rs2466990

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

AADAT : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0443 (13283/29924,GnomAD)
A==0397 (11574/29118,TOPMED)
A==0311 (1558/5008,1000G)
G=0456 (1757/3854,ALSPAC)
G=0446 (1653/3708,TWINSUK)

Position: chr4:170072620 (GRCh38.p7) (4q33)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 26 Enhancers around

Promoter: 28 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 4	NC_000004.12:g.170072620A>G
GRCh37.p13 chr 4	NC_000004.11:g.170993771A>G

Molecule type	Change	Amino acid[Codon]	SO Term
AADAT transcript variant 3	NM_001286682.1:c.	N/A	Intron Variant
AADAT transcript variant 4	NM_001286683.1:c.	N/A	Intron Variant
AADAT transcript variant 1	NM_016228.3:c.	N/A	Intron Variant
AADAT transcript variant 2	NM_182662.1:c.	N/A	Intron Variant
AADAT transcript variant X1	XM_006714231.2:c.	N/A	Intron Variant
AADAT transcript variant X3	XM_011532020.2:c.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.223	G=0.777
1000Genomes	American	Sub	694	A=0.480	G=0.520
1000Genomes	East Asian	Sub	1008	A=0.022	G=0.978
1000Genomes	Europe	Sub	1006	A=0.575	G=0.425
1000Genomes	Global	Study-wide	5008	A=0.311	G=0.689
1000Genomes	South Asian	Sub	978	A=0.340	G=0.660
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.544	G=0.456
The Genome Aggregation Database	African	Sub	8704	A=0.267	G=0.733
The Genome Aggregation Database	American	Sub	834	A=0.460	G=0.540
The Genome Aggregation Database	East Asian	Sub	1616	A=0.027	G=0.973
The Genome Aggregation Database	Europe	Sub	18468	A=0.562	G=0.437
The Genome Aggregation Database	Global	Study-wide	29924	A=0.443	G=0.556
The Genome Aggregation Database	Other	Sub	302	A=0.470	G=0.530
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.397	G=0.602
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.554	G=0.446

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)

SNP ID	p-value	Traits	Study
rs2466990	4.94E-05	alcohol withdrawal symptoms	22072270

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

There is no significant Hi-C chromatin interaction data for this SNP.

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr4	170944347	170944541	E067	-49230
chr4	170969247	170969336	E067	-24435
chr4	170969353	170969488	E067	-24283
chr4	170944347	170944541	E068	-49230
chr4	170979119	170979398	E068	-14373
chr4	170944347	170944541	E069	-49230
chr4	170969247	170969336	E069	-24435
chr4	170969353	170969488	E069	-24283
chr4	171030622	171030727	E069	36851
chr4	171030774	171031326	E069	37003
chr4	170970760	170970810	E070	-22961
chr4	170971005	170971195	E070	-22576
chr4	171008571	171008748	E070	14800
chr4	170949015	170949108	E071	-44663
chr4	170949327	170949405	E071	-44366
chr4	170944347	170944541	E072	-49230
chr4	170969247	170969336	E072	-24435
chr4	170969353	170969488	E072	-24283
chr4	170944347	170944541	E073	-49230
chr4	170969247	170969336	E073	-24435
chr4	170969353	170969488	E073	-24283
chr4	170944347	170944541	E074	-49230
chr4	171030622	171030727	E081	36851
chr4	171030774	171031326	E081	37003
chr4	170979875	170979925	E082	-13846
chr4	171030774	171031326	E082	37003

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr4	170946712	170947382	E067	-46389
chr4	170947398	170949009	E067	-44762
chr4	171010296	171012296	E067	16525
chr4	170946712	170947382	E068	-46389
chr4	170947398	170949009	E068	-44762
chr4	171010296	171012296	E068	16525
chr4	170946712	170947382	E069	-46389
chr4	170947398	170949009	E069	-44762
chr4	171010296	171012296	E069	16525
chr4	170947398	170949009	E070	-44762
chr4	171010296	171012296	E070	16525
chr4	170946712	170947382	E071	-46389
chr4	170947398	170949009	E071	-44762
chr4	171010296	171012296	E071	16525
chr4	170946712	170947382	E072	-46389
chr4	170947398	170949009	E072	-44762
chr4	171010296	171012296	E072	16525
chr4	170946712	170947382	E073	-46389
chr4	170947398	170949009	E073	-44762
chr4	171010296	171012296	E073	16525
chr4	170946712	170947382	E074	-46389
chr4	170947398	170949009	E074	-44762
chr4	171010296	171012296	E074	16525
chr4	170947398	170949009	E081	-44762
chr4	171010296	171012296	E081	16525
chr4	170946712	170947382	E082	-46389
chr4	170947398	170949009	E082	-44762
chr4	171010296	171012296	E082	16525