rs2381750

Organism: Homo sapiens

Alleles: G>A / G>T

Gene : Feature

LOC105373664 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0102 (3071/29910,GnomAD)
T=0102 (2975/29118,TOPMED)
T=0085 (428/5008,1000G)
T=0102 (393/3854,ALSPAC)
T=0100 (370/3708,TWINSUK)

Position: chr2:145624668 (GRCh38.p7) (2q22.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 66 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.145624668G>A
GRCh38.p7 chr 2	NC_000002.12:g.145624668G>T
GRCh37.p13 chr 2	NC_000002.11:g.146382236G>A
GRCh37.p13 chr 2	NC_000002.11:g.146382236G>T

Gene: LOC105373664, uncharacterized LOC105373664(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105373664 transcript variant X2	XR_001739724.1:n.	N/A	Intron Variant
LOC105373664 transcript variant X1	XR_923414.1:n.	N/A	Intron Variant
LOC105373664 transcript variant X2	XR_923415.1:n.	N/A	Intron Variant
LOC105373664 transcript variant X3	XR_923416.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.894	T=0.106
1000Genomes	American	Sub	694	G=0.890	T=0.110
1000Genomes	East Asian	Sub	1008	G=0.949	T=0.051
1000Genomes	Europe	Sub	1006	G=0.916	T=0.084
1000Genomes	Global	Study-wide	5008	G=0.915	T=0.085
1000Genomes	South Asian	Sub	978	G=0.920	T=0.080
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.898	T=0.102
The Genome Aggregation Database	African	Sub	8714	G=0.889	T=0.111
The Genome Aggregation Database	American	Sub	836	G=0.890	T=0.11,
The Genome Aggregation Database	East Asian	Sub	1590	G=0.970	T=0.030
The Genome Aggregation Database	Europe	Sub	18468	G=0.895	T=0.104
The Genome Aggregation Database	Global	Study-wide	29910	G=0.897	T=0.102
The Genome Aggregation Database	Other	Sub	302	G=0.890	T=0.11,
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.897	T=0.102
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.900	T=0.100

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

P-Value

SNP ID	p-value	Traits	Study
rs2381750	0.00086	alcohol dependence	20201924

eQTL of rs2381750 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 rs2381750 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	33546954	33547150	E067	-39690
chr2	33547173	33547621	E067	-39219
chr2	33591063	33591172	E067	4223
chr2	33591487	33591960	E067	4647
chr2	33596943	33597010	E067	10103
chr2	33597210	33597260	E067	10370
chr2	33603808	33603933	E067	16968
chr2	33604001	33604213	E067	17161
chr2	33590421	33590557	E068	3581
chr2	33590646	33590735	E068	3806
chr2	33591063	33591172	E068	4223
chr2	33591487	33591960	E068	4647
chr2	33595632	33596301	E068	8792
chr2	33596943	33597010	E068	10103
chr2	33597210	33597260	E068	10370
chr2	33603565	33603629	E068	16725
chr2	33603681	33603763	E068	16841
chr2	33603808	33603933	E068	16968
chr2	33604001	33604213	E068	17161
chr2	33547173	33547621	E069	-39219
chr2	33591063	33591172	E069	4223
chr2	33591487	33591960	E069	4647
chr2	33595632	33596301	E069	8792
chr2	33596943	33597010	E069	10103
chr2	33597210	33597260	E069	10370
chr2	33603808	33603933	E069	16968
chr2	33604001	33604213	E069	17161
chr2	33591487	33591960	E070	4647
chr2	33547173	33547621	E071	-39219
chr2	33547874	33547930	E071	-38910
chr2	33590646	33590735	E071	3806
chr2	33591063	33591172	E071	4223
chr2	33591487	33591960	E071	4647
chr2	33595409	33595589	E071	8569
chr2	33595632	33596301	E071	8792
chr2	33596943	33597010	E071	10103
chr2	33597210	33597260	E071	10370
chr2	33600242	33600396	E071	13402
chr2	33603565	33603629	E071	16725
chr2	33603681	33603763	E071	16841
chr2	33603808	33603933	E071	16968
chr2	33604001	33604213	E071	17161
chr2	33604808	33604858	E071	17968
chr2	33605223	33605356	E071	18383
chr2	33616414	33616663	E071	29574
chr2	33591063	33591172	E072	4223
chr2	33591487	33591960	E072	4647
chr2	33595632	33596301	E072	8792
chr2	33596943	33597010	E072	10103
chr2	33597210	33597260	E072	10370
chr2	33603808	33603933	E072	16968
chr2	33604001	33604213	E072	17161
chr2	33604808	33604858	E072	17968
chr2	33595632	33596301	E073	8792
chr2	33603808	33603933	E073	16968
chr2	33604001	33604213	E073	17161
chr2	33595632	33596301	E074	8792
chr2	33596943	33597010	E074	10103
chr2	33597210	33597260	E074	10370
chr2	33600242	33600396	E074	13402
chr2	33603565	33603629	E074	16725
chr2	33603681	33603763	E074	16841
chr2	33603808	33603933	E074	16968
chr2	33604001	33604213	E074	17161
chr2	33547173	33547621	E081	-39219
chr2	33547874	33547930	E081	-38910