rs9294269

Organism: Homo sapiens

Alleles: A>C

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0472 (14129/29918,GnomAD)
C=0394 (11476/29118,TOPMED)
C=0434 (2172/5008,1000G)
A==0451 (1737/3854,ALSPAC)
A==0455 (1687/3708,TWINSUK)

Position: chr6:63627392 (GRCh38.p7) (6q12)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 162 Enhancers around

Promoter: 50 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 6	NC_000006.12:g.63627392A>C
GRCh37.p13 chr 6	NC_000006.11:g.64337297A>C

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.801	C=0.199
1000Genomes	American	Sub	694	A=0.580	C=0.420
1000Genomes	East Asian	Sub	1008	A=0.450	C=0.550
1000Genomes	Europe	Sub	1006	A=0.416	C=0.584
1000Genomes	Global	Study-wide	5008	A=0.566	C=0.434
1000Genomes	South Asian	Sub	978	A=0.510	C=0.490
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.451	C=0.549
The Genome Aggregation Database	African	Sub	8706	A=0.769	C=0.231
The Genome Aggregation Database	American	Sub	838	A=0.590	C=0.410
The Genome Aggregation Database	East Asian	Sub	1608	A=0.453	C=0.547
The Genome Aggregation Database	Europe	Sub	18464	A=0.420	C=0.579
The Genome Aggregation Database	Global	Study-wide	29918	A=0.527	C=0.472
The Genome Aggregation Database	Other	Sub	302	A=0.380	C=0.620
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.605	C=0.394
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.455	C=0.545

PMID	Title	Author	Journal
22096494	A novel, functional and replicable risk gene region for alcohol dependence identified by genome-wide association study.	Zuo L	PLoS One

SNP ID	p-value	Traits	Study
rs9294269	3.7E-06	alcohol dependence	22096494

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr6:64337297	LGSN	ENSG00000146166.12	A>C	1.9599e-12	307415	Brain_Spinal_cord_cervical

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 )
chr6	64307610	64307749	E067	-29548
chr6	64350032	64350267	E067	12735
chr6	64350310	64350429	E067	13013
chr6	64351522	64351562	E067	14225
chr6	64351664	64351729	E067	14367
chr6	64353265	64353367	E067	15968
chr6	64353403	64353453	E067	16106
chr6	64353550	64353597	E067	16253
chr6	64353799	64354122	E067	16502
chr6	64354164	64354298	E067	16867
chr6	64354766	64354995	E067	17469
chr6	64356484	64356589	E067	19187
chr6	64359391	64359514	E067	22094
chr6	64359879	64359966	E067	22582
chr6	64369793	64369833	E067	32496
chr6	64369956	64370043	E067	32659
chr6	64370465	64370839	E067	33168
chr6	64373408	64373737	E067	36111
chr6	64384616	64384840	E067	47319
chr6	64386745	64387006	E067	49448
chr6	64387067	64387235	E067	49770
chr6	64348152	64348219	E068	10855
chr6	64348304	64348374	E068	11007
chr6	64349166	64349250	E068	11869
chr6	64350032	64350267	E068	12735
chr6	64350310	64350429	E068	13013
chr6	64353403	64353453	E068	16106
chr6	64353550	64353597	E068	16253
chr6	64353799	64354122	E068	16502
chr6	64354164	64354298	E068	16867
chr6	64354766	64354995	E068	17469
chr6	64355005	64355161	E068	17708
chr6	64359391	64359514	E068	22094
chr6	64359879	64359966	E068	22582
chr6	64360034	64360162	E068	22737
chr6	64369793	64369833	E068	32496
chr6	64369956	64370043	E068	32659
chr6	64370465	64370839	E068	33168
chr6	64373195	64373307	E068	35898
chr6	64374078	64374118	E068	36781
chr6	64385497	64385541	E068	48200
chr6	64386464	64386529	E068	49167
chr6	64386745	64387006	E068	49448
chr6	64387067	64387235	E068	49770
chr6	64299831	64300142	E069	-37155
chr6	64348152	64348219	E069	10855
chr6	64348304	64348374	E069	11007
chr6	64350032	64350267	E069	12735
chr6	64350310	64350429	E069	13013
chr6	64353265	64353367	E069	15968
chr6	64353403	64353453	E069	16106
chr6	64353550	64353597	E069	16253
chr6	64353799	64354122	E069	16502
chr6	64354164	64354298	E069	16867
chr6	64354766	64354995	E069	17469
chr6	64355005	64355161	E069	17708
chr6	64359391	64359514	E069	22094
chr6	64359879	64359966	E069	22582
chr6	64365985	64366056	E069	28688
chr6	64369793	64369833	E069	32496
chr6	64369956	64370043	E069	32659
chr6	64370465	64370839	E069	33168
chr6	64373834	64373908	E069	36537
chr6	64384616	64384840	E069	47319
chr6	64385086	64385323	E069	47789
chr6	64385340	64385412	E069	48043
chr6	64385497	64385541	E069	48200
chr6	64386464	64386529	E069	49167
chr6	64386745	64387006	E069	49448
chr6	64387067	64387235	E069	49770
chr6	64348152	64348219	E070	10855
chr6	64295649	64295699	E071	-41598
chr6	64307610	64307749	E071	-29548
chr6	64348152	64348219	E071	10855
chr6	64348304	64348374	E071	11007
chr6	64349166	64349250	E071	11869
chr6	64350032	64350267	E071	12735
chr6	64350310	64350429	E071	13013
chr6	64353265	64353367	E071	15968
chr6	64353403	64353453	E071	16106
chr6	64353550	64353597	E071	16253
chr6	64353799	64354122	E071	16502
chr6	64354164	64354298	E071	16867
chr6	64354766	64354995	E071	17469
chr6	64355005	64355161	E071	17708
chr6	64359391	64359514	E071	22094
chr6	64359879	64359966	E071	22582
chr6	64360034	64360162	E071	22737
chr6	64369793	64369833	E071	32496
chr6	64369956	64370043	E071	32659
chr6	64370465	64370839	E071	33168
chr6	64373195	64373307	E071	35898
chr6	64373408	64373737	E071	36111
chr6	64373834	64373908	E071	36537
chr6	64374078	64374118	E071	36781
chr6	64384616	64384840	E071	47319
chr6	64385086	64385323	E071	47789
chr6	64385340	64385412	E071	48043
chr6	64385497	64385541	E071	48200
chr6	64386464	64386529	E071	49167
chr6	64386745	64387006	E071	49448
chr6	64387067	64387235	E071	49770
chr6	64350032	64350267	E072	12735
chr6	64350310	64350429	E072	13013
chr6	64351522	64351562	E072	14225
chr6	64351664	64351729	E072	14367
chr6	64353265	64353367	E072	15968
chr6	64353403	64353453	E072	16106
chr6	64353550	64353597	E072	16253
chr6	64353799	64354122	E072	16502
chr6	64354164	64354298	E072	16867
chr6	64354766	64354995	E072	17469
chr6	64355005	64355161	E072	17708
chr6	64359391	64359514	E072	22094
chr6	64359879	64359966	E072	22582
chr6	64367948	64368043	E072	30651
chr6	64368128	64368168	E072	30831
chr6	64370465	64370839	E072	33168
chr6	64386464	64386529	E072	49167
chr6	64386745	64387006	E072	49448
chr6	64387067	64387235	E072	49770
chr6	64350032	64350267	E073	12735
chr6	64350310	64350429	E073	13013
chr6	64354164	64354298	E073	16867
chr6	64354766	64354995	E073	17469
chr6	64359391	64359514	E073	22094
chr6	64344535	64344923	E074	7238
chr6	64349166	64349250	E074	11869
chr6	64350032	64350267	E074	12735
chr6	64350310	64350429	E074	13013
chr6	64351522	64351562	E074	14225
chr6	64351664	64351729	E074	14367
chr6	64353265	64353367	E074	15968
chr6	64353403	64353453	E074	16106
chr6	64353550	64353597	E074	16253
chr6	64353799	64354122	E074	16502
chr6	64354164	64354298	E074	16867
chr6	64354766	64354995	E074	17469
chr6	64355005	64355161	E074	17708
chr6	64359391	64359514	E074	22094
chr6	64359879	64359966	E074	22582
chr6	64360034	64360162	E074	22737
chr6	64369793	64369833	E074	32496
chr6	64369956	64370043	E074	32659
chr6	64370465	64370839	E074	33168
chr6	64383758	64383814	E074	46461
chr6	64384616	64384840	E074	47319
chr6	64385086	64385323	E074	47789
chr6	64385340	64385412	E074	48043
chr6	64385497	64385541	E074	48200
chr6	64386464	64386529	E074	49167
chr6	64386745	64387006	E074	49448
chr6	64387067	64387235	E074	49770
chr6	64349166	64349250	E081	11869
chr6	64350032	64350267	E081	12735
chr6	64350310	64350429	E081	13013
chr6	64387067	64387235	E081	49770
chr6	64348152	64348219	E082	10855
chr6	64348304	64348374	E082	11007
chr6	64349166	64349250	E082	11869
chr6	64353799	64354122	E082	16502
chr6	64354164	64354298	E082	16867

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr6	64307757	64309034	E067	-28263
chr6	64345072	64347052	E067	7775
chr6	64347077	64347265	E067	9780
chr6	64347307	64347377	E067	10010
chr6	64347388	64347481	E067	10091
chr6	64307757	64309034	E068	-28263
chr6	64345072	64347052	E068	7775
chr6	64347077	64347265	E068	9780
chr6	64347307	64347377	E068	10010
chr6	64347388	64347481	E068	10091
chr6	64307757	64309034	E069	-28263
chr6	64345072	64347052	E069	7775
chr6	64347077	64347265	E069	9780
chr6	64347307	64347377	E069	10010
chr6	64347388	64347481	E069	10091
chr6	64307757	64309034	E070	-28263
chr6	64345072	64347052	E070	7775
chr6	64347077	64347265	E070	9780
chr6	64347307	64347377	E070	10010
chr6	64347388	64347481	E070	10091
chr6	64307757	64309034	E071	-28263
chr6	64345072	64347052	E071	7775
chr6	64347077	64347265	E071	9780
chr6	64347307	64347377	E071	10010
chr6	64347388	64347481	E071	10091
chr6	64307757	64309034	E072	-28263
chr6	64345072	64347052	E072	7775
chr6	64347077	64347265	E072	9780
chr6	64347307	64347377	E072	10010
chr6	64347388	64347481	E072	10091
chr6	64307757	64309034	E073	-28263
chr6	64345072	64347052	E073	7775
chr6	64347077	64347265	E073	9780
chr6	64347307	64347377	E073	10010
chr6	64347388	64347481	E073	10091
chr6	64307757	64309034	E074	-28263
chr6	64345072	64347052	E074	7775
chr6	64347077	64347265	E074	9780
chr6	64347307	64347377	E074	10010
chr6	64347388	64347481	E074	10091
chr6	64307757	64309034	E081	-28263
chr6	64345072	64347052	E081	7775
chr6	64347077	64347265	E081	9780
chr6	64347307	64347377	E081	10010
chr6	64347388	64347481	E081	10091
chr6	64307757	64309034	E082	-28263
chr6	64345072	64347052	E082	7775
chr6	64347077	64347265	E082	9780
chr6	64347307	64347377	E082	10010
chr6	64347388	64347481	E082	10091

rs9294269

Genomic Coordinates

Population Frequency

P-Value

eQTL of rs9294269 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs9294269 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Promoter Annotation (GRCh37.p13)