rs2642001

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

KANK1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T==0187 (5605/29856,GnomAD)
T==0210 (1052/5008,1000G)
T==0207 (796/3854,ALSPAC)
T==0204 (756/3708,TWINSUK)

Position: chr9:593229 (GRCh38.p7) (9p24.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 383 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.593229T>C
GRCh37.p13 chr 9	NC_000009.11:g.593229T>C
KANK1 RefSeqGene	NG_016331.2:g.127936T>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=0.094	C=0.906
1000Genomes	American	Sub	694	T=0.280	C=0.720
1000Genomes	East Asian	Sub	1008	T=0.312	C=0.688
1000Genomes	Europe	Sub	1006	T=0.219	C=0.781
1000Genomes	Global	Study-wide	5008	T=0.210	C=0.790
1000Genomes	South Asian	Sub	978	T=0.210	C=0.790
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.207	C=0.793
The Genome Aggregation Database	African	Sub	8640	T=0.105	C=0.895
The Genome Aggregation Database	American	Sub	838	T=0.220	C=0.780
The Genome Aggregation Database	East Asian	Sub	1614	T=0.312	C=0.688
The Genome Aggregation Database	Europe	Sub	18462	T=0.211	C=0.788
The Genome Aggregation Database	Global	Study-wide	29856	T=0.187	C=0.812
The Genome Aggregation Database	Other	Sub	302	T=0.350	C=0.650
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.204	C=0.796

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
rs2642001	7.98E-05	alcohol consumption	23743675

eQTL of rs2642001 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 rs2642001 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	-48670
chr9	544637	544773	E067	-48456
chr9	544890	545079	E067	-48150
chr9	545245	545352	E067	-47877
chr9	545536	545720	E067	-47509
chr9	545724	545829	E067	-47400
chr9	546262	547628	E067	-45601
chr9	547741	547856	E067	-45373
chr9	547891	548104	E067	-45125
chr9	548193	548243	E067	-44986
chr9	549261	549344	E067	-43885
chr9	558445	558593	E067	-34636
chr9	560046	560243	E067	-32986
chr9	560348	560446	E067	-32783
chr9	560500	560550	E067	-32679
chr9	560701	560789	E067	-32440
chr9	560845	561205	E067	-32024
chr9	561468	561924	E067	-31305
chr9	562439	562642	E067	-30587
chr9	562912	563844	E067	-29385
chr9	563874	564064	E067	-29165
chr9	569032	570658	E067	-22571
chr9	570713	570786	E067	-22443
chr9	570925	570999	E067	-22230
chr9	571096	571215	E067	-22014
chr9	571221	571532	E067	-21697
chr9	571582	572115	E067	-21114
chr9	572958	573162	E067	-20067
chr9	573583	574603	E067	-18626
chr9	589168	589389	E067	-3840
chr9	589520	589584	E067	-3645
chr9	589600	590159	E067	-3070
chr9	590160	590507	E067	-2722
chr9	591279	591734	E067	-1495
chr9	591999	592597	E067	-632
chr9	596434	596484	E067	3205
chr9	611236	611286	E067	18007
chr9	611471	611521	E067	18242
chr9	613610	614810	E067	20381
chr9	614921	614971	E067	21692
chr9	614997	615051	E067	21768
chr9	625970	626215	E067	32741
chr9	626378	626418	E067	33149
chr9	626554	626692	E067	33325
chr9	626731	626962	E067	33502
chr9	627032	627454	E067	33803
chr9	544239	544289	E068	-48940
chr9	544406	544559	E068	-48670
chr9	544637	544773	E068	-48456
chr9	544890	545079	E068	-48150
chr9	545245	545352	E068	-47877
chr9	545536	545720	E068	-47509
chr9	545724	545829	E068	-47400
chr9	547891	548104	E068	-45125
chr9	548193	548243	E068	-44986
chr9	548384	548463	E068	-44766
chr9	552035	552935	E068	-40294
chr9	560845	561205	E068	-32024
chr9	561468	561924	E068	-31305
chr9	562439	562642	E068	-30587
chr9	564319	564395	E068	-28834
chr9	564787	564837	E068	-28392
chr9	570713	570786	E068	-22443
chr9	570925	570999	E068	-22230
chr9	571096	571215	E068	-22014
chr9	571221	571532	E068	-21697
chr9	571582	572115	E068	-21114
chr9	573583	574603	E068	-18626
chr9	574613	574653	E068	-18576
chr9	574754	574818	E068	-18411
chr9	579663	579718	E068	-13511
chr9	589168	589389	E068	-3840
chr9	589520	589584	E068	-3645
chr9	589600	590159	E068	-3070
chr9	590160	590507	E068	-2722
chr9	590828	590904	E068	-2325
chr9	590966	591151	E068	-2078
chr9	591279	591734	E068	-1495
chr9	591999	592597	E068	-632
chr9	608530	608829	E068	15301
chr9	608920	609108	E068	15691
chr9	611236	611286	E068	18007
chr9	611471	611521	E068	18242
chr9	615882	615993	E068	22653
chr9	616662	617026	E068	23433
chr9	617361	617943	E068	24132
chr9	619108	619185	E068	25879
chr9	619431	619591	E068	26202
chr9	621214	621897	E068	27985
chr9	624987	625545	E068	31758
chr9	625570	625630	E068	32341
chr9	625687	625737	E068	32458
chr9	625760	625951	E068	32531
chr9	625970	626215	E068	32741
chr9	626378	626418	E068	33149
chr9	627032	627454	E068	33803
chr9	627620	627910	E068	34391
chr9	628077	628139	E068	34848
chr9	628176	628272	E068	34947
chr9	628389	628472	E068	35160
chr9	628480	628617	E068	35251
chr9	628640	628731	E068	35411
chr9	629215	629404	E068	35986
chr9	629442	629570	E068	36213
chr9	638055	638151	E068	44826
chr9	638197	638452	E068	44968
chr9	639026	639122	E068	45797
chr9	639186	639236	E068	45957
chr9	641365	641539	E068	48136
chr9	641793	641883	E068	48564
chr9	641977	642547	E068	48748
chr9	544239	544289	E069	-48940
chr9	544406	544559	E069	-48670
chr9	544637	544773	E069	-48456
chr9	544890	545079	E069	-48150
chr9	545245	545352	E069	-47877
chr9	545536	545720	E069	-47509
chr9	545724	545829	E069	-47400
chr9	546262	547628	E069	-45601
chr9	547741	547856	E069	-45373
chr9	547891	548104	E069	-45125
chr9	548193	548243	E069	-44986
chr9	549261	549344	E069	-43885
chr9	549370	550149	E069	-43080
chr9	552035	552935	E069	-40294
chr9	560348	560446	E069	-32783
chr9	560500	560550	E069	-32679
chr9	560701	560789	E069	-32440
chr9	560845	561205	E069	-32024
chr9	561468	561924	E069	-31305
chr9	562439	562642	E069	-30587
chr9	562912	563844	E069	-29385
chr9	563874	564064	E069	-29165
chr9	564319	564395	E069	-28834
chr9	564787	564837	E069	-28392
chr9	564856	564906	E069	-28323
chr9	564910	564998	E069	-28231
chr9	567283	567458	E069	-25771
chr9	567464	567885	E069	-25344
chr9	569032	570658	E069	-22571
chr9	570713	570786	E069	-22443
chr9	570925	570999	E069	-22230
chr9	571096	571215	E069	-22014
chr9	571221	571532	E069	-21697
chr9	571582	572115	E069	-21114
chr9	573583	574603	E069	-18626
chr9	588968	589039	E069	-4190
chr9	589168	589389	E069	-3840
chr9	589520	589584	E069	-3645
chr9	589600	590159	E069	-3070
chr9	590160	590507	E069	-2722
chr9	590828	590904	E069	-2325
chr9	590966	591151	E069	-2078
chr9	591279	591734	E069	-1495
chr9	596434	596484	E069	3205
chr9	608530	608829	E069	15301
chr9	608920	609108	E069	15691
chr9	610709	610872	E069	17480
chr9	610900	610999	E069	17671
chr9	611236	611286	E069	18007
chr9	613610	614810	E069	20381
chr9	614921	614971	E069	21692
chr9	614997	615051	E069	21768
chr9	619431	619591	E069	26202
chr9	621214	621897	E069	27985
chr9	624987	625545	E069	31758
chr9	625570	625630	E069	32341
chr9	625687	625737	E069	32458
chr9	625760	625951	E069	32531
chr9	625970	626215	E069	32741
chr9	626378	626418	E069	33149
chr9	626554	626692	E069	33325
chr9	626731	626962	E069	33502
chr9	627032	627454	E069	33803
chr9	627620	627910	E069	34391
chr9	628077	628139	E069	34848
chr9	628176	628272	E069	34947
chr9	628389	628472	E069	35160
chr9	628480	628617	E069	35251
chr9	628640	628731	E069	35411
chr9	629215	629404	E069	35986
chr9	630950	631064	E069	37721
chr9	544239	544289	E071	-48940
chr9	544406	544559	E071	-48670
chr9	544637	544773	E071	-48456
chr9	544890	545079	E071	-48150
chr9	545245	545352	E071	-47877
chr9	545536	545720	E071	-47509
chr9	545724	545829	E071	-47400
chr9	549261	549344	E071	-43885
chr9	549370	550149	E071	-43080
chr9	551166	551357	E071	-41872
chr9	551636	551714	E071	-41515
chr9	552035	552935	E071	-40294
chr9	553489	553539	E071	-39690
chr9	557794	558197	E071	-35032
chr9	558445	558593	E071	-34636
chr9	559734	560039	E071	-33190
chr9	560046	560243	E071	-32986
chr9	560348	560446	E071	-32783
chr9	560500	560550	E071	-32679
chr9	560701	560789	E071	-32440
chr9	560845	561205	E071	-32024
chr9	561468	561924	E071	-31305
chr9	562439	562642	E071	-30587
chr9	564787	564837	E071	-28392
chr9	564856	564906	E071	-28323
chr9	564910	564998	E071	-28231
chr9	567283	567458	E071	-25771
chr9	567464	567885	E071	-25344
chr9	570713	570786	E071	-22443
chr9	570925	570999	E071	-22230
chr9	571096	571215	E071	-22014
chr9	571221	571532	E071	-21697
chr9	571582	572115	E071	-21114
chr9	572190	572355	E071	-20874
chr9	572408	572499	E071	-20730
chr9	572634	572717	E071	-20512
chr9	572958	573162	E071	-20067
chr9	573583	574603	E071	-18626
chr9	574613	574653	E071	-18576
chr9	574754	574818	E071	-18411
chr9	574933	575460	E071	-17769
chr9	578859	578948	E071	-14281
chr9	578963	579071	E071	-14158
chr9	588763	588891	E071	-4338
chr9	588968	589039	E071	-4190
chr9	589168	589389	E071	-3840
chr9	589520	589584	E071	-3645
chr9	589600	590159	E071	-3070
chr9	591279	591734	E071	-1495
chr9	591999	592597	E071	-632
chr9	592742	592795	E071	-434
chr9	592890	592970	E071	-259
chr9	596434	596484	E071	3205
chr9	608530	608829	E071	15301
chr9	608920	609108	E071	15691
chr9	610633	610683	E071	17404
chr9	610709	610872	E071	17480
chr9	610900	610999	E071	17671
chr9	613610	614810	E071	20381
chr9	614921	614971	E071	21692
chr9	614997	615051	E071	21768
chr9	615455	615495	E071	22226
chr9	615882	615993	E071	22653
chr9	616662	617026	E071	23433
chr9	618535	618774	E071	25306
chr9	618781	618874	E071	25552
chr9	619108	619185	E071	25879
chr9	619431	619591	E071	26202
chr9	621214	621897	E071	27985
chr9	624857	624934	E071	31628
chr9	624987	625545	E071	31758
chr9	625570	625630	E071	32341
chr9	625687	625737	E071	32458
chr9	625760	625951	E071	32531
chr9	625970	626215	E071	32741
chr9	626378	626418	E071	33149
chr9	626554	626692	E071	33325
chr9	626731	626962	E071	33502
chr9	627032	627454	E071	33803
chr9	544890	545079	E072	-48150
chr9	545245	545352	E072	-47877
chr9	545536	545720	E072	-47509
chr9	545724	545829	E072	-47400
chr9	547891	548104	E072	-45125
chr9	549261	549344	E072	-43885
chr9	549370	550149	E072	-43080
chr9	552035	552935	E072	-40294
chr9	560845	561205	E072	-32024
chr9	561468	561924	E072	-31305
chr9	562439	562642	E072	-30587
chr9	562912	563844	E072	-29385
chr9	563874	564064	E072	-29165
chr9	564319	564395	E072	-28834
chr9	564787	564837	E072	-28392
chr9	564856	564906	E072	-28323
chr9	564910	564998	E072	-28231
chr9	569032	570658	E072	-22571
chr9	570713	570786	E072	-22443
chr9	570925	570999	E072	-22230
chr9	571096	571215	E072	-22014
chr9	571221	571532	E072	-21697
chr9	573583	574603	E072	-18626
chr9	574933	575460	E072	-17769
chr9	587598	587704	E072	-5525
chr9	589168	589389	E072	-3840
chr9	589520	589584	E072	-3645
chr9	589600	590159	E072	-3070
chr9	590160	590507	E072	-2722
chr9	591279	591734	E072	-1495
chr9	591999	592597	E072	-632
chr9	596434	596484	E072	3205
chr9	608530	608829	E072	15301
chr9	608920	609108	E072	15691
chr9	611236	611286	E072	18007
chr9	613610	614810	E072	20381
chr9	619431	619591	E072	26202
chr9	624857	624934	E072	31628
chr9	624987	625545	E072	31758
chr9	625570	625630	E072	32341
chr9	625687	625737	E072	32458
chr9	625760	625951	E072	32531
chr9	625970	626215	E072	32741
chr9	626378	626418	E072	33149
chr9	626554	626692	E072	33325
chr9	626731	626962	E072	33502
chr9	627032	627454	E072	33803
chr9	627620	627910	E072	34391
chr9	637287	637489	E072	44058
chr9	544890	545079	E073	-48150
chr9	545245	545352	E073	-47877
chr9	545536	545720	E073	-47509
chr9	545724	545829	E073	-47400
chr9	546262	547628	E073	-45601
chr9	573583	574603	E073	-18626
chr9	589600	590159	E073	-3070
chr9	613610	614810	E073	20381
chr9	615882	615993	E073	22653
chr9	616040	616350	E073	22811
chr9	621214	621897	E073	27985
chr9	624857	624934	E073	31628
chr9	624987	625545	E073	31758
chr9	625570	625630	E073	32341
chr9	625687	625737	E073	32458
chr9	625760	625951	E073	32531
chr9	625970	626215	E073	32741
chr9	626378	626418	E073	33149
chr9	626554	626692	E073	33325
chr9	626731	626962	E073	33502
chr9	627032	627454	E073	33803
chr9	544239	544289	E074	-48940
chr9	544406	544559	E074	-48670
chr9	544637	544773	E074	-48456
chr9	544890	545079	E074	-48150
chr9	545245	545352	E074	-47877
chr9	545536	545720	E074	-47509
chr9	545724	545829	E074	-47400
chr9	546262	547628	E074	-45601
chr9	547741	547856	E074	-45373
chr9	547891	548104	E074	-45125
chr9	548193	548243	E074	-44986
chr9	552035	552935	E074	-40294
chr9	562439	562642	E074	-30587
chr9	569032	570658	E074	-22571
chr9	570713	570786	E074	-22443
chr9	570925	570999	E074	-22230
chr9	571096	571215	E074	-22014
chr9	571221	571532	E074	-21697
chr9	572958	573162	E074	-20067
chr9	573583	574603	E074	-18626
chr9	588968	589039	E074	-4190
chr9	589168	589389	E074	-3840
chr9	589520	589584	E074	-3645
chr9	589600	590159	E074	-3070
chr9	590160	590507	E074	-2722
chr9	591279	591734	E074	-1495
chr9	591999	592597	E074	-632
chr9	596434	596484	E074	3205
chr9	613610	614810	E074	20381
chr9	614921	614971	E074	21692
chr9	614997	615051	E074	21768
chr9	617361	617943	E074	24132
chr9	618781	618874	E074	25552
chr9	619108	619185	E074	25879
chr9	619431	619591	E074	26202
chr9	624857	624934	E074	31628
chr9	624987	625545	E074	31758
chr9	625570	625630	E074	32341
chr9	625687	625737	E074	32458
chr9	625760	625951	E074	32531
chr9	625970	626215	E074	32741
chr9	626378	626418	E074	33149
chr9	626554	626692	E074	33325
chr9	626731	626962	E074	33502
chr9	627032	627454	E074	33803
chr9	627620	627910	E074	34391
chr9	628077	628139	E074	34848
chr9	628176	628272	E074	34947
chr9	628389	628472	E074	35160
chr9	546262	547628	E081	-45601
chr9	547741	547856	E081	-45373
chr9	552035	552935	E081	-40294