rs13294002

Organism: Homo sapiens

Alleles: T>G

Gene : Feature

LOC105376136 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0096 (2887/29974,GnomAD)
G=0085 (2474/29118,TOPMED)
G=0048 (241/5008,1000G)
G=0153 (591/3854,ALSPAC)
G=0148 (550/3708,TWINSUK)

Position: chr9:89291224 (GRCh38.p7) (9q22.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 54 Enhancers around

Promoter: 34 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 9	NC_000009.12:g.89291224T>G
GRCh37.p13 chr 9	NC_000009.11:g.91906139T>G

Gene: LOC105376136, uncharacterized LOC105376136(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105376136 transcript variant X1	XR_930100.2:n.	N/A	Intron Variant
LOC105376136 transcript variant X2	XR_930101.2:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.993	G=0.007
1000Genomes	American	Sub	694	T=0.950	G=0.050
1000Genomes	East Asian	Sub	1008	T=0.994	G=0.006
1000Genomes	Europe	Sub	1006	T=0.870	G=0.130
1000Genomes	Global	Study-wide	5008	T=0.952	G=0.048
1000Genomes	South Asian	Sub	978	T=0.940	G=0.060
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.847	G=0.153
The Genome Aggregation Database	African	Sub	8726	T=0.971	G=0.029
The Genome Aggregation Database	American	Sub	838	T=0.940	G=0.060
The Genome Aggregation Database	East Asian	Sub	1622	T=0.993	G=0.007
The Genome Aggregation Database	Europe	Sub	18488	T=0.861	G=0.138
The Genome Aggregation Database	Global	Study-wide	29974	T=0.903	G=0.096
The Genome Aggregation Database	Other	Sub	300	T=0.940	G=0.060
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.915	G=0.085
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.852	G=0.148

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

SNP ID	p-value	Traits	Study
rs13294002	0.000072	alcoholism	pha002893
rs13294002	0.000072	alcohol dependence	20201924
rs13294002	0.0002	alcohol dependence(early age of onset)	20201924

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

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 )
chr9	91932296	91932742	E067	26157
chr9	91937101	91937212	E067	30962
chr9	91937254	91937305	E067	31115
chr9	91937575	91937633	E067	31436
chr9	91938799	91938860	E067	32660
chr9	91939143	91939183	E067	33004
chr9	91939837	91939916	E067	33698
chr9	91940311	91940361	E067	34172
chr9	91940378	91940466	E067	34239
chr9	91940500	91940550	E067	34361
chr9	91932296	91932742	E068	26157
chr9	91935344	91935417	E068	29205
chr9	91935488	91935532	E068	29349
chr9	91935958	91936011	E068	29819
chr9	91936126	91936186	E068	29987
chr9	91939837	91939916	E068	33698
chr9	91896178	91896267	E069	-9872
chr9	91932296	91932742	E069	26157
chr9	91935086	91935231	E069	28947
chr9	91935344	91935417	E069	29205
chr9	91935488	91935532	E069	29349
chr9	91929746	91929992	E070	23607
chr9	91932296	91932742	E070	26157
chr9	91937254	91937305	E070	31115
chr9	91937575	91937633	E070	31436
chr9	91937659	91937699	E070	31520
chr9	91938267	91938754	E070	32128
chr9	91938799	91938860	E070	32660
chr9	91939837	91939916	E070	33698
chr9	91932296	91932742	E071	26157
chr9	91935086	91935231	E071	28947
chr9	91938267	91938754	E071	32128
chr9	91938799	91938860	E071	32660
chr9	91932296	91932742	E073	26157
chr9	91935086	91935231	E073	28947
chr9	91896178	91896267	E074	-9872
chr9	91932296	91932742	E074	26157
chr9	91867583	91868346	E081	-37793
chr9	91871344	91871398	E081	-34741
chr9	91871515	91871567	E081	-34572
chr9	91935086	91935231	E081	28947
chr9	91935344	91935417	E081	29205
chr9	91935958	91936011	E081	29819
chr9	91936126	91936186	E081	29987
chr9	91936203	91936278	E081	30064
chr9	91936585	91936629	E081	30446
chr9	91936837	91936932	E081	30698
chr9	91937101	91937212	E081	30962
chr9	91937254	91937305	E081	31115
chr9	91937575	91937633	E081	31436
chr9	91937659	91937699	E081	31520
chr9	91871515	91871567	E082	-34572
chr9	91929746	91929992	E082	23607
chr9	91930047	91930215	E082	23908

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr9	91924062	91927592	E067	17923
chr9	91932778	91934974	E067	26639
chr9	91924062	91927592	E068	17923
chr9	91932778	91934974	E068	26639
chr9	91924062	91927592	E069	17923
chr9	91932778	91934974	E069	26639
chr9	91897040	91897208	E070	-8931
chr9	91897347	91897471	E070	-8668
chr9	91897742	91897785	E070	-8354
chr9	91924062	91927592	E070	17923
chr9	91927625	91927801	E070	21486
chr9	91928214	91928283	E070	22075
chr9	91928490	91928540	E070	22351
chr9	91932778	91934974	E070	26639
chr9	91924062	91927592	E071	17923
chr9	91932778	91934974	E071	26639
chr9	91897347	91897471	E072	-8668
chr9	91897742	91897785	E072	-8354
chr9	91924062	91927592	E072	17923
chr9	91932778	91934974	E072	26639
chr9	91924062	91927592	E073	17923
chr9	91932778	91934974	E073	26639
chr9	91924062	91927592	E074	17923
chr9	91932778	91934974	E074	26639
chr9	91924062	91927592	E081	17923
chr9	91932778	91934974	E081	26639
chr9	91897040	91897208	E082	-8931
chr9	91897347	91897471	E082	-8668
chr9	91897742	91897785	E082	-8354
chr9	91924062	91927592	E082	17923
chr9	91927625	91927801	E082	21486
chr9	91928214	91928283	E082	22075
chr9	91928490	91928540	E082	22351
chr9	91932778	91934974	E082	26639

rs13294002

Genomic Coordinates

Gene: LOC105376136, uncharacterized LOC105376136(minus strand)

Population Frequency

P-Value

eQTL of rs13294002 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs13294002 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Promoter Annotation (GRCh37.p13)