	560500	560550	E069	-31679
chr9	560701	560789	E069	-31440
chr9	560845	561205	E069	-31024
chr9	561468	561924	E069	-30305
chr9	562439	562642	E069	-29587
chr9	562912	563844	E069	-28385
chr9	563874	564064	E069	-28165
chr9	564319	564395	E069	-27834
chr9	564787	564837	E069	-27392
chr9	564856	564906	E069	-27323
chr9	564910	564998	E069	-27231
chr9	567283	567458	E069	-24771
chr9	567464	567885	E069	-24344
chr9	569032	570658	E069	-21571
chr9	570713	570786	E069	-21443
chr9	570925	570999	E069	-21230
chr9	571096	571215	E069	-21014
chr9	571221	571532	E069	-20697
chr9	571582	572115	E069	-20114
chr9	573583	574603	E069	-17626
chr9	588968	589039	E069	-3190
chr9	589168	589389	E069	-2840
chr9	589520	589584	E069	-2645
chr9	589600	590159	E069	-2070
chr9	590160	590507	E069	-1722
chr9	590828	590904	E069	-1325
chr9	590966	591151	E069	-1078
chr9	591279	591734	E069	-495
chr9	596434	596484	E069	4205
chr9	608530	608829	E069	16301
chr9	608920	609108	E069	16691
chr9	610709	610872	E069	18480
chr9	610900	610999	E069	18671
chr9	611236	611286	E069	19007
chr9	613610	614810	E069	21381
chr9	614921	614971	E069	22692
chr9	614997	615051	E069	22768
chr9	619431	619591	E069	27202
chr9	621214	621897	E069	28985
chr9	624987	625545	E069	32758
chr9	625570	625630	E069	33341
chr9	625687	625737	E069	33458
chr9	625760	625951	E069	33531
chr9	625970	626215	E069	33741
chr9	626378	626418	E069	34149
chr9	626554	626692	E069	34325
chr9	626731	626962	E069	34502
chr9	627032	627454	E069	34803
chr9	627620	627910	E069	35391
chr9	628077	628139	E069	35848
chr9	628176	628272	E069	35947
chr9	628389	628472	E069	36160
chr9	628480	628617	E069	36251
chr9	628640	628731	E069	36411
chr9	629215	629404	E069	36986
chr9	630950	631064	E069	38721
chr9	544239	544289	E071	-47940
chr9	544406	544559	E071	-47670
chr9	544637	544773	E071	-47456
chr9	544890	545079	E071	-47150
chr9	545245	545352	E071	-46877
chr9	545536	545720	E071	-46509
chr9	545724	545829	E071	-46400
chr9	549261	549344	E071	-42885
chr9	549370	550149	E071	-42080
chr9	551166	551357	E071	-40872
chr9	551636	551714	E071	-40515
chr9	552035	552935	E071	-39294
chr9	553489	553539	E071	-38690
chr9	557794	558197	E071	-34032
chr9	558445	558593	E071	-33636
chr9	559734	560039	E071	-32190
chr9	560046	560243	E071	-31986
chr9	560348	560446	E071	-31783
chr9	560500	560550	E071	-31679
chr9	560701	560789	E071	-31440
chr9	560845	561205	E071	-31024
chr9	561468	561924	E071	-30305
chr9	562439	562642	E071	-29587
chr9	564787	564837	E071	-27392
chr9	564856	564906	E071	-27323
chr9	564910	564998	E071	-27231
chr9	567283	567458	E071	-24771
chr9	567464	567885	E071	-24344
chr9	570713	570786	E071	-21443
chr9	570925	570999	E071	-21230
chr9	571096	571215	E071	-21014
chr9	571221	571532	E071	-20697
chr9	571582	572115	E071	-20114
chr9	572190	572355	E071	-19874
chr9	572408	572499	E071	-19730
chr9	572634	572717	E071	-19512
chr9	572958	573162	E071	-19067
chr9	573583	574603	E071	-17626
chr9	574613	574653	E071	-17576
chr9	574754	574818	E071	-17411
chr9	574933	575460	E071	-16769
chr9	578859	578948	E071	-13281
chr9	578963	579071	E071	-13158
chr9	588763	588891	E071	-3338
chr9	588968	589039	E071	-3190
chr9	589168	589389	E071	-2840
chr9	589520	589584	E071	-2645
chr9	589600	590159	E071	-2070
chr9	591279	591734	E071	-495
chr9	591999	592597	E071	0
chr9	592742	592795	E071	513
chr9	592890	592970	E071	661
chr9	596434	596484	E071	4205
chr9	608530	608829	E071	16301
chr9	608920	609108	E071	16691
chr9	610633	610683	E071	18404
chr9	610709	610872	E071	18480
chr9	610900	610999	E071	18671
chr9	613610	614810	E071	21381
chr9	614921	614971	E071	22692
chr9	614997	615051	E071	22768
chr9	615455	615495	E071	23226
chr9	615882	615993	E071	23653
chr9	616662	617026	E071	24433
chr9	618535	618774	E071	26306
chr9	618781	618874	E071	26552
chr9	619108	619185	E071	26879
chr9	619431	619591	E071	27202
chr9	621214	621897	E071	28985
chr9	624857	624934	E071	32628
chr9	624987	625545	E071	32758
chr9	625570	625630	E071	33341
chr9	625687	625737	E071	33458
chr9	625760	625951	E071	33531
chr9	625970	626215	E071	33741
chr9	626378	626418	E071	34149
chr9	626554	626692	E071	34325
chr9	626731	626962	E071	34502
chr9	627032	627454	E071	34803
chr9	544890	545079	E072	-47150
chr9	545245	545352	E072	-46877
chr9	545536	545720	E072	-46509
chr9	545724	545829	E072	-46400
chr9	547891	548104	E072	-44125
chr9	549261	549344	E072	-42885
chr9	549370	550149	E072	-42080
chr9	552035	552935	E072	-39294
chr9	560845	561205	E072	-31024
chr9	561468	561924	E072	-30305
chr9	562439	562642	E072	-29587
chr9	562912	563844	E072	-28385
chr9	563874	564064	E072	-28165
chr9	564319	564395	E072	-27834
chr9	564787	564837	E072	-27392
chr9	564856	564906	E072	-27323
chr9	564910	564998	E072	-27231
chr9	569032	570658	E072	-21571
chr9	570713	570786	E072	-21443
chr9	570925	570999	E072	-21230
chr9	571096	571215	E072	-21014
chr9	571221	571532	E072	-20697
chr9	573583	574603	E072	-17626
chr9	574933	575460	E072	-16769
chr9	587598	587704	E072	-4525
chr9	589168	589389	E072	-2840
chr9	589520	589584	E072	-2645
chr9	589600	590159	E072	-2070
chr9	590160	590507	E072	-1722
chr9	591279	591734	E072	-495
chr9	591999	592597	E072	0
chr9	596434	596484	E072	4205
chr9	608530	608829	E072	16301
chr9	608920	609108	E072	16691
chr9	611236	611286	E072	19007
chr9	613610	614810	E072	21381
chr9	619431	619591	E072	27202
chr9	624857	624934	E072	32628
chr9	624987	625545	E072	32758
chr9	625570	625630	E072	33341
chr9	625687	625737	E072	33458
chr9	625760	625951	E072	33531
chr9	625970	626215	E072	33741
chr9	626378	626418	E072	34149
chr9	626554	626692	E072	34325
chr9	626731	626962	E072	34502
chr9	627032	627454	E072	34803
chr9	627620	627910	E072	35391
chr9	637287	637489	E072	45058
chr9	544890	545079	E073	-47150
chr9	545245	545352	E073	-46877
chr9	545536	545720	E073	-46509
chr9	545724	545829	E073	-46400
chr9	546262	547628	E073	-44601
chr9	573583	574603	E073	-17626
chr9	589600	590159	E073	-2070
chr9	613610	614810	E073	21381
chr9	615882	615993	E073	23653
chr9	616040	616350	E073	23811
chr9	621214	621897	E073	28985
chr9	624857	624934	E073	32628
chr9	624987	625545	E073	32758
chr9	625570	625630	E073	33341
chr9	625687	625737	E073	33458
chr9	625760	625951	E073	33531
chr9	625970	626215	E073	33741
chr9	626378	626418	E073	34149
chr9	626554	626692	E073	34325
chr9	626731	626962	E073	34502
chr9	627032	627454	E073	34803
chr9	544239	544289	E074	-47940
chr9	544406	544559	E074	-47670
chr9	544637	544773	E074	-47456
chr9	544890	545079	E074	-47150
chr9	545245	545352	E074	-46877
chr9	545536	545720	E074	-46509
chr9	545724	545829	E074	-46400
chr9	546262	547628	E074	-44601
chr9	547741	547856	E074	-44373
chr9	547891	548104	E074	-44125
chr9	548193	548243	E074	-43986
chr9	552035	552935	E074	-39294
chr9	562439	562642	E074	-29587
chr9	569032	570658	E074	-21571
chr9	570713	570786	E074	-21443
chr9	570925	570999	E074	-21230
chr9	571096	571215	E074	-21014
chr9	571221	571532	E074	-20697
chr9	572958	573162	E074	-19067
chr9	573583	574603	E074	-17626
chr9	588968	589039	E074	-3190
chr9	589168	589389	E074	-2840
chr9	589520	589584	E074	-2645
chr9	589600	590159	E074	-2070
chr9	590160	590507	E074	-1722
chr9	591279	591734	E074	-495
chr9	591999	592597	E074	0
chr9	596434	596484	E074	4205
chr9	613610	614810	E074	21381
chr9	614921	614971	E074	22692
chr9	614997	615051	E074	22768
chr9	617361	617943	E074	25132
chr9	618781	618874	E074	26552
chr9	619108	619185	E074	26879
chr9	619431	619591	E074	27202
chr9	624857	624934	E074	32628
chr9	624987	625545	E074	32758
chr9	625570	625630	E074	33341
chr9	625687	625737	E074	33458
chr9	625760	625951	E074	33531
chr9	625970	626215	E074	33741
chr9	626378	626418	E074	34149
chr9	626554	626692	E074	34325
chr9	626731	626962	E074	34502
chr9	627032	627454	E074	34803
chr9	627620	627910	E074	35391
chr9	628077	628139	E074	35848
chr9	628176	628272	E074	35947
chr9	628389	628472	E074	36160
chr9	546262	547628	E081	-44601
chr9	547741	547856	E081	-44373
chr9	552035	552935	E081	-39294