rs6697886

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0215 (6439/29890,GnomAD)
A=0244 (7132/29118,TOPMED)
A=0221 (1105/5008,1000G)
A=0141 (542/3854,ALSPAC)
A=0149 (553/3708,TWINSUK)

Position: chr1:1238231 (GRCh38.p7) (1p36.33)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 134 Enhancers around

Promoter: 26 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.1238231G>A
GRCh37.p13 chr 1	NC_000001.10:g.1173611G>A

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.579	A=0.421
1000Genomes	American	Sub	694	G=0.880	A=0.120
1000Genomes	East Asian	Sub	1008	G=0.831	A=0.169
1000Genomes	Europe	Sub	1006	G=0.871	A=0.129
1000Genomes	Global	Study-wide	5008	G=0.779	A=0.221
1000Genomes	South Asian	Sub	978	G=0.830	A=0.170
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.859	A=0.141
The Genome Aggregation Database	African	Sub	8690	G=0.618	A=0.382
The Genome Aggregation Database	American	Sub	838	G=0.880	A=0.120
The Genome Aggregation Database	East Asian	Sub	1620	G=0.812	A=0.188
The Genome Aggregation Database	Europe	Sub	18440	G=0.854	A=0.145
The Genome Aggregation Database	Global	Study-wide	29890	G=0.784	A=0.215
The Genome Aggregation Database	Other	Sub	302	G=0.880	A=0.120
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.755	A=0.244
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.851	A=0.149

PMID	Title	Author	Journal
21703634	A meta-analysis of two genome-wide association studies identifies 3 new loci for alcohol dependence.	Wang KS	J Psychiatr Res

P-Value

SNP ID	p-value	Traits	Study
rs6697886	9.7E-05	alcohol dependence	21703634

eQTL of rs6697886 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:1173611	TNFRSF18	ENSG00000186891.9	G>A	8.9439e-5	31540	Cerebellum
Chr1:1173611	B3GALT6	ENSG00000176022.3	G>A	1.8238e-15	5982	Cerebellum
Chr1:1173611	ANKRD65	ENSG00000235098.4	G>A	0.0000e+0	-183538	Cerebellum
Chr1:1173611	B3GALT6	ENSG00000176022.3	G>A	1.9847e-8	5982	Cerebellar_Hemisphere
Chr1:1173611	B3GALT6	ENSG00000176022.3	G>A	7.8577e-6	5982	Caudate_basal_ganglia
Chr1:1173611	RP5-902P8.12	ENSG00000260179.1	G>A	4.5432e-3	-13103	Caudate_basal_ganglia
Chr1:1173611	B3GALT6	ENSG00000176022.3	G>A	3.3209e-7	5982	Putamen_basal_ganglia
Chr1:1173611	B3GALT6	ENSG00000176022.3	G>A	2.1829e-4	5982	Anterior_cingulate_cortex

meQTL of rs6697886 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 )
chr1	1165140	1165194	E067	-8417
chr1	1165282	1165336	E067	-8275
chr1	1205978	1206032	E067	32367
chr1	1206280	1206568	E067	32669
chr1	1206884	1206956	E067	33273
chr1	1207508	1207548	E067	33897
chr1	1210684	1210820	E067	37073
chr1	1210869	1210937	E067	37258
chr1	1165140	1165194	E068	-8417
chr1	1165282	1165336	E068	-8275
chr1	1165432	1165533	E068	-8078
chr1	1165701	1165780	E068	-7831
chr1	1168943	1169040	E068	-4571
chr1	1169075	1169219	E068	-4392
chr1	1205600	1205733	E068	31989
chr1	1205777	1205848	E068	32166
chr1	1205978	1206032	E068	32367
chr1	1206280	1206568	E068	32669
chr1	1206884	1206956	E068	33273
chr1	1207508	1207548	E068	33897
chr1	1143415	1144181	E069	-29430
chr1	1144374	1144552	E069	-29059
chr1	1164416	1164466	E069	-9145
chr1	1164488	1164548	E069	-9063
chr1	1164626	1164676	E069	-8935
chr1	1165140	1165194	E069	-8417
chr1	1165432	1165533	E069	-8078
chr1	1165701	1165780	E069	-7831
chr1	1168943	1169040	E069	-4571
chr1	1205600	1205733	E069	31989
chr1	1205777	1205848	E069	32166
chr1	1205978	1206032	E069	32367
chr1	1206280	1206568	E069	32669
chr1	1206884	1206956	E069	33273
chr1	1207508	1207548	E069	33897
chr1	1210400	1210600	E069	36789
chr1	1210684	1210820	E069	37073
chr1	1210869	1210937	E069	37258
chr1	1165282	1165336	E070	-8275
chr1	1169634	1169684	E070	-3927
chr1	1169775	1169819	E070	-3792
chr1	1169950	1170011	E070	-3600
chr1	1170012	1170071	E070	-3540
chr1	1205600	1205733	E070	31989
chr1	1205777	1205848	E070	32166
chr1	1205978	1206032	E070	32367
chr1	1206280	1206568	E070	32669
chr1	1206884	1206956	E070	33273
chr1	1207508	1207548	E070	33897
chr1	1210400	1210600	E070	36789
chr1	1140734	1140952	E071	-32659
chr1	1143415	1144181	E071	-29430
chr1	1165140	1165194	E071	-8417
chr1	1165282	1165336	E071	-8275
chr1	1165432	1165533	E071	-8078
chr1	1165701	1165780	E071	-7831
chr1	1168943	1169040	E071	-4571
chr1	1185268	1185318	E071	11657
chr1	1196406	1196533	E071	22795
chr1	1196582	1196649	E071	22971
chr1	1205600	1205733	E071	31989
chr1	1205777	1205848	E071	32166
chr1	1205978	1206032	E071	32367
chr1	1206280	1206568	E071	32669
chr1	1206884	1206956	E071	33273
chr1	1207508	1207548	E071	33897
chr1	1210400	1210600	E071	36789
chr1	1143415	1144181	E072	-29430
chr1	1144374	1144552	E072	-29059
chr1	1160713	1160888	E072	-12723
chr1	1161319	1161601	E072	-12010
chr1	1165140	1165194	E072	-8417
chr1	1165282	1165336	E072	-8275
chr1	1165432	1165533	E072	-8078
chr1	1168943	1169040	E072	-4571
chr1	1181445	1181510	E072	7834
chr1	1205600	1205733	E072	31989
chr1	1205777	1205848	E072	32166
chr1	1205978	1206032	E072	32367
chr1	1206280	1206568	E072	32669
chr1	1206884	1206956	E072	33273
chr1	1207508	1207548	E072	33897
chr1	1210400	1210600	E072	36789
chr1	1210684	1210820	E072	37073
chr1	1161319	1161601	E073	-12010
chr1	1162376	1162430	E073	-11181
chr1	1164022	1164085	E073	-9526
chr1	1165140	1165194	E073	-8417
chr1	1165701	1165780	E073	-7831
chr1	1205777	1205848	E073	32166
chr1	1205978	1206032	E073	32367
chr1	1206280	1206568	E073	32669
chr1	1206884	1206956	E073	33273
chr1	1207508	1207548	E073	33897
chr1	1219138	1219178	E073	45527
chr1	1219181	1219275	E073	45570
chr1	1219295	1219468	E073	45684
chr1	1165140	1165194	E074	-8417
chr1	1165282	1165336	E074	-8275
chr1	1165432	1165533	E074	-8078
chr1	1165701	1165780	E074	-7831
chr1	1205600	1205733	E074	31989
chr1	1205777	1205848	E074	32166
chr1	1205978	1206032	E074	32367
chr1	1206280	1206568	E074	32669
chr1	1206884	1206956	E074	33273
chr1	1207508	1207548	E074	33897
chr1	1143415	1144181	E081	-29430
chr1	1144374	1144552	E081	-29059
chr1	1165282	1165336	E081	-8275
chr1	1165432	1165533	E081	-8078
chr1	1165701	1165780	E081	-7831
chr1	1168943	1169040	E081	-4571
chr1	1169075	1169219	E081	-4392
chr1	1169511	1169587	E081	-4024
chr1	1169634	1169684	E081	-3927
chr1	1169775	1169819	E081	-3792
chr1	1169950	1170011	E081	-3600
chr1	1205777	1205848	E081	32166
chr1	1205978	1206032	E081	32367
chr1	1206280	1206568	E081	32669
chr1	1206884	1206956	E081	33273
chr1	1207508	1207548	E081	33897
chr1	1210400	1210600	E081	36789
chr1	1210684	1210820	E081	37073
chr1	1210869	1210937	E081	37258
chr1	1143415	1144181	E082	-29430
chr1	1165140	1165194	E082	-8417
chr1	1165282	1165336	E082	-8275
chr1	1165432	1165533	E082	-8078
chr1	1169775	1169819	E082	-3792
chr1	1206280	1206568	E082	32669
chr1	1206884	1206956	E082	33273
chr1	1207508	1207548	E082	33897

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	1166122	1168143	E067	-5468
chr1	1208993	1209933	E067	35382
chr1	1166122	1168143	E068	-5468
chr1	1208993	1209933	E068	35382
chr1	1136717	1137192	E069	-36419
chr1	1166122	1168143	E069	-5468
chr1	1208993	1209933	E069	35382
chr1	1136024	1136620	E070	-36991
chr1	1136717	1137192	E070	-36419
chr1	1166122	1168143	E070	-5468
chr1	1208993	1209933	E070	35382
chr1	1136024	1136620	E071	-36991
chr1	1136717	1137192	E071	-36419
chr1	1166122	1168143	E071	-5468
chr1	1208993	1209933	E071	35382
chr1	1166122	1168143	E072	-5468
chr1	1208993	1209933	E072	35382
chr1	1166122	1168143	E073	-5468
chr1	1208993	1209933	E073	35382
chr1	1166122	1168143	E074	-5468
chr1	1208993	1209933	E074	35382
chr1	1166122	1168143	E081	-5468
chr1	1136024	1136620	E082	-36991
chr1	1136717	1137192	E082	-36419
chr1	1166122	1168143	E082	-5468
chr1	1208993	1209933	E082	35382