rs7643379

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

MB21D2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A==0463 (13840/29870,GnomAD)
A==0486 (14161/29118,TOPMED)
A==0500 (2504/5008,1000G)
G=0500 (2504/5008,1000G)
A==0468 (1804/3854,ALSPAC)
A==0470 (1744/3708,TWINSUK)

Position: chr3:192901594 (GRCh38.p7) (3q29)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 113 Enhancers around

Promoter: 20 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 3	NC_000003.12:g.192901594A>G
GRCh37.p13 chr 3	NC_000003.11:g.192619383A>G

Gene: MB21D2, Mab-21 domain containing 2(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MB21D2 transcript	NM_178496.3:c.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.483	G=0.517
1000Genomes	American	Sub	694	A=0.420	G=0.580
1000Genomes	East Asian	Sub	1008	A=0.669	G=0.331
1000Genomes	Europe	Sub	1006	A=0.453	G=0.547
1000Genomes	Global	Study-wide	5008	A=0.500	G=0.500
1000Genomes	South Asian	Sub	978	A=0.450	G=0.550
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.468	G=0.532
The Genome Aggregation Database	African	Sub	8678	A=0.491	G=0.509
The Genome Aggregation Database	American	Sub	832	A=0.360	G=0.640
The Genome Aggregation Database	East Asian	Sub	1608	A=0.698	G=0.302
The Genome Aggregation Database	Europe	Sub	18452	A=0.433	G=0.566
The Genome Aggregation Database	Global	Study-wide	29870	A=0.463	G=0.536
The Genome Aggregation Database	Other	Sub	300	A=0.520	G=0.480
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.486	G=0.513
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.470	G=0.530

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
rs7643379	0.0000052	alcohol dependence	20201924
rs7643379	0.00000525	alcoholism	pha002892

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 )
chr3	192575065	192575337	E067	-44046
chr3	192575418	192575591	E067	-43792
chr3	192576856	192576934	E067	-42449
chr3	192632576	192633097	E067	13193
chr3	192633135	192633436	E067	13752
chr3	192636682	192636784	E067	17299
chr3	192636985	192637035	E067	17602
chr3	192569598	192570301	E068	-49082
chr3	192632576	192633097	E068	13193
chr3	192633135	192633436	E068	13752
chr3	192574807	192574865	E069	-44518
chr3	192575065	192575337	E069	-44046
chr3	192622373	192622457	E069	2990
chr3	192622458	192623020	E069	3075
chr3	192636682	192636784	E069	17299
chr3	192575065	192575337	E070	-44046
chr3	192584720	192584862	E070	-34521
chr3	192584884	192584966	E070	-34417
chr3	192585040	192585191	E070	-34192
chr3	192585316	192585433	E070	-33950
chr3	192585536	192585731	E070	-33652
chr3	192610688	192611529	E070	-7854
chr3	192611676	192611794	E070	-7589
chr3	192611948	192612035	E070	-7348
chr3	192612199	192612264	E070	-7119
chr3	192622373	192622457	E070	2990
chr3	192622458	192623020	E070	3075
chr3	192623923	192624094	E070	4540
chr3	192624214	192624339	E070	4831
chr3	192624407	192624498	E070	5024
chr3	192624539	192624663	E070	5156
chr3	192624691	192625188	E070	5308
chr3	192625264	192625347	E070	5881
chr3	192632017	192632219	E070	12634
chr3	192632272	192632329	E070	12889
chr3	192632359	192632458	E070	12976
chr3	192569598	192570301	E071	-49082
chr3	192587198	192587486	E071	-31897
chr3	192587554	192587604	E071	-31779
chr3	192587648	192587723	E071	-31660
chr3	192622373	192622457	E071	2990
chr3	192622458	192623020	E071	3075
chr3	192632359	192632458	E071	12976
chr3	192632576	192633097	E071	13193
chr3	192633135	192633436	E071	13752
chr3	192636682	192636784	E071	17299
chr3	192636985	192637035	E071	17602
chr3	192569598	192570301	E072	-49082
chr3	192576856	192576934	E072	-42449
chr3	192622373	192622457	E072	2990
chr3	192622458	192623020	E072	3075
chr3	192632359	192632458	E072	12976
chr3	192632576	192633097	E072	13193
chr3	192636682	192636784	E072	17299
chr3	192639723	192639850	E072	20340
chr3	192639872	192639995	E072	20489
chr3	192569598	192570301	E073	-49082
chr3	192587554	192587604	E073	-31779
chr3	192587648	192587723	E073	-31660
chr3	192632359	192632458	E073	12976
chr3	192632576	192633097	E073	13193
chr3	192636682	192636784	E073	17299
chr3	192636985	192637035	E073	17602
chr3	192569598	192570301	E074	-49082
chr3	192574807	192574865	E074	-44518
chr3	192575065	192575337	E074	-44046
chr3	192622458	192623020	E074	3075
chr3	192633135	192633436	E074	13752
chr3	192636682	192636784	E074	17299
chr3	192575065	192575337	E081	-44046
chr3	192575418	192575591	E081	-43792
chr3	192576685	192576761	E081	-42622
chr3	192576797	192576847	E081	-42536
chr3	192576856	192576934	E081	-42449
chr3	192577042	192577102	E081	-42281
chr3	192577120	192577215	E081	-42168
chr3	192577954	192578004	E081	-41379
chr3	192578280	192578605	E081	-40778
chr3	192578786	192578905	E081	-40478
chr3	192579717	192579767	E081	-39616
chr3	192579921	192580086	E081	-39297
chr3	192584720	192584862	E081	-34521
chr3	192584884	192584966	E081	-34417
chr3	192585040	192585191	E081	-34192
chr3	192585316	192585433	E081	-33950
chr3	192587198	192587486	E081	-31897
chr3	192622373	192622457	E081	2990
chr3	192622458	192623020	E081	3075
chr3	192623923	192624094	E081	4540
chr3	192624214	192624339	E081	4831
chr3	192624407	192624498	E081	5024
chr3	192624539	192624663	E081	5156
chr3	192624691	192625188	E081	5308
chr3	192625264	192625347	E081	5881
chr3	192625591	192626089	E081	6208
chr3	192630529	192630643	E081	11146
chr3	192632017	192632219	E081	12634
chr3	192632272	192632329	E081	12889
chr3	192633135	192633436	E081	13752
chr3	192577042	192577102	E082	-42281
chr3	192577120	192577215	E082	-42168
chr3	192577954	192578004	E082	-41379
chr3	192578280	192578605	E082	-40778
chr3	192578786	192578905	E082	-40478
chr3	192579717	192579767	E082	-39616
chr3	192579921	192580086	E082	-39297
chr3	192584720	192584862	E082	-34521
chr3	192584884	192584966	E082	-34417
chr3	192610688	192611529	E082	-7854
chr3	192622373	192622457	E082	2990
chr3	192622458	192623020	E082	3075
chr3	192630529	192630643	E082	11146
chr3	192631566	192631636	E082	12183

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr3	192633990	192636323	E067	14607
chr3	192636395	192636441	E067	17012
chr3	192633990	192636323	E068	14607
chr3	192636395	192636441	E068	17012
chr3	192633990	192636323	E069	14607
chr3	192636395	192636441	E069	17012
chr3	192633990	192636323	E070	14607
chr3	192636395	192636441	E070	17012
chr3	192633990	192636323	E071	14607
chr3	192636395	192636441	E071	17012
chr3	192633990	192636323	E072	14607
chr3	192636395	192636441	E072	17012
chr3	192633990	192636323	E073	14607
chr3	192636395	192636441	E073	17012
chr3	192633990	192636323	E074	14607
chr3	192636395	192636441	E074	17012
chr3	192633990	192636323	E081	14607
chr3	192636395	192636441	E081	17012
chr3	192633990	192636323	E082	14607
chr3	192636395	192636441	E082	17012

rs7643379

Genomic Coordinates

Gene: MB21D2, Mab-21 domain containing 2(minus strand)

Population Frequency

P-Value

eQTL of rs7643379 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs7643379 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Promoter Annotation (GRCh37.p13)