rs7132890

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

LOC105369901 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0441 (13185/29840,GnomAD)
G==0460 (13417/29118,TOPMED)
G==0454 (2272/5008,1000G)
G==0369 (1424/3854,ALSPAC)
G==0370 (1373/3708,TWINSUK)

Position: chr12:91966063 (GRCh38.p7) (12q21.33)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 57 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.91966063G>A
GRCh37.p13 chr 12	NC_000012.11:g.92359839G>A

Gene: LOC105369901, uncharacterized LOC105369901(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105369901 transcript variant X2	XR_001749253.1:n.	N/A	Intron Variant
LOC105369901 transcript variant X3	XR_001749254.1:n.	N/A	Intron Variant
LOC105369901 transcript variant X4	XR_001749255.1:n.	N/A	Intron Variant
LOC105369901 transcript variant X5	XR_001749256.1:n.	N/A	Intron Variant
LOC105369901 transcript variant X1	XR_945202.2:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.601	A=0.399
1000Genomes	American	Sub	694	G=0.470	A=0.530
1000Genomes	East Asian	Sub	1008	G=0.367	A=0.633
1000Genomes	Europe	Sub	1006	G=0.393	A=0.607
1000Genomes	Global	Study-wide	5008	G=0.454	A=0.546
1000Genomes	South Asian	Sub	978	G=0.390	A=0.610
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.369	A=0.631
The Genome Aggregation Database	African	Sub	8686	G=0.570	A=0.430
The Genome Aggregation Database	American	Sub	838	G=0.490	A=0.510
The Genome Aggregation Database	East Asian	Sub	1612	G=0.356	A=0.644
The Genome Aggregation Database	Europe	Sub	18402	G=0.388	A=0.611
The Genome Aggregation Database	Global	Study-wide	29840	G=0.441	A=0.558
The Genome Aggregation Database	Other	Sub	302	G=0.320	A=0.680
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.460	A=0.539
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.370	A=0.630

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
rs7132890	0.0006	alcohol dependence	20201924

eQTL of rs7132890 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 rs7132890 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 )
chr12	92379086	92379878	E067	19247
chr12	92379927	92380182	E067	20088
chr12	92380341	92380598	E067	20502
chr12	92378409	92378679	E068	18570
chr12	92379927	92380182	E068	20088
chr12	92380341	92380598	E068	20502
chr12	92381858	92382373	E068	22019
chr12	92382394	92382520	E068	22555
chr12	92382545	92382624	E068	22706
chr12	92381858	92382373	E069	22019
chr12	92377261	92377311	E070	17422
chr12	92377358	92377408	E070	17519
chr12	92377410	92377494	E070	17571
chr12	92377792	92377997	E070	17953
chr12	92378222	92378408	E070	18383
chr12	92378409	92378679	E070	18570
chr12	92378892	92379063	E070	19053
chr12	92379086	92379878	E070	19247
chr12	92379927	92380182	E070	20088
chr12	92380341	92380598	E070	20502
chr12	92380738	92380790	E070	20899
chr12	92380969	92381013	E070	21130
chr12	92381357	92381684	E070	21518
chr12	92381858	92382373	E070	22019
chr12	92382394	92382520	E070	22555
chr12	92386323	92386403	E070	26484
chr12	92386503	92386662	E070	26664
chr12	92386814	92386867	E070	26975
chr12	92387236	92387286	E070	27397
chr12	92387468	92387522	E070	27629
chr12	92387597	92387694	E070	27758
chr12	92387703	92387822	E070	27864
chr12	92387934	92388056	E070	28095
chr12	92388107	92388176	E070	28268
chr12	92389323	92389447	E070	29484
chr12	92397283	92397343	E070	37444
chr12	92397496	92397540	E070	37657
chr12	92397627	92397712	E070	37788
chr12	92397720	92397824	E070	37881
chr12	92378892	92379063	E071	19053
chr12	92379086	92379878	E071	19247
chr12	92379927	92380182	E071	20088
chr12	92380341	92380598	E071	20502
chr12	92380738	92380790	E071	20899
chr12	92380969	92381013	E071	21130
chr12	92381357	92381684	E071	21518
chr12	92381858	92382373	E072	22019
chr12	92382394	92382520	E072	22555
chr12	92382545	92382624	E072	22706
chr12	92379086	92379878	E074	19247
chr12	92379927	92380182	E074	20088
chr12	92381858	92382373	E074	22019
chr12	92382394	92382520	E074	22555
chr12	92387703	92387822	E081	27864
chr12	92387934	92388056	E081	28095
chr12	92388107	92388176	E081	28268
chr12	92381357	92381684	E082	21518