SNP Detail Info-rs2832278

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

LINC00189 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0125 (3763/29974,GnomAD)
A==0108 (3152/29118,TOPMED)
A==0169 (847/5008,1000G)
A==0125 (483/3854,ALSPAC)
A==0116 (431/3708,TWINSUK)

Position: chr21:29239169 (GRCh38.p7) (21q21.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 22 Enhancers around

Promoter: 1 Promoter around

Sequence Name	Change(s)
GRCh38.p7 chr 21	NC_000021.9:g.29239169A>G
GRCh37.p13 chr 21	NC_000021.8:g.30611490A>G

Molecule type	Change	Amino acid[Codon]	SO Term
LINC00189 transcript	NR_027072.2:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.037	G=0.963
1000Genomes	American	Sub	694	A=0.330	G=0.670
1000Genomes	East Asian	Sub	1008	A=0.371	G=0.629
1000Genomes	Europe	Sub	1006	A=0.137	G=0.863
1000Genomes	Global	Study-wide	5008	A=0.169	G=0.831
1000Genomes	South Asian	Sub	978	A=0.060	G=0.940
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.125	G=0.875
The Genome Aggregation Database	African	Sub	8730	A=0.051	G=0.949
The Genome Aggregation Database	American	Sub	836	A=0.350	G=0.650
The Genome Aggregation Database	East Asian	Sub	1616	A=0.348	G=0.652
The Genome Aggregation Database	Europe	Sub	18490	A=0.131	G=0.868
The Genome Aggregation Database	Global	Study-wide	29974	A=0.125	G=0.874
The Genome Aggregation Database	Other	Sub	302	A=0.100	G=0.900
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.108	G=0.891
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.116	G=0.884

PMID	Title	Author	Journal
23743675	A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.	Kapoor M	Hum Genet

SNP ID	p-value	Traits	Study
rs2832278	0.000623	alcohol consumption	23743675

eQTL of rs2832278 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr21:30611490	RWDD2B	ENSG00000156253.2	A>G	2.1847e-20	219791	Cerebellum
Chr21:30611490	USP16	ENSG00000156256.10	A>G	6.0550e-9	213460	Cerebellum
Chr21:30611490	RWDD2B	ENSG00000156253.2	A>G	5.7170e-15	219791	Frontal_Cortex_BA9
Chr21:30611490	RWDD2B	ENSG00000156253.2	A>G	5.8446e-15	219791	Hypothalamus
Chr21:30611490	RWDD2B	ENSG00000156253.2	A>G	3.6385e-21	219791	Cortex
Chr21:30611490	RWDD2B	ENSG00000156253.2	A>G	5.0980e-12	219791	Cerebellar_Hemisphere
Chr21:30611490	RWDD2B	ENSG00000156253.2	A>G	3.5867e-21	219791	Caudate_basal_ganglia
Chr21:30611490	RWDD2B	ENSG00000156253.2	A>G	3.6379e-12	219791	Anterior_cingulate_cortex

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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr21	30566576	30566859	E068	-44631
chr21	30566865	30566964	E068	-44526
chr21	30567101	30567466	E068	-44024
chr21	30567489	30567677	E068	-43813
chr21	30567745	30567799	E068	-43691
chr21	30610409	30610972	E070	-518
chr21	30610999	30611127	E070	-363
chr21	30611214	30611543	E070	0
chr21	30566126	30566198	E071	-45292
chr21	30566286	30566398	E071	-45092
chr21	30566411	30566570	E071	-44920
chr21	30566576	30566859	E071	-44631
chr21	30566865	30566964	E071	-44526
chr21	30609008	30609084	E071	-2406
chr21	30609102	30609320	E071	-2170
chr21	30609324	30609824	E071	-1666
chr21	30609830	30610407	E071	-1083
chr21	30566126	30566198	E074	-45292
chr21	30566286	30566398	E074	-45092
chr21	30566411	30566570	E074	-44920
chr21	30566576	30566859	E074	-44631
chr21	30566865	30566964	E074	-44526

rs2832278