rs5745331

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

MSH4 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0219 (6591/29988,GnomAD)
G=0193 (5629/29118,TOPMED)
G=0154 (771/5008,1000G)
G=0297 (1145/3854,ALSPAC)
G=0258 (957/3708,TWINSUK)

Position: chr1:75807628 (GRCh38.p7) (1p31.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 10 Enhancers around

Promoter: 64 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.75807628A>G
GRCh37.p13 chr 1	NC_000001.10:g.76273313A>G
MSH4 RefSeqGene	NG_029861.1:g.15758A>G

Gene: MSH4, mutS homolog 4(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MSH4 transcript	NM_002440.3:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.911	G=0.089
1000Genomes	American	Sub	694	A=0.810	G=0.190
1000Genomes	East Asian	Sub	1008	A=0.977	G=0.023
1000Genomes	Europe	Sub	1006	A=0.694	G=0.306
1000Genomes	Global	Study-wide	5008	A=0.846	G=0.154
1000Genomes	South Asian	Sub	978	A=0.800	G=0.200
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.703	G=0.297
The Genome Aggregation Database	African	Sub	8734	A=0.893	G=0.107
The Genome Aggregation Database	American	Sub	838	A=0.820	G=0.180
The Genome Aggregation Database	East Asian	Sub	1622	A=0.981	G=0.019
The Genome Aggregation Database	Europe	Sub	18492	A=0.711	G=0.288
The Genome Aggregation Database	Global	Study-wide	29988	A=0.780	G=0.219
The Genome Aggregation Database	Other	Sub	302	A=0.540	G=0.460
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.806	G=0.193
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.742	G=0.258

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
rs5745331	0.000347	alcohol dependence	20201924

eQTL of rs5745331 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 rs5745331 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 )
chr1	76255876	76255926	E067	-17387
chr1	76254905	76255305	E069	-18008
chr1	76254905	76255305	E070	-18008
chr1	76254905	76255305	E071	-18008
chr1	76254905	76255305	E072	-18008
chr1	76255876	76255926	E072	-17387
chr1	76256795	76257021	E072	-16292
chr1	76254905	76255305	E073	-18008
chr1	76254905	76255305	E074	-18008
chr1	76254905	76255305	E081	-18008

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	76251277	76252556	E067	-20757
chr1	76252654	76252744	E067	-20569
chr1	76252947	76253029	E067	-20284
chr1	76253138	76253245	E067	-20068
chr1	76253371	76253468	E067	-19845
chr1	76253506	76253604	E067	-19709
chr1	76250968	76251254	E068	-22059
chr1	76251277	76252556	E068	-20757
chr1	76252654	76252744	E068	-20569
chr1	76252947	76253029	E068	-20284
chr1	76253138	76253245	E068	-20068
chr1	76253371	76253468	E068	-19845
chr1	76253506	76253604	E068	-19709
chr1	76251277	76252556	E069	-20757
chr1	76252654	76252744	E069	-20569
chr1	76252947	76253029	E069	-20284
chr1	76253138	76253245	E069	-20068
chr1	76253371	76253468	E069	-19845
chr1	76253506	76253604	E069	-19709
chr1	76251277	76252556	E070	-20757
chr1	76252654	76252744	E070	-20569
chr1	76252947	76253029	E070	-20284
chr1	76253138	76253245	E070	-20068
chr1	76253371	76253468	E070	-19845
chr1	76253506	76253604	E070	-19709
chr1	76250968	76251254	E071	-22059
chr1	76251277	76252556	E071	-20757
chr1	76252654	76252744	E071	-20569
chr1	76252947	76253029	E071	-20284
chr1	76253138	76253245	E071	-20068
chr1	76253371	76253468	E071	-19845
chr1	76253506	76253604	E071	-19709
chr1	76251277	76252556	E072	-20757
chr1	76252654	76252744	E072	-20569
chr1	76252947	76253029	E072	-20284
chr1	76253138	76253245	E072	-20068
chr1	76253371	76253468	E072	-19845
chr1	76253506	76253604	E072	-19709
chr1	76251277	76252556	E073	-20757
chr1	76252654	76252744	E073	-20569
chr1	76252947	76253029	E073	-20284
chr1	76253138	76253245	E073	-20068
chr1	76253371	76253468	E073	-19845
chr1	76253506	76253604	E073	-19709
chr1	76251277	76252556	E074	-20757
chr1	76252654	76252744	E074	-20569
chr1	76252947	76253029	E074	-20284
chr1	76253138	76253245	E074	-20068
chr1	76253371	76253468	E074	-19845
chr1	76253506	76253604	E074	-19709
chr1	76250968	76251254	E081	-22059
chr1	76251277	76252556	E081	-20757
chr1	76252654	76252744	E081	-20569
chr1	76252947	76253029	E081	-20284
chr1	76253138	76253245	E081	-20068
chr1	76253371	76253468	E081	-19845
chr1	76253506	76253604	E081	-19709
chr1	76250968	76251254	E082	-22059
chr1	76251277	76252556	E082	-20757
chr1	76252654	76252744	E082	-20569
chr1	76252947	76253029	E082	-20284
chr1	76253138	76253245	E082	-20068
chr1	76253371	76253468	E082	-19845
chr1	76253506	76253604	E082	-19709