SNP Detail Info-rs11909745

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

LINC00189 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0122 (3659/29978,GnomAD)
A==0100 (2926/29118,TOPMED)
A==0165 (826/5008,1000G)
A==0126 (484/3854,ALSPAC)
A==0117 (432/3708,TWINSUK)

Position: chr21:29238300 (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.29238300A>G
GRCh37.p13 chr 21	NC_000021.8:g.30610621A>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=0.015	G=0.985
1000Genomes	American	Sub	694	A=0.330	G=0.670
1000Genomes	East Asian	Sub	1008	A=0.376	G=0.624
1000Genomes	Europe	Sub	1006	A=0.140	G=0.860
1000Genomes	Global	Study-wide	5008	A=0.165	G=0.835
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=0.126	G=0.874
The Genome Aggregation Database	African	Sub	8732	A=0.032	G=0.968
The Genome Aggregation Database	American	Sub	838	A=0.350	G=0.650
The Genome Aggregation Database	East Asian	Sub	1614	A=0.365	G=0.635
The Genome Aggregation Database	Europe	Sub	18492	A=0.133	G=0.866
The Genome Aggregation Database	Global	Study-wide	29978	A=0.122	G=0.877
The Genome Aggregation Database	Other	Sub	302	A=0.110	G=0.890
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.100	G=0.899
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.117	G=0.883

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
rs11909745	0.000679	alcohol consumption	23743675

eQTL of rs11909745 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr21:30610621	RWDD2B	ENSG00000156253.2	A>G	2.1847e-20	218922	Cerebellum
Chr21:30610621	USP16	ENSG00000156256.10	A>G	6.0550e-9	212591	Cerebellum
Chr21:30610621	RWDD2B	ENSG00000156253.2	A>G	5.7170e-15	218922	Frontal_Cortex_BA9
Chr21:30610621	RWDD2B	ENSG00000156253.2	A>G	5.8446e-15	218922	Hypothalamus
Chr21:30610621	RWDD2B	ENSG00000156253.2	A>G	3.6385e-21	218922	Cortex
Chr21:30610621	RWDD2B	ENSG00000156253.2	A>G	5.0980e-12	218922	Cerebellar_Hemisphere
Chr21:30610621	RWDD2B	ENSG00000156253.2	A>G	3.5867e-21	218922	Caudate_basal_ganglia
Chr21:30610621	RWDD2B	ENSG00000156253.2	A>G	3.6379e-12	218922	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	-43762
chr21	30566865	30566964	E068	-43657
chr21	30567101	30567466	E068	-43155
chr21	30567489	30567677	E068	-42944
chr21	30567745	30567799	E068	-42822
chr21	30610409	30610972	E070	0
chr21	30610999	30611127	E070	378
chr21	30611214	30611543	E070	593
chr21	30566126	30566198	E071	-44423
chr21	30566286	30566398	E071	-44223
chr21	30566411	30566570	E071	-44051
chr21	30566576	30566859	E071	-43762
chr21	30566865	30566964	E071	-43657
chr21	30609008	30609084	E071	-1537
chr21	30609102	30609320	E071	-1301
chr21	30609324	30609824	E071	-797
chr21	30609830	30610407	E071	-214
chr21	30566126	30566198	E074	-44423
chr21	30566286	30566398	E074	-44223
chr21	30566411	30566570	E074	-44051
chr21	30566576	30566859	E074	-43762
chr21	30566865	30566964	E074	-43657

rs11909745