rs2642002

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

KANK1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0198 (5941/29906,GnomAD)
C==0222 (1111/5008,1000G)
C==0206 (794/3854,ALSPAC)
C==0204 (757/3708,TWINSUK)

Position: chr9:592718 (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.592718C>T
GRCh37.p13 chr 9	NC_000009.11:g.592718C>T
KANK1 RefSeqGene	NG_016331.2:g.127425C>T

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	C=0.137	T=0.863
1000Genomes	American	Sub	694	C=0.280	T=0.720
1000Genomes	East Asian	Sub	1008	C=0.312	T=0.688
1000Genomes	Europe	Sub	1006	C=0.220	T=0.780
1000Genomes	Global	Study-wide	5008	C=0.222	T=0.778
1000Genomes	South Asian	Sub	978	C=0.200	T=0.800
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.206	T=0.794
The Genome Aggregation Database	African	Sub	8658	C=0.144	T=0.856
The Genome Aggregation Database	American	Sub	838	C=0.220	T=0.780
The Genome Aggregation Database	East Asian	Sub	1618	C=0.313	T=0.687
The Genome Aggregation Database	Europe	Sub	18490	C=0.210	T=0.789
The Genome Aggregation Database	Global	Study-wide	29906	C=0.198	T=0.801
The Genome Aggregation Database	Other	Sub	302	C=0.350	T=0.650
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.204	T=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
rs2642002	0.000114	alcohol consumption	23743675

eQTL of rs2642002 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 rs2642002 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	-48159
chr9	544637	544773	E067	-47945
chr9	544890	545079	E067	-47639
chr9	545245	545352	E067	-47366
chr9	545536	545720	E067	-46998
chr9	545724	545829	E067	-46889
chr9	546262	547628	E067	-45090
chr9	547741	547856	E067	-44862
chr9	547891	548104	E067	-44614
chr9	548193	548243	E067	-44475
chr9	549261	549344	E067	-43374
chr9	558445	558593	E067	-34125
chr9	560046	560243	E067	-32475
chr9	560348	560446	E067	-32272
chr9	560500	560550	E067	-32168
chr9	560701	560789	E067	-31929
chr9	560845	561205	E067	-31513
chr9	561468	561924	E067	-30794
chr9	562439	562642	E067	-30076
chr9	562912	563844	E067	-28874
chr9	563874	564064	E067	-28654
chr9	569032	570658	E067	-22060
chr9	570713	570786	E067	-21932
chr9	570925	570999	E067	-21719
chr9	571096	571215	E067	-21503
chr9	571221	571532	E067	-21186
chr9	571582	572115	E067	-20603
chr9	572958	573162	E067	-19556
chr9	573583	574603	E067	-18115
chr9	589168	589389	E067	-3329
chr9	589520	589584	E067	-3134
chr9	589600	590159	E067	-2559
chr9	590160	590507	E067	-2211
chr9	591279	591734	E067	-984
chr9	591999	592597	E067	-121
chr9	596434	596484	E067	3716
chr9	611236	611286	E067	18518
chr9	611471	611521	E067	18753
chr9	613610	614810	E067	20892
chr9	614921	614971	E067	22203
chr9	614997	615051	E067	22279
chr9	625970	626215	E067	33252
chr9	626378	626418	E067	33660
chr9	626554	626692	E067	33836
chr9	626731	626962	E067	34013
chr9	627032	627454	E067	34314
chr9	544239	544289	E068	-48429
chr9	544406	544559	E068	-48159
chr9	544637	544773	E068	-47945
chr9	544890	545079	E068	-47639
chr9	545245	545352	E068	-47366
chr9	545536	545720	E068	-46998
chr9	545724	545829	E068	-46889
chr9	547891	548104	E068	-44614
chr9	548193	548243	E068	-44475
chr9	548384	548463	E068	-44255
chr9	552035	552935	E068	-39783
chr9	560845	561205	E068	-31513
chr9	561468	561924	E068	-30794
chr9	562439	562642	E068	-30076
chr9	564319	564395	E068	-28323
chr9	564787	564837	E068	-27881
chr9	570713	570786	E068	-21932
chr9	570925	570999	E068	-21719
chr9	571096	571215	E068	-21503
chr9	571221	571532	E068	-21186
chr9	571582	572115	E068	-20603
chr9	573583	574603	E068	-18115
chr9	574613	574653	E068	-18065
chr9	574754	574818	E068	-17900
chr9	579663	579718	E068	-13000
chr9	589168	589389	E068	-3329
chr9	589520	589584	E068	-3134
chr9	589600	590159	E068	-2559
chr9	590160	590507	E068	-2211
chr9	590828	590904	E068	-1814
chr9	590966	591151	E068	-1567
chr9	591279	591734	E068	-984
chr9	591999	592597	E068	-121
chr9	608530	608829	E068	15812
chr9	608920	609108	E068	16202
chr9	611236	611286	E068	18518
chr9	611471	611521	E068	18753
chr9	615882	615993	E068	23164
chr9	616662	617026	E068	23944
chr9	617361	617943	E068	24643
chr9	619108	619185	E068	26390
chr9	619431	619591	E068	26713
chr9	621214	621897	E068	28496
chr9	624987	625545	E068	32269
chr9	625570	625630	E068	32852
chr9	625687	625737	E068	32969
chr9	625760	625951	E068	33042
chr9	625970	626215	E068	33252
chr9	626378	626418	E068	33660
chr9	627032	627454	E068	34314
chr9	627620	627910	E068	34902
chr9	628077	628139	E068	35359
chr9	628176	628272	E068	35458
chr9	628389	628472	E068	35671
chr9	628480	628617	E068	35762
chr9	628640	628731	E068	35922
chr9	629215	629404	E068	36497
chr9	629442	629570	E068	36724
chr9	638055	638151	E068	45337
chr9	638197	638452	E068	45479
chr9	639026	639122	E068	46308
chr9	639186	639236	E068	46468
chr9	641365	641539	E068	48647
chr9	641793	641883	E068	49075
chr9	641977	642547	E068	49259
chr9	544239	544289	E069	-48429
chr9	544406	544559	E069	-48159
chr9	544637	544773	E069	-47945
chr9	544890	545079	E069	-47639
chr9	545245	545352	E069	-47366
chr9	545536	545720	E069	-46998
chr9	545724	545829	E069	-46889
chr9	546262	547628	E069	-45090
chr9	547741	547856	E069	-44862
chr9	547891	548104	E069	-44614
chr9	548193	548243	E069	-44475
chr9	549261	549344	E069	-43374
chr9	549370	550149	E069	-42569
chr9	552035	552935	E069	-39783
chr9	560348	560446	E069	-32272
chr9	560500	560550	E069	-32168
chr9	560701	560789	E069	-31929
chr9	560845	561205	E069	-31513
chr9	561468	561924	E069	-30794
chr9	562439	562642	E069	-30076
chr9	562912	563844	E069	-28874
chr9	563874	564064	E069	-28654
chr9	564319	564395	E069	-28323
chr9	564787	564837	E069	-27881
chr9	564856	564906	E069	-27812
chr9	564910	564998	E069	-27720
chr9	567283	567458	E069	-25260
chr9	567464	567885	E069	-24833
chr9	569032	570658	E069	-22060
chr9	570713	570786	E069	-21932
chr9	570925	570999	E069	-21719
chr9	571096	571215	E069	-21503
chr9	571221	571532	E069	-21186
chr9	571582	572115	E069	-20603
chr9	573583	574603	E069	-18115
chr9	588968	589039	E069	-3679
chr9	589168	589389	E069	-3329
chr9	589520	589584	E069	-3134
chr9	589600	590159	E069	-2559
chr9	590160	590507	E069	-2211
chr9	590828	590904	E069	-1814
chr9	590966	591151	E069	-1567
chr9	591279	591734	E069	-984
chr9	596434	596484	E069	3716
chr9	608530	608829	E069	15812
chr9	608920	609108	E069	16202
chr9	610709	610872	E069	17991
chr9	610900	610999	E069	18182
chr9	611236	611286	E069	18518
chr9	613610	614810	E069	20892
chr9	614921	614971	E069	22203
chr9	614997	615051	E069	22279
chr9	619431	619591	E069	26713
chr9	621214	621897	E069	28496
chr9	624987	625545	E069	32269
chr9	625570	625630	E069	32852
chr9	625687	625737	E069	32969
chr9	625760	625951	E069	33042
chr9	625970	626215	E069	33252
chr9	626378	626418	E069	33660
chr9	626554	626692	E069	33836
chr9	626731	626962	E069	34013
chr9	627032	627454	E069	34314
chr9	627620	627910	E069	34902
chr9	628077	628139	E069	35359
chr9	628176	628272	E069	35458
chr9	628389	628472	E069	35671
chr9	628480	628617	E069	35762
chr9	628640	628731	E069	35922
chr9	629215	629404	E069	36497
chr9	630950	631064	E069	38232
chr9	544239	544289	E071	-48429
chr9	544406	544559	E071	-48159
chr9	544637	544773	E071	-47945
chr9	544890	545079	E071	-47639
chr9	545245	545352	E071	-47366
chr9	545536	545720	E071	-46998
chr9	545724	545829	E071	-46889
chr9	549261	549344	E071	-43374
chr9	549370	550149	E071	-42569
chr9	551166	551357	E071	-41361
chr9	551636	551714	E071	-41004
chr9	552035	552935	E071	-39783
chr9	553489	553539	E071	-39179
chr9	557794	558197	E071	-34521
chr9	558445	558593	E071	-34125
chr9	559734	560039	E071	-32679
chr9	560046	560243	E071	-32475
chr9	560348	560446	E071	-32272
chr9	560500	560550	E071	-32168
chr9	560701	560789	E071	-31929
chr9	560845	561205	E071	-31513
chr9	561468	561924	E071	-30794
chr9	562439	562642	E071	-30076
chr9	564787	564837	E071	-27881
chr9	564856	564906	E071	-27812
chr9	564910	564998	E071	-27720
chr9	567283	567458	E071	-25260
chr9	567464	567885	E071	-24833
chr9	570713	570786	E071	-21932
chr9	570925	570999	E071	-21719
chr9	571096	571215	E071	-21503
chr9	571221	571532	E071	-21186
chr9	571582	572115	E071	-20603
chr9	572190	572355	E071	-20363
chr9	572408	572499	E071	-20219
chr9	572634	572717	E071	-20001
chr9	572958	573162	E071	-19556
chr9	573583	574603	E071	-18115
chr9	574613	574653	E071	-18065
chr9	574754	574818	E071	-17900
chr9	574933	575460	E071	-17258
chr9	578859	578948	E071	-13770
chr9	578963	579071	E071	-13647
chr9	588763	588891	E071	-3827
chr9	588968	589039	E071	-3679
chr9	589168	589389	E071	-3329
chr9	589520	589584	E071	-3134
chr9	589600	590159	E071	-2559
chr9	591279	591734	E071	-984
chr9	591999	592597	E071	-121
chr9	592742	592795	E071	24
chr9	592890	592970	E071	172
chr9	596434	596484	E071	3716
chr9	608530	608829	E071	15812
chr9	608920	609108	E071	16202
chr9	610633	610683	E071	17915
chr9	610709	610872	E071	17991
chr9	610900	610999	E071	18182
chr9	613610	614810	E071	20892
chr9	614921	614971	E071	22203
chr9	614997	615051	E071	22279
chr9	615455	615495	E071	22737
chr9	615882	615993	E071	23164
chr9	616662	617026	E071	23944
chr9	618535	618774	E071	25817
chr9	618781	618874	E071	26063
chr9	619108	619185	E071	26390
chr9	619431	619591	E071	26713
chr9	621214	621897	E071	28496
chr9	624857	624934	E071	32139
chr9	624987	625545	E071	32269
chr9	625570	625630	E071	32852
chr9	625687	625737	E071	32969
chr9	625760	625951	E071	33042
chr9	625970	626215	E071	33252
chr9	626378	626418	E071	33660
chr9	626554	626692	E071	33836
chr9	626731	626962	E071	34013
chr9	627032	627454	E071	34314
chr9	544890	545079	E072	-47639
chr9	545245	545352	E072	-47366
chr9	545536	545720	E072	-46998
chr9	545724	545829	E072	-46889
chr9	547891	548104	E072	-44614
chr9	549261	549344	E072	-43374
chr9	549370	550149	E072	-42569
chr9	552035	552935	E072	-39783
chr9	560845	561205	E072	-31513
chr9	561468	561924	E072	-30794
chr9	562439	562642	E072	-30076
chr9	562912	563844	E072	-28874
chr9	563874	564064	E072	-28654
chr9	564319	564395	E072	-28323
chr9	564787	564837	E072	-27881
chr9	564856	564906	E072	-27812
chr9	564910	564998	E072	-27720
chr9	569032	570658	E072	-22060
chr9	570713	570786	E072	-21932
chr9	570925	570999	E072	-21719
chr9	571096	571215	E072	-21503
chr9	571221	571532	E072	-21186
chr9	573583	574603	E072	-18115
chr9	574933	575460	E072	-17258
chr9	587598	587704	E072	-5014
chr9	589168	589389	E072	-3329
chr9	589520	589584	E072	-3134
chr9	589600	590159	E072	-2559
chr9	590160	590507	E072	-2211
chr9	591279	591734	E072	-984
chr9	591999	592597	E072	-121
chr9	596434	596484	E072	3716
chr9	608530	608829	E072	15812
chr9	608920	609108	E072	16202
chr9	611236	611286	E072	18518
chr9	613610	614810	E072	20892
chr9	619431	619591	E072	26713
chr9	624857	624934	E072	32139
chr9	624987	625545	E072	32269
chr9	625570	625630	E072	32852
chr9	625687	625737	E072	32969
chr9	625760	625951	E072	33042
chr9	625970	626215	E072	33252
chr9	626378	626418	E072	33660
chr9	626554	626692	E072	33836
chr9	626731	626962	E072	34013
chr9	627032	627454	E072	34314
chr9	627620	627910	E072	34902
chr9	637287	637489	E072	44569
chr9	544890	545079	E073	-47639
chr9	545245	545352	E073	-47366
chr9	545536	545720	E073	-46998
chr9	545724	545829	E073	-46889
chr9	546262	547628	E073	-45090
chr9	573583	574603	E073	-18115
chr9	589600	590159	E073	-2559
chr9	613610	614810	E073	20892
chr9	615882	615993	E073	23164
chr9	616040	616350	E073	23322
chr9	621214	621897	E073	28496
chr9	624857	624934	E073	32139
chr9	624987	625545	E073	32269
chr9	625570	625630	E073	32852
chr9	625687	625737	E073	32969
chr9	625760	625951	E073	33042
chr9	625970	626215	E073	33252
chr9	626378	626418	E073	33660
chr9	626554	626692	E073	33836
chr9	626731	626962	E073	34013
chr9	627032	627454	E073	34314
chr9	544239	544289	E074	-48429
chr9	544406	544559	E074	-48159
chr9	544637	544773	E074	-47945
chr9	544890	545079	E074	-47639
chr9	545245	545352	E074	-47366
chr9	545536	545720	E074	-46998
chr9	545724	545829	E074	-46889
chr9	546262	547628	E074	-45090
chr9	547741	547856	E074	-44862
chr9	547891	548104	E074	-44614
chr9	548193	548243	E074	-44475
chr9	552035	552935	E074	-39783
chr9	562439	562642	E074	-30076
chr9	569032	570658	E074	-22060
chr9	570713	570786	E074	-21932
chr9	570925	570999	E074	-21719
chr9	571096	571215	E074	-21503
chr9	571221	571532	E074	-21186
chr9	572958	573162	E074	-19556
chr9	573583	574603	E074	-18115
chr9	588968	589039	E074	-3679
chr9	589168	589389	E074	-3329
chr9	589520	589584	E074	-3134
chr9	589600	590159	E074	-2559
chr9	590160	590507	E074	-2211
chr9	591279	591734	E074	-984
chr9	591999	592597	E074	-121
chr9	596434	596484	E074	3716
chr9	613610	614810	E074	20892
chr9	614921	614971	E074	22203
chr9	614997	615051	E074	22279
chr9	617361	617943	E074	24643
chr9	618781	618874	E074	26063
chr9	619108	619185	E074	26390
chr9	619431	619591	E074	26713
chr9	624857	624934	E074	32139
chr9	624987	625545	E074	32269
chr9	625570	625630	E074	32852
chr9	625687	625737	E074	32969
chr9	625760	625951	E074	33042
chr9	625970	626215	E074	33252
chr9	626378	626418	E074	33660
chr9	626554	626692	E074	33836
chr9	626731	626962	E074	34013
chr9	627032	627454	E074	34314
chr9	627620	627910	E074	34902
chr9	628077	628139	E074	35359
chr9	628176	628272	E074	35458
chr9	628389	628472	E074	35671
chr9	546262	547628	E081	-45090
chr9	547741	547856	E081	-44862
chr9	552035	552935	E081	-39783