rs11804222

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0136 (4101/29950,GnomAD)
A=0163 (4756/29118,TOPMED)
A=0139 (698/5008,1000G)
A=0130 (501/3854,ALSPAC)
A=0135 (500/3708,TWINSUK)

Position: chr1:11876457 (GRCh38.p7) (1p36.22)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 112 Enhancers around

Promoter: 48 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.11876457G>A
GRCh37.p13 chr 1	NC_000001.10:g.11936514G>A

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.775	A=0.225
1000Genomes	American	Sub	694	G=0.930	A=0.070
1000Genomes	East Asian	Sub	1008	G=0.950	A=0.050
1000Genomes	Europe	Sub	1006	G=0.904	A=0.096
1000Genomes	Global	Study-wide	5008	G=0.861	A=0.139
1000Genomes	South Asian	Sub	978	G=0.790	A=0.210
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.870	A=0.130
The Genome Aggregation Database	African	Sub	8720	G=0.791	A=0.209
The Genome Aggregation Database	American	Sub	838	G=0.930	A=0.070
The Genome Aggregation Database	East Asian	Sub	1618	G=0.948	A=0.052
The Genome Aggregation Database	Europe	Sub	18472	G=0.885	A=0.114
The Genome Aggregation Database	Global	Study-wide	29950	G=0.863	A=0.136
The Genome Aggregation Database	Other	Sub	302	G=0.900	A=0.100
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.836	A=0.163
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.865	A=0.135

PMID	Title	Author	Journal
22072270	Genome-wide association study identifies 5q21 and 9p24.1 (KDM4C) loci associated with alcohol withdrawal symptoms.	Wang KS	J Neural Transm (Vienna)

P-Value

SNP ID	p-value	Traits	Study
rs11804222	3.23E-05	alcohol withdrawal symptoms	22072270

eQTL of rs11804222 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 rs11804222 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	11908471	11908643	E067	-27871
chr1	11940227	11940565	E067	3713
chr1	11940714	11941660	E067	4200
chr1	11978786	11978897	E067	42272
chr1	11978950	11979249	E067	42436
chr1	11979383	11979467	E067	42869
chr1	11980051	11980105	E067	43537
chr1	11980390	11980594	E067	43876
chr1	11980732	11980800	E067	44218
chr1	11981223	11981273	E067	44709
chr1	11983512	11983592	E067	46998
chr1	11983686	11983875	E067	47172
chr1	11983990	11984034	E067	47476
chr1	11940227	11940565	E068	3713
chr1	11940714	11941660	E068	4200
chr1	11978786	11978897	E068	42272
chr1	11978950	11979249	E068	42436
chr1	11979383	11979467	E068	42869
chr1	11980051	11980105	E068	43537
chr1	11980390	11980594	E068	43876
chr1	11981223	11981273	E068	44709
chr1	11983512	11983592	E068	46998
chr1	11983686	11983875	E068	47172
chr1	11983990	11984034	E068	47476
chr1	11940227	11940565	E069	3713
chr1	11940714	11941660	E069	4200
chr1	11941685	11941782	E069	5171
chr1	11959081	11959164	E069	22567
chr1	11978246	11978310	E069	41732
chr1	11978786	11978897	E069	42272
chr1	11978950	11979249	E069	42436
chr1	11979383	11979467	E069	42869
chr1	11980051	11980105	E069	43537
chr1	11980390	11980594	E069	43876
chr1	11980732	11980800	E069	44218
chr1	11981223	11981273	E069	44709
chr1	11983512	11983592	E069	46998
chr1	11983686	11983875	E069	47172
chr1	11983990	11984034	E069	47476
chr1	11902136	11903044	E070	-33470
chr1	11908814	11908973	E070	-27541
chr1	11909414	11909485	E070	-27029
chr1	11940227	11940565	E070	3713
chr1	11980732	11980800	E070	44218
chr1	11981223	11981273	E070	44709
chr1	11983512	11983592	E070	46998
chr1	11902136	11903044	E071	-33470
chr1	11940227	11940565	E071	3713
chr1	11940714	11941660	E071	4200
chr1	11941685	11941782	E071	5171
chr1	11978246	11978310	E071	41732
chr1	11978786	11978897	E071	42272
chr1	11978950	11979249	E071	42436
chr1	11979383	11979467	E071	42869
chr1	11980051	11980105	E071	43537
chr1	11980390	11980594	E071	43876
chr1	11981223	11981273	E071	44709
chr1	11983512	11983592	E071	46998
chr1	11983686	11983875	E071	47172
chr1	11983990	11984034	E071	47476
chr1	11908137	11908438	E072	-28076
chr1	11908471	11908643	E072	-27871
chr1	11940227	11940565	E072	3713
chr1	11940714	11941660	E072	4200
chr1	11978786	11978897	E072	42272
chr1	11978950	11979249	E072	42436
chr1	11979383	11979467	E072	42869
chr1	11980051	11980105	E072	43537
chr1	11983512	11983592	E072	46998
chr1	11908137	11908438	E073	-28076
chr1	11940227	11940565	E073	3713
chr1	11940714	11941660	E073	4200
chr1	11941685	11941782	E073	5171
chr1	11959081	11959164	E073	22567
chr1	11978786	11978897	E073	42272
chr1	11978950	11979249	E073	42436
chr1	11979383	11979467	E073	42869
chr1	11980051	11980105	E073	43537
chr1	11981223	11981273	E073	44709
chr1	11983512	11983592	E073	46998
chr1	11983686	11983875	E073	47172
chr1	11983990	11984034	E073	47476
chr1	11940227	11940565	E074	3713
chr1	11940714	11941660	E074	4200
chr1	11978786	11978897	E074	42272
chr1	11978950	11979249	E074	42436
chr1	11979383	11979467	E074	42869
chr1	11980051	11980105	E074	43537
chr1	11980390	11980594	E074	43876
chr1	11980732	11980800	E074	44218
chr1	11981223	11981273	E074	44709
chr1	11983512	11983592	E074	46998
chr1	11983686	11983875	E074	47172
chr1	11983990	11984034	E074	47476
chr1	11908137	11908438	E081	-28076
chr1	11908471	11908643	E081	-27871
chr1	11908814	11908973	E081	-27541
chr1	11909414	11909485	E081	-27029
chr1	11910332	11910576	E081	-25938
chr1	11959081	11959164	E081	22567
chr1	11981223	11981273	E081	44709
chr1	11983512	11983592	E081	46998
chr1	11983686	11983875	E081	47172
chr1	11983990	11984034	E081	47476
chr1	11908137	11908438	E082	-28076
chr1	11908471	11908643	E082	-27871
chr1	11959081	11959164	E082	22567
chr1	11980390	11980594	E082	43876
chr1	11980732	11980800	E082	44218
chr1	11981223	11981273	E082	44709
chr1	11983686	11983875	E082	47172
chr1	11983990	11984034	E082	47476

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	11967386	11970388	E067	30872
chr1	11985272	11985419	E067	48758
chr1	11985615	11985699	E067	49101
chr1	11985822	11985876	E067	49308
chr1	11986031	11986202	E067	49517
chr1	11967386	11970388	E068	30872
chr1	11985272	11985419	E068	48758
chr1	11985615	11985699	E068	49101
chr1	11985822	11985876	E068	49308
chr1	11986031	11986202	E068	49517
chr1	11967386	11970388	E069	30872
chr1	11985272	11985419	E069	48758
chr1	11985615	11985699	E069	49101
chr1	11985822	11985876	E069	49308
chr1	11986031	11986202	E069	49517
chr1	11907121	11907476	E070	-29038
chr1	11967386	11970388	E070	30872
chr1	11985272	11985419	E070	48758
chr1	11985615	11985699	E070	49101
chr1	11985822	11985876	E070	49308
chr1	11986031	11986202	E070	49517
chr1	11967386	11970388	E071	30872
chr1	11985272	11985419	E071	48758
chr1	11985615	11985699	E071	49101
chr1	11985822	11985876	E071	49308
chr1	11986031	11986202	E071	49517
chr1	11967386	11970388	E072	30872
chr1	11985272	11985419	E072	48758
chr1	11985615	11985699	E072	49101
chr1	11985822	11985876	E072	49308
chr1	11986031	11986202	E072	49517
chr1	11967386	11970388	E073	30872
chr1	11985272	11985419	E073	48758
chr1	11985615	11985699	E073	49101
chr1	11985822	11985876	E073	49308
chr1	11986031	11986202	E073	49517
chr1	11967386	11970388	E074	30872
chr1	11985272	11985419	E074	48758
chr1	11985615	11985699	E074	49101
chr1	11985822	11985876	E074	49308
chr1	11986031	11986202	E074	49517
chr1	11967386	11970388	E081	30872
chr1	11985272	11985419	E081	48758
chr1	11967386	11970388	E082	30872
chr1	11985272	11985419	E082	48758
chr1	11985615	11985699	E082	49101
chr1	11985822	11985876	E082	49308
chr1	11986031	11986202	E082	49517