rs11589188

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

LOC107985208 : Intron Variant
LOC107985210 : 500B Downstream Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0022 (682/29870,GnomAD)
C=0025 (748/29118,TOPMED)
C=0015 (75/5008,1000G)
C=0043 (164/3854,ALSPAC)
C=0042 (154/3708,TWINSUK)

Position: chr1:156002096 (GRCh38.p7) (1q22)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 203 Enhancers around

Promoter: 20 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.156002096T>C
GRCh37.p13 chr 1	NC_000001.10:g.155971887T>C

Gene: LOC107985208, uncharacterized LOC107985208(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC107985208 transcript	XR_001738245.1:n.	N/A	Intron Variant

Gene: LOC107985210, uncharacterized LOC107985210(plus strand): 500B Downstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
LOC107985210 transcript	XR_001738248.1:n.	N/A	Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.998	C=0.002
1000Genomes	American	Sub	694	T=0.980	C=0.020
1000Genomes	East Asian	Sub	1008	T=1.000	C=0.000
1000Genomes	Europe	Sub	1006	T=0.956	C=0.044
1000Genomes	Global	Study-wide	5008	T=0.985	C=0.015
1000Genomes	South Asian	Sub	978	T=0.990	C=0.010
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.957	C=0.043
The Genome Aggregation Database	African	Sub	8720	T=0.993	C=0.007
The Genome Aggregation Database	American	Sub	826	T=0.970	C=0.030
The Genome Aggregation Database	East Asian	Sub	1622	T=1.000	C=0.000
The Genome Aggregation Database	Europe	Sub	18400	T=0.968	C=0.031
The Genome Aggregation Database	Global	Study-wide	29870	T=0.977	C=0.022
The Genome Aggregation Database	Other	Sub	302	T=0.930	C=0.070
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.974	C=0.025
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.958	C=0.042

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
rs11589188	6E-05	alcohol dependence	21703634

eQTL of rs11589188 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 rs11589188 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	155927773	155927821	E067	-44066
chr1	155927897	155927947	E067	-43940
chr1	155930054	155930246	E067	-41641
chr1	155930278	155930479	E067	-41408
chr1	155930724	155930817	E067	-41070
chr1	155930853	155930913	E067	-40974
chr1	155930987	155931079	E067	-40808
chr1	155931398	155931484	E067	-40403
chr1	155931628	155932676	E067	-39211
chr1	155932857	155932954	E067	-38933
chr1	155936061	155936196	E067	-35691
chr1	155939794	155939918	E067	-31969
chr1	155939980	155940034	E067	-31853
chr1	155943607	155944085	E067	-27802
chr1	155950352	155950465	E067	-21422
chr1	155952913	155953996	E067	-17891
chr1	155960836	155961246	E067	-10641
chr1	156020719	156020807	E067	48832
chr1	156021107	156021174	E067	49220
chr1	155927773	155927821	E068	-44066
chr1	155927897	155927947	E068	-43940
chr1	155929154	155929222	E068	-42665
chr1	155929289	155929421	E068	-42466
chr1	155929467	155929723	E068	-42164
chr1	155930054	155930246	E068	-41641
chr1	155930278	155930479	E068	-41408
chr1	155930724	155930817	E068	-41070
chr1	155930853	155930913	E068	-40974
chr1	155930987	155931079	E068	-40808
chr1	155931398	155931484	E068	-40403
chr1	155931628	155932676	E068	-39211
chr1	155932857	155932954	E068	-38933
chr1	155934137	155934264	E068	-37623
chr1	155934767	155934815	E068	-37072
chr1	155950352	155950465	E068	-21422
chr1	155950740	155950790	E068	-21097
chr1	155950875	155950997	E068	-20890
chr1	155951000	155951583	E068	-20304
chr1	155970884	155971076	E068	-811
chr1	155971694	155971770	E068	-117
chr1	155974587	155975446	E068	2700
chr1	155929289	155929421	E069	-42466
chr1	155929467	155929723	E069	-42164
chr1	155930054	155930246	E069	-41641
chr1	155930278	155930479	E069	-41408
chr1	155930724	155930817	E069	-41070
chr1	155930853	155930913	E069	-40974
chr1	155930987	155931079	E069	-40808
chr1	155931398	155931484	E069	-40403
chr1	155931628	155932676	E069	-39211
chr1	155932857	155932954	E069	-38933
chr1	155936061	155936196	E069	-35691
chr1	155939794	155939918	E069	-31969
chr1	155943607	155944085	E069	-27802
chr1	155950352	155950465	E069	-21422
chr1	155950740	155950790	E069	-21097
chr1	155970884	155971076	E069	-811
chr1	155971105	155971153	E069	-734
chr1	155971183	155971290	E069	-597
chr1	155971439	155971568	E069	-319
chr1	156020146	156020231	E069	48259
chr1	156020234	156020596	E069	48347
chr1	156020719	156020807	E069	48832
chr1	156021107	156021174	E069	49220
chr1	156021258	156021451	E069	49371
chr1	156021650	156021717	E069	49763
chr1	156021758	156021817	E069	49871
chr1	155936061	155936196	E070	-35691
chr1	155952913	155953996	E070	-17891
chr1	155988897	155989045	E070	17010
chr1	155989207	155989269	E070	17320
chr1	156021650	156021717	E070	49763
chr1	156021758	156021817	E070	49871
chr1	155929154	155929222	E071	-42665
chr1	155929289	155929421	E071	-42466
chr1	155929467	155929723	E071	-42164
chr1	155930054	155930246	E071	-41641
chr1	155930278	155930479	E071	-41408
chr1	155930724	155930817	E071	-41070
chr1	155930853	155930913	E071	-40974
chr1	155930987	155931079	E071	-40808
chr1	155931398	155931484	E071	-40403
chr1	155931628	155932676	E071	-39211
chr1	155932857	155932954	E071	-38933
chr1	155936061	155936196	E071	-35691
chr1	155936586	155936652	E071	-35235
chr1	155943607	155944085	E071	-27802
chr1	155950352	155950465	E071	-21422
chr1	155950740	155950790	E071	-21097
chr1	155950875	155950997	E071	-20890
chr1	155951000	155951583	E071	-20304
chr1	155952913	155953996	E071	-17891
chr1	155960836	155961246	E071	-10641
chr1	155965797	155965853	E071	-6034
chr1	155965902	155965969	E071	-5918
chr1	155966069	155966390	E071	-5497
chr1	155970884	155971076	E071	-811
chr1	155971105	155971153	E071	-734
chr1	155971183	155971290	E071	-597
chr1	155971439	155971568	E071	-319
chr1	155971694	155971770	E071	-117
chr1	155971786	155971990	E071	0
chr1	155976506	155977144	E071	4619
chr1	156020146	156020231	E071	48259
chr1	156020234	156020596	E071	48347
chr1	156020719	156020807	E071	48832
chr1	156021107	156021174	E071	49220
chr1	156021258	156021451	E071	49371
chr1	155929154	155929222	E072	-42665
chr1	155929289	155929421	E072	-42466
chr1	155929467	155929723	E072	-42164
chr1	155930054	155930246	E072	-41641
chr1	155930278	155930479	E072	-41408
chr1	155930724	155930817	E072	-41070
chr1	155930853	155930913	E072	-40974
chr1	155930987	155931079	E072	-40808
chr1	155931398	155931484	E072	-40403
chr1	155931628	155932676	E072	-39211
chr1	155932857	155932954	E072	-38933
chr1	155934137	155934264	E072	-37623
chr1	155934767	155934815	E072	-37072
chr1	155943607	155944085	E072	-27802
chr1	155952913	155953996	E072	-17891
chr1	155960836	155961246	E072	-10641
chr1	155965797	155965853	E072	-6034
chr1	155965902	155965969	E072	-5918
chr1	155966069	155966390	E072	-5497
chr1	155976506	155977144	E072	4619
chr1	156020719	156020807	E072	48832
chr1	156021107	156021174	E072	49220
chr1	156021258	156021451	E072	49371
chr1	156021650	156021717	E072	49763
chr1	155927378	155927442	E073	-44445
chr1	155927773	155927821	E073	-44066
chr1	155930054	155930246	E073	-41641
chr1	155930278	155930479	E073	-41408
chr1	155930724	155930817	E073	-41070
chr1	155930853	155930913	E073	-40974
chr1	155930987	155931079	E073	-40808
chr1	155931398	155931484	E073	-40403
chr1	155931628	155932676	E073	-39211
chr1	155932857	155932954	E073	-38933
chr1	155934137	155934264	E073	-37623
chr1	155934767	155934815	E073	-37072
chr1	155936061	155936196	E073	-35691
chr1	155950352	155950465	E073	-21422
chr1	155950740	155950790	E073	-21097
chr1	155950875	155950997	E073	-20890
chr1	155952451	155952550	E073	-19337
chr1	155952913	155953996	E073	-17891
chr1	155960836	155961246	E073	-10641
chr1	155930278	155930479	E074	-41408
chr1	155930724	155930817	E074	-41070
chr1	155930853	155930913	E074	-40974
chr1	155930987	155931079	E074	-40808
chr1	155931398	155931484	E074	-40403
chr1	155931628	155932676	E074	-39211
chr1	155932857	155932954	E074	-38933
chr1	155936061	155936196	E074	-35691
chr1	155936586	155936652	E074	-35235
chr1	155936720	155936846	E074	-35041
chr1	155939505	155939779	E074	-32108
chr1	155943607	155944085	E074	-27802
chr1	155950352	155950465	E074	-21422
chr1	155950740	155950790	E074	-21097
chr1	155950875	155950997	E074	-20890
chr1	155951000	155951583	E074	-20304
chr1	155951669	155951757	E074	-20130
chr1	155952913	155953996	E074	-17891
chr1	155965797	155965853	E074	-6034
chr1	155965902	155965969	E074	-5918
chr1	155966069	155966390	E074	-5497
chr1	155995680	155996034	E074	23793
chr1	155996328	155996396	E074	24441
chr1	156020234	156020596	E074	48347
chr1	156020719	156020807	E074	48832
chr1	156021107	156021174	E074	49220
chr1	155936586	155936652	E081	-35235
chr1	155936720	155936846	E081	-35041
chr1	155937194	155937413	E081	-34474
chr1	155937428	155937964	E081	-33923
chr1	155938072	155938122	E081	-33765
chr1	155938176	155938284	E081	-33603
chr1	155938291	155939047	E081	-32840
chr1	155939052	155939315	E081	-32572
chr1	155939505	155939779	E081	-32108
chr1	155939794	155939918	E081	-31969
chr1	155939980	155940034	E081	-31853
chr1	155940203	155940968	E081	-30919
chr1	155941818	155941868	E081	-30019
chr1	155941889	155941949	E081	-29938
chr1	155943607	155944085	E081	-27802
chr1	155988897	155989045	E081	17010
chr1	155989207	155989269	E081	17320
chr1	156021650	156021717	E081	49763
chr1	156021758	156021817	E081	49871
chr1	155937194	155937413	E082	-34474
chr1	155939505	155939779	E082	-32108
chr1	155939794	155939918	E082	-31969
chr1	155939980	155940034	E082	-31853
chr1	155941818	155941868	E082	-30019
chr1	155941889	155941949	E082	-29938
chr1	155988897	155989045	E082	17010

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	155945509	155950112	E067	-21775
chr1	155990026	155991243	E067	18139
chr1	155945509	155950112	E068	-21775
chr1	155990026	155991243	E068	18139
chr1	155945509	155950112	E069	-21775
chr1	155990026	155991243	E069	18139
chr1	155945509	155950112	E070	-21775
chr1	155990026	155991243	E070	18139
chr1	155945509	155950112	E071	-21775
chr1	155990026	155991243	E071	18139
chr1	155945509	155950112	E072	-21775
chr1	155990026	155991243	E072	18139
chr1	155945509	155950112	E073	-21775
chr1	155990026	155991243	E073	18139
chr1	155945509	155950112	E074	-21775
chr1	155990026	155991243	E074	18139
chr1	155945509	155950112	E081	-21775
chr1	155990026	155991243	E081	18139
chr1	155945509	155950112	E082	-21775
chr1	155990026	155991243	E082	18139