rs2804280

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

KANK1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0193 (5793/29876,GnomAD)
C==0192 (5592/29118,TOPMED)
C==0222 (1112/5008,1000G)
C==0209 (804/3854,ALSPAC)
C==0204 (756/3708,TWINSUK)

Position: chr9:589511 (GRCh38.p7) (9p24.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 380 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.589511C>T
GRCh37.p13 chr 9	NC_000009.11:g.589511C>T
KANK1 RefSeqGene	NG_016331.2:g.124218C>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=0.114	T=0.886
1000Genomes	American	Sub	694	C=0.280	T=0.720
1000Genomes	East Asian	Sub	1008	C=0.335	T=0.665
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=0.210	T=0.790
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.209	T=0.791
The Genome Aggregation Database	African	Sub	8704	C=0.124	T=0.876
The Genome Aggregation Database	American	Sub	836	C=0.220	T=0.780
The Genome Aggregation Database	East Asian	Sub	1610	C=0.339	T=0.661
The Genome Aggregation Database	Europe	Sub	18424	C=0.210	T=0.789
The Genome Aggregation Database	Global	Study-wide	29876	C=0.193	T=0.806
The Genome Aggregation Database	Other	Sub	302	C=0.350	T=0.650
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.192	T=0.808
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
rs2804280	7.7E-05	alcohol consumption	23743675

eQTL of rs2804280 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 rs2804280 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	-44952
chr9	544637	544773	E067	-44738
chr9	544890	545079	E067	-44432
chr9	545245	545352	E067	-44159
chr9	545536	545720	E067	-43791
chr9	545724	545829	E067	-43682
chr9	546262	547628	E067	-41883
chr9	547741	547856	E067	-41655
chr9	547891	548104	E067	-41407
chr9	548193	548243	E067	-41268
chr9	549261	549344	E067	-40167
chr9	558445	558593	E067	-30918
chr9	560046	560243	E067	-29268
chr9	560348	560446	E067	-29065
chr9	560500	560550	E067	-28961
chr9	560701	560789	E067	-28722
chr9	560845	561205	E067	-28306
chr9	561468	561924	E067	-27587
chr9	562439	562642	E067	-26869
chr9	562912	563844	E067	-25667
chr9	563874	564064	E067	-25447
chr9	569032	570658	E067	-18853
chr9	570713	570786	E067	-18725
chr9	570925	570999	E067	-18512
chr9	571096	571215	E067	-18296
chr9	571221	571532	E067	-17979
chr9	571582	572115	E067	-17396
chr9	572958	573162	E067	-16349
chr9	573583	574603	E067	-14908
chr9	589168	589389	E067	-122
chr9	589520	589584	E067	9
chr9	589600	590159	E067	89
chr9	590160	590507	E067	649
chr9	591279	591734	E067	1768
chr9	591999	592597	E067	2488
chr9	596434	596484	E067	6923
chr9	611236	611286	E067	21725
chr9	611471	611521	E067	21960
chr9	613610	614810	E067	24099
chr9	614921	614971	E067	25410
chr9	614997	615051	E067	25486
chr9	625970	626215	E067	36459
chr9	626378	626418	E067	36867
chr9	626554	626692	E067	37043
chr9	626731	626962	E067	37220
chr9	627032	627454	E067	37521
chr9	544239	544289	E068	-45222
chr9	544406	544559	E068	-44952
chr9	544637	544773	E068	-44738
chr9	544890	545079	E068	-44432
chr9	545245	545352	E068	-44159
chr9	545536	545720	E068	-43791
chr9	545724	545829	E068	-43682
chr9	547891	548104	E068	-41407
chr9	548193	548243	E068	-41268
chr9	548384	548463	E068	-41048
chr9	552035	552935	E068	-36576
chr9	560845	561205	E068	-28306
chr9	561468	561924	E068	-27587
chr9	562439	562642	E068	-26869
chr9	564319	564395	E068	-25116
chr9	564787	564837	E068	-24674
chr9	570713	570786	E068	-18725
chr9	570925	570999	E068	-18512
chr9	571096	571215	E068	-18296
chr9	571221	571532	E068	-17979
chr9	571582	572115	E068	-17396
chr9	573583	574603	E068	-14908
chr9	574613	574653	E068	-14858
chr9	574754	574818	E068	-14693
chr9	579663	579718	E068	-9793
chr9	589168	589389	E068	-122
chr9	589520	589584	E068	9
chr9	589600	590159	E068	89
chr9	590160	590507	E068	649
chr9	590828	590904	E068	1317
chr9	590966	591151	E068	1455
chr9	591279	591734	E068	1768
chr9	591999	592597	E068	2488
chr9	608530	608829	E068	19019
chr9	608920	609108	E068	19409
chr9	611236	611286	E068	21725
chr9	611471	611521	E068	21960
chr9	615882	615993	E068	26371
chr9	616662	617026	E068	27151
chr9	617361	617943	E068	27850
chr9	619108	619185	E068	29597
chr9	619431	619591	E068	29920
chr9	621214	621897	E068	31703
chr9	624987	625545	E068	35476
chr9	625570	625630	E068	36059
chr9	625687	625737	E068	36176
chr9	625760	625951	E068	36249
chr9	625970	626215	E068	36459
chr9	626378	626418	E068	36867
chr9	627032	627454	E068	37521
chr9	627620	627910	E068	38109
chr9	628077	628139	E068	38566
chr9	628176	628272	E068	38665
chr9	628389	628472	E068	38878
chr9	628480	628617	E068	38969
chr9	628640	628731	E068	39129
chr9	629215	629404	E068	39704
chr9	629442	629570	E068	39931
chr9	638055	638151	E068	48544
chr9	638197	638452	E068	48686
chr9	639026	639122	E068	49515
chr9	639186	639236	E068	49675
chr9	544239	544289	E069	-45222
chr9	544406	544559	E069	-44952
chr9	544637	544773	E069	-44738
chr9	544890	545079	E069	-44432
chr9	545245	545352	E069	-44159
chr9	545536	545720	E069	-43791
chr9	545724	545829	E069	-43682
chr9	546262	547628	E069	-41883
chr9	547741	547856	E069	-41655
chr9	547891	548104	E069	-41407
chr9	548193	548243	E069	-41268
chr9	549261	549344	E069	-40167
chr9	549370	550149	E069	-39362
chr9	552035	552935	E069	-36576
chr9	560348	560446	E069	-29065
chr9	560500	560550	E069	-28961
chr9	560701	560789	E069	-28722
chr9	560845	561205	E069	-28306
chr9	561468	561924	E069	-27587
chr9	562439	562642	E069	-26869
chr9	562912	563844	E069	-25667
chr9	563874	564064	E069	-25447
chr9	564319	564395	E069	-25116
chr9	564787	564837	E069	-24674
chr9	564856	564906	E069	-24605
chr9	564910	564998	E069	-24513
chr9	567283	567458	E069	-22053
chr9	567464	567885	E069	-21626
chr9	569032	570658	E069	-18853
chr9	570713	570786	E069	-18725
chr9	570925	570999	E069	-18512
chr9	571096	571215	E069	-18296
chr9	571221	571532	E069	-17979
chr9	571582	572115	E069	-17396
chr9	573583	574603	E069	-14908
chr9	588968	589039	E069	-472
chr9	589168	589389	E069	-122
chr9	589520	589584	E069	9
chr9	589600	590159	E069	89
chr9	590160	590507	E069	649
chr9	590828	590904	E069	1317
chr9	590966	591151	E069	1455
chr9	591279	591734	E069	1768
chr9	596434	596484	E069	6923
chr9	608530	608829	E069	19019
chr9	608920	609108	E069	19409
chr9	610709	610872	E069	21198
chr9	610900	610999	E069	21389
chr9	611236	611286	E069	21725
chr9	613610	614810	E069	24099
chr9	614921	614971	E069	25410
chr9	614997	615051	E069	25486
chr9	619431	619591	E069	29920
chr9	621214	621897	E069	31703
chr9	624987	625545	E069	35476
chr9	625570	625630	E069	36059
chr9	625687	625737	E069	36176
chr9	625760	625951	E069	36249
chr9	625970	626215	E069	36459
chr9	626378	626418	E069	36867
chr9	626554	626692	E069	37043
chr9	626731	626962	E069	37220
chr9	627032	627454	E069	37521
chr9	627620	627910	E069	38109
chr9	628077	628139	E069	38566
chr9	628176	628272	E069	38665
chr9	628389	628472	E069	38878
chr9	628480	628617	E069	38969
chr9	628640	628731	E069	39129
chr9	629215	629404	E069	39704
chr9	630950	631064	E069	41439
chr9	544239	544289	E071	-45222
chr9	544406	544559	E071	-44952
chr9	544637	544773	E071	-44738
chr9	544890	545079	E071	-44432
chr9	545245	545352	E071	-44159
chr9	545536	545720	E071	-43791
chr9	545724	545829	E071	-43682
chr9	549261	549344	E071	-40167
chr9	549370	550149	E071	-39362
chr9	551166	551357	E071	-38154
chr9	551636	551714	E071	-37797
chr9	552035	552935	E071	-36576
chr9	553489	553539	E071	-35972
chr9	557794	558197	E071	-31314
chr9	558445	558593	E071	-30918
chr9	559734	560039	E071	-29472
chr9	560046	560243	E071	-29268
chr9	560348	560446	E071	-29065
chr9	560500	560550	E071	-28961
chr9	560701	560789	E071	-28722
chr9	560845	561205	E071	-28306
chr9	561468	561924	E071	-27587
chr9	562439	562642	E071	-26869
chr9	564787	564837	E071	-24674
chr9	564856	564906	E071	-24605
chr9	564910	564998	E071	-24513
chr9	567283	567458	E071	-22053
chr9	567464	567885	E071	-21626
chr9	570713	570786	E071	-18725
chr9	570925	570999	E071	-18512
chr9	571096	571215	E071	-18296
chr9	571221	571532	E071	-17979
chr9	571582	572115	E071	-17396
chr9	572190	572355	E071	-17156
chr9	572408	572499	E071	-17012
chr9	572634	572717	E071	-16794
chr9	572958	573162	E071	-16349
chr9	573583	574603	E071	-14908
chr9	574613	574653	E071	-14858
chr9	574754	574818	E071	-14693
chr9	574933	575460	E071	-14051
chr9	578859	578948	E071	-10563
chr9	578963	579071	E071	-10440
chr9	588763	588891	E071	-620
chr9	588968	589039	E071	-472
chr9	589168	589389	E071	-122
chr9	589520	589584	E071	9
chr9	589600	590159	E071	89
chr9	591279	591734	E071	1768
chr9	591999	592597	E071	2488
chr9	592742	592795	E071	3231
chr9	592890	592970	E071	3379
chr9	596434	596484	E071	6923
chr9	608530	608829	E071	19019
chr9	608920	609108	E071	19409
chr9	610633	610683	E071	21122
chr9	610709	610872	E071	21198
chr9	610900	610999	E071	21389
chr9	613610	614810	E071	24099
chr9	614921	614971	E071	25410
chr9	614997	615051	E071	25486
chr9	615455	615495	E071	25944
chr9	615882	615993	E071	26371
chr9	616662	617026	E071	27151
chr9	618535	618774	E071	29024
chr9	618781	618874	E071	29270
chr9	619108	619185	E071	29597
chr9	619431	619591	E071	29920
chr9	621214	621897	E071	31703
chr9	624857	624934	E071	35346
chr9	624987	625545	E071	35476
chr9	625570	625630	E071	36059
chr9	625687	625737	E071	36176
chr9	625760	625951	E071	36249
chr9	625970	626215	E071	36459
chr9	626378	626418	E071	36867
chr9	626554	626692	E071	37043
chr9	626731	626962	E071	37220
chr9	627032	627454	E071	37521
chr9	544890	545079	E072	-44432
chr9	545245	545352	E072	-44159
chr9	545536	545720	E072	-43791
chr9	545724	545829	E072	-43682
chr9	547891	548104	E072	-41407
chr9	549261	549344	E072	-40167
chr9	549370	550149	E072	-39362
chr9	552035	552935	E072	-36576
chr9	560845	561205	E072	-28306
chr9	561468	561924	E072	-27587
chr9	562439	562642	E072	-26869
chr9	562912	563844	E072	-25667
chr9	563874	564064	E072	-25447
chr9	564319	564395	E072	-25116
chr9	564787	564837	E072	-24674
chr9	564856	564906	E072	-24605
chr9	564910	564998	E072	-24513
chr9	569032	570658	E072	-18853
chr9	570713	570786	E072	-18725
chr9	570925	570999	E072	-18512
chr9	571096	571215	E072	-18296
chr9	571221	571532	E072	-17979
chr9	573583	574603	E072	-14908
chr9	574933	575460	E072	-14051
chr9	587598	587704	E072	-1807
chr9	589168	589389	E072	-122
chr9	589520	589584	E072	9
chr9	589600	590159	E072	89
chr9	590160	590507	E072	649
chr9	591279	591734	E072	1768
chr9	591999	592597	E072	2488
chr9	596434	596484	E072	6923
chr9	608530	608829	E072	19019
chr9	608920	609108	E072	19409
chr9	611236	611286	E072	21725
chr9	613610	614810	E072	24099
chr9	619431	619591	E072	29920
chr9	624857	624934	E072	35346
chr9	624987	625545	E072	35476
chr9	625570	625630	E072	36059
chr9	625687	625737	E072	36176
chr9	625760	625951	E072	36249
chr9	625970	626215	E072	36459
chr9	626378	626418	E072	36867
chr9	626554	626692	E072	37043
chr9	626731	626962	E072	37220
chr9	627032	627454	E072	37521
chr9	627620	627910	E072	38109
chr9	637287	637489	E072	47776
chr9	544890	545079	E073	-44432
chr9	545245	545352	E073	-44159
chr9	545536	545720	E073	-43791
chr9	545724	545829	E073	-43682
chr9	546262	547628	E073	-41883
chr9	573583	574603	E073	-14908
chr9	589600	590159	E073	89
chr9	613610	614810	E073	24099
chr9	615882	615993	E073	26371
chr9	616040	616350	E073	26529
chr9	621214	621897	E073	31703
chr9	624857	624934	E073	35346
chr9	624987	625545	E073	35476
chr9	625570	625630	E073	36059
chr9	625687	625737	E073	36176
chr9	625760	625951	E073	36249
chr9	625970	626215	E073	36459
chr9	626378	626418	E073	36867
chr9	626554	626692	E073	37043
chr9	626731	626962	E073	37220
chr9	627032	627454	E073	37521
chr9	544239	544289	E074	-45222
chr9	544406	544559	E074	-44952
chr9	544637	544773	E074	-44738
chr9	544890	545079	E074	-44432
chr9	545245	545352	E074	-44159
chr9	545536	545720	E074	-43791
chr9	545724	545829	E074	-43682
chr9	546262	547628	E074	-41883
chr9	547741	547856	E074	-41655
chr9	547891	548104	E074	-41407
chr9	548193	548243	E074	-41268
chr9	552035	552935	E074	-36576
chr9	562439	562642	E074	-26869
chr9	569032	570658	E074	-18853
chr9	570713	570786	E074	-18725
chr9	570925	570999	E074	-18512
chr9	571096	571215	E074	-18296
chr9	571221	571532	E074	-17979
chr9	572958	573162	E074	-16349
chr9	573583	574603	E074	-14908
chr9	588968	589039	E074	-472
chr9	589168	589389	E074	-122
chr9	589520	589584	E074	9
chr9	589600	590159	E074	89
chr9	590160	590507	E074	649
chr9	591279	591734	E074	1768
chr9	591999	592597	E074	2488
chr9	596434	596484	E074	6923
chr9	613610	614810	E074	24099
chr9	614921	614971	E074	25410
chr9	614997	615051	E074	25486
chr9	617361	617943	E074	27850
chr9	618781	618874	E074	29270
chr9	619108	619185	E074	29597
chr9	619431	619591	E074	29920
chr9	624857	624934	E074	35346
chr9	624987	625545	E074	35476
chr9	625570	625630	E074	36059
chr9	625687	625737	E074	36176
chr9	625760	625951	E074	36249
chr9	625970	626215	E074	36459
chr9	626378	626418	E074	36867
chr9	626554	626692	E074	37043
chr9	626731	626962	E074	37220
chr9	627032	627454	E074	37521
chr9	627620	627910	E074	38109
chr9	628077	628139	E074	38566
chr9	628176	628272	E074	38665
chr9	628389	628472	E074	38878
chr9	546262	547628	E081	-41883
chr9	547741	547856	E081	-41655
chr9	552035	552935	E081	-36576