SNP Detail Info-rs2707653

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

LOC107985945 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0358 (10749/29948,GnomAD)
T=0278 (8101/29118,TOPMED)
T=0355 (1777/5008,1000G)
T=0410 (1580/3854,ALSPAC)
T=0414 (1535/3708,TWINSUK)

Position: chr2:129805369 (GRCh38.p7) (2q21.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 32 Enhancers around

Promoter: 0 Promoter around

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.129805369C>T
GRCh37.p13 chr 2	NC_000002.11:g.130562942C>T

Molecule type	Change	Amino acid[Codon]	SO Term
LOC107985945 transcript	XR_001739711.1:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.979	T=0.021
1000Genomes	American	Sub	694	C=0.560	T=0.440
1000Genomes	East Asian	Sub	1008	C=0.443	T=0.557
1000Genomes	Europe	Sub	1006	C=0.548	T=0.452
1000Genomes	Global	Study-wide	5008	C=0.645	T=0.355
1000Genomes	South Asian	Sub	978	C=0.560	T=0.440
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.590	T=0.410
The Genome Aggregation Database	African	Sub	8728	C=0.916	T=0.084
The Genome Aggregation Database	American	Sub	836	C=0.570	T=0.430
The Genome Aggregation Database	East Asian	Sub	1612	C=0.492	T=0.508
The Genome Aggregation Database	Europe	Sub	18470	C=0.527	T=0.472
The Genome Aggregation Database	Global	Study-wide	29948	C=0.641	T=0.358
The Genome Aggregation Database	Other	Sub	302	C=0.660	T=0.340
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.721	T=0.278
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.586	T=0.414

PMID	Title	Author	Journal
21703634	A meta-analysis of two genome-wide association studies identifies 3 new loci for alcohol dependence.	Wang KS	J Psychiatr Res

SNP ID	p-value	Traits	Study
rs2707653	6.09E-05	alcohol dependence	21703634

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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr2	130515443	130516325	E069	-46617
chr2	130514385	130514525	E070	-48417
chr2	130515443	130516325	E070	-46617
chr2	130551002	130551500	E070	-11442
chr2	130551711	130551908	E070	-11034
chr2	130552014	130552074	E070	-10868
chr2	130560809	130560923	E070	-2019
chr2	130564612	130564708	E070	1670
chr2	130564745	130564827	E070	1803
chr2	130584827	130584924	E070	21885
chr2	130586417	130586702	E070	23475
chr2	130523139	130523179	E073	-39763
chr2	130523295	130523397	E073	-39545
chr2	130515443	130516325	E081	-46617
chr2	130538574	130538722	E081	-24220
chr2	130539541	130539591	E081	-23351
chr2	130539699	130539767	E081	-23175
chr2	130549450	130549573	E081	-13369
chr2	130551002	130551500	E081	-11442
chr2	130551711	130551908	E081	-11034
chr2	130552014	130552074	E081	-10868
chr2	130577251	130577386	E081	14309
chr2	130578656	130578729	E081	15714
chr2	130579066	130579412	E081	16124
chr2	130579715	130579843	E081	16773
chr2	130579959	130580074	E081	17017
chr2	130515443	130516325	E082	-46617
chr2	130551002	130551500	E082	-11442
chr2	130551711	130551908	E082	-11034
chr2	130552014	130552074	E082	-10868
chr2	130564612	130564708	E082	1670
chr2	130564745	130564827	E082	1803

rs2707653