rs837899

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

LOC151121 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0146 (4398/29958,GnomAD)
G==0148 (4314/29118,TOPMED)
G==0167 (836/5008,1000G)
G==0086 (333/3854,ALSPAC)
G==0094 (348/3708,TWINSUK)

Position: chr2:129266460 (GRCh38.p7) (2q21.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 74 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.129266460G>A
GRCh37.p13 chr 2	NC_000002.11:g.130024033G>A

Gene: LOC151121, uncharacterized LOC151121(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LINC01854 transcript variant 1	NR_122040.1:n.	N/A	Intron Variant
LINC01854 transcript variant 2	NR_122041.1:n.	N/A	Intron Variant
LINC01854 transcript variant 3	NR_122042.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.250	A=0.750
1000Genomes	American	Sub	694	G=0.090	A=0.910
1000Genomes	East Asian	Sub	1008	G=0.180	A=0.820
1000Genomes	Europe	Sub	1006	G=0.094	A=0.906
1000Genomes	Global	Study-wide	5008	G=0.167	A=0.833
1000Genomes	South Asian	Sub	978	G=0.170	A=0.830
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.086	A=0.914
The Genome Aggregation Database	African	Sub	8714	G=0.224	A=0.776
The Genome Aggregation Database	American	Sub	838	G=0.110	A=0.890
The Genome Aggregation Database	East Asian	Sub	1620	G=0.141	A=0.859
The Genome Aggregation Database	Europe	Sub	18484	G=0.112	A=0.887
The Genome Aggregation Database	Global	Study-wide	29958	G=0.146	A=0.853
The Genome Aggregation Database	Other	Sub	302	G=0.160	A=0.840
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.148	A=0.851
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.094	A=0.906

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
rs837899	6.21E-05	alcohol withdrawal symptoms	22072270

eQTL of rs837899 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 rs837899 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 )
chr2	130058723	130058784	E067	34690
chr2	130059024	130059502	E067	34991
chr2	130059592	130059681	E067	35559
chr2	130059767	130060015	E067	35734
chr2	130059024	130059502	E068	34991
chr2	130059592	130059681	E068	35559
chr2	130059767	130060015	E068	35734
chr2	130060148	130060684	E068	36115
chr2	130059024	130059502	E069	34991
chr2	130059592	130059681	E069	35559
chr2	130059767	130060015	E069	35734
chr2	130060148	130060684	E069	36115
chr2	129990903	129991022	E070	-33011
chr2	129991443	129991904	E070	-32129
chr2	130059024	130059502	E070	34991
chr2	130059592	130059681	E070	35559
chr2	130059767	130060015	E070	35734
chr2	130060148	130060684	E070	36115
chr2	130060734	130060787	E070	36701
chr2	130058723	130058784	E071	34690
chr2	130059024	130059502	E071	34991
chr2	130059592	130059681	E071	35559
chr2	130059767	130060015	E071	35734
chr2	130060148	130060684	E071	36115
chr2	130059024	130059502	E072	34991
chr2	130059592	130059681	E072	35559
chr2	130059767	130060015	E072	35734
chr2	130060148	130060684	E072	36115
chr2	130054088	130054995	E073	30055
chr2	130055135	130055241	E073	31102
chr2	130055547	130055759	E073	31514
chr2	130058723	130058784	E073	34690
chr2	130059024	130059502	E073	34991
chr2	130059592	130059681	E073	35559
chr2	130059767	130060015	E073	35734
chr2	130060148	130060684	E073	36115
chr2	130058723	130058784	E074	34690
chr2	130059024	130059502	E074	34991
chr2	130059592	130059681	E074	35559
chr2	130059767	130060015	E074	35734
chr2	129990903	129991022	E081	-33011
chr2	129991443	129991904	E081	-32129
chr2	129996773	129997036	E081	-26997
chr2	130010223	130010353	E081	-13680
chr2	130010398	130011293	E081	-12740
chr2	130038915	130039052	E081	14882
chr2	130039472	130039687	E081	15439
chr2	130039843	130039996	E081	15810
chr2	130050579	130050658	E081	26546
chr2	130050695	130050812	E081	26662
chr2	130054088	130054995	E081	30055
chr2	130055135	130055241	E081	31102
chr2	130055547	130055759	E081	31514
chr2	130058723	130058784	E081	34690
chr2	130059024	130059502	E081	34991
chr2	130060148	130060684	E081	36115
chr2	130060734	130060787	E081	36701
chr2	129996773	129997036	E082	-26997
chr2	130010223	130010353	E082	-13680
chr2	130038591	130038845	E082	14558
chr2	130038915	130039052	E082	14882
chr2	130039472	130039687	E082	15439
chr2	130039843	130039996	E082	15810
chr2	130050579	130050658	E082	26546
chr2	130050695	130050812	E082	26662
chr2	130054088	130054995	E082	30055
chr2	130055135	130055241	E082	31102
chr2	130055547	130055759	E082	31514
chr2	130058723	130058784	E082	34690
chr2	130059024	130059502	E082	34991
chr2	130059592	130059681	E082	35559
chr2	130059767	130060015	E082	35734
chr2	130060148	130060684	E082	36115
chr2	130060734	130060787	E082	36701