rs4245815

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

MSH2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0164 (4921/29958,GnomAD)
G==0196 (5711/29116,TOPMED)
G==0169 (845/5008,1000G)
G==0099 (383/3854,ALSPAC)
G==0095 (352/3708,TWINSUK)

Position: chr2:47592833 (GRCh38.p7) (2p16.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 57 Enhancers around

Promoter: 20 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.47592833G>A
GRCh37.p13 chr 2	NC_000002.11:g.47819972G>A

Gene: MSH2, mutS homolog 2(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MSH2 transcript variant 1	NM_000251.2:c.	N/A	Genic Downstream Transcript Variant
MSH2 transcript variant 2	NM_001258281.1:c.	N/A	Genic Downstream Transcript Variant
MSH2 transcript variant X1	XM_005264332.3:c.	N/A	Genic Downstream Transcript Variant
MSH2 transcript variant X3	XM_011532867.1:c.	N/A	Genic Downstream Transcript Variant
MSH2 transcript variant X2	XR_001738747.1:n.	N/A	Intron Variant
MSH2 transcript variant X4	XR_939685.1:n.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.357	A=0.643
1000Genomes	American	Sub	694	G=0.090	A=0.910
1000Genomes	East Asian	Sub	1008	G=0.071	A=0.929
1000Genomes	Europe	Sub	1006	G=0.091	A=0.909
1000Genomes	Global	Study-wide	5008	G=0.169	A=0.831
1000Genomes	South Asian	Sub	978	G=0.150	A=0.850
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.099	A=0.901
The Genome Aggregation Database	African	Sub	8708	G=0.319	A=0.681
The Genome Aggregation Database	American	Sub	838	G=0.070	A=0.930
The Genome Aggregation Database	East Asian	Sub	1620	G=0.062	A=0.938
The Genome Aggregation Database	Europe	Sub	18492	G=0.105	A=0.894
The Genome Aggregation Database	Global	Study-wide	29958	G=0.164	A=0.835
The Genome Aggregation Database	Other	Sub	300	G=0.090	A=0.910
Trans-Omics for Precision Medicine	Global	Study-wide	29116	G=0.196	A=0.803
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.095	A=0.905

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
rs4245815	0.000662	alcohol dependence	20201924

eQTL of rs4245815 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 rs4245815 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	47785333	47785484	E067	-34488
chr2	47785583	47786154	E067	-33818
chr2	47786278	47786437	E067	-33535
chr2	47844297	47844875	E067	24325
chr2	47844886	47845021	E067	24914
chr2	47848098	47848175	E067	28126
chr2	47844297	47844875	E068	24325
chr2	47785333	47785484	E069	-34488
chr2	47785583	47786154	E069	-33818
chr2	47843523	47844133	E069	23551
chr2	47844297	47844875	E069	24325
chr2	47844886	47845021	E069	24914
chr2	47845193	47845243	E069	25221
chr2	47848098	47848175	E069	28126
chr2	47784729	47784856	E070	-35116
chr2	47785333	47785484	E070	-34488
chr2	47785583	47786154	E070	-33818
chr2	47786278	47786437	E070	-33535
chr2	47786544	47786655	E070	-33317
chr2	47868666	47868724	E070	48694
chr2	47785333	47785484	E071	-34488
chr2	47785583	47786154	E071	-33818
chr2	47786278	47786437	E071	-33535
chr2	47786544	47786655	E071	-33317
chr2	47795437	47795914	E071	-24058
chr2	47843523	47844133	E071	23551
chr2	47844297	47844875	E071	24325
chr2	47844886	47845021	E071	24914
chr2	47845193	47845243	E071	25221
chr2	47845287	47845361	E071	25315
chr2	47848098	47848175	E071	28126
chr2	47784729	47784856	E072	-35116
chr2	47785333	47785484	E072	-34488
chr2	47785583	47786154	E072	-33818
chr2	47789179	47789356	E072	-30616
chr2	47843523	47844133	E072	23551
chr2	47844297	47844875	E072	24325
chr2	47844886	47845021	E072	24914
chr2	47845193	47845243	E072	25221
chr2	47845287	47845361	E072	25315
chr2	47785333	47785484	E073	-34488
chr2	47785583	47786154	E073	-33818
chr2	47786278	47786437	E073	-33535
chr2	47843523	47844133	E074	23551
chr2	47844297	47844875	E074	24325
chr2	47844886	47845021	E074	24914
chr2	47845193	47845243	E074	25221
chr2	47845287	47845361	E074	25315
chr2	47780359	47780459	E081	-39513
chr2	47784729	47784856	E081	-35116
chr2	47785333	47785484	E081	-34488
chr2	47785583	47786154	E081	-33818
chr2	47786278	47786437	E081	-33535
chr2	47786544	47786655	E081	-33317
chr2	47793690	47793861	E081	-26111
chr2	47795437	47795914	E081	-24058
chr2	47795437	47795914	E082	-24058

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	47796885	47797111	E067	-22861
chr2	47797121	47797374	E067	-22598
chr2	47797872	47798990	E067	-20982
chr2	47796885	47797111	E068	-22861
chr2	47797121	47797374	E068	-22598
chr2	47797872	47798990	E068	-20982
chr2	47796885	47797111	E069	-22861
chr2	47797121	47797374	E069	-22598
chr2	47797872	47798990	E069	-20982
chr2	47797121	47797374	E071	-22598
chr2	47797872	47798990	E071	-20982
chr2	47797121	47797374	E072	-22598
chr2	47797872	47798990	E072	-20982
chr2	47796885	47797111	E073	-22861
chr2	47797121	47797374	E073	-22598
chr2	47797872	47798990	E073	-20982
chr2	47797121	47797374	E074	-22598
chr2	47797872	47798990	E074	-20982
chr2	47796885	47797111	E082	-22861
chr2	47797121	47797374	E082	-22598