rs2306371

Homo sapiens
T>C
MSH3 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0152 (4571/29962,GnomAD)
C=0163 (4750/29118,TOPMED)
C=0176 (881/5008,1000G)
C=0105 (403/3854,ALSPAC)
C=0115 (427/3708,TWINSUK)
chr5:80813439 (GRCh38.p7) (5q14.1)
AD
GWASdb2
1   publication(s)
See rs on genome
5 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.80813439T>C
GRCh37.p13 chr 5NC_000005.9:g.80109258T>C
MSH3 RefSeqGeneNG_016607.1:g.163965T>C

Gene: MSH3, mutS homolog 3(plus strand)

Molecule type Change Amino acid[Codon] SO Term
MSH3 transcriptNM_002439.4:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.767C=0.233
1000GenomesAmericanSub694T=0.820C=0.180
1000GenomesEast AsianSub1008T=0.758C=0.242
1000GenomesEuropeSub1006T=0.879C=0.121
1000GenomesGlobalStudy-wide5008T=0.824C=0.176
1000GenomesSouth AsianSub978T=0.910C=0.090
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.895C=0.105
The Genome Aggregation DatabaseAfricanSub8724T=0.788C=0.212
The Genome Aggregation DatabaseAmericanSub838T=0.840C=0.160
The Genome Aggregation DatabaseEast AsianSub1612T=0.742C=0.258
The Genome Aggregation DatabaseEuropeSub18486T=0.884C=0.115
The Genome Aggregation DatabaseGlobalStudy-wide29962T=0.847C=0.152
The Genome Aggregation DatabaseOtherSub302T=0.900C=0.100
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.836C=0.163
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.885C=0.115
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs23063710.00012alcohol dependence(early age of onset)20201924
rs23063710.00059alcohol dependence20201924

eQTL of rs2306371 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr5:80109258MSH3ENSG00000113318.9T>C2.6526e-3158287Cerebellum
Chr5:80109258MSH3ENSG00000113318.9T>C7.1973e-6158287Cerebellar_Hemisphere

meQTL of rs2306371 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 )
chr58012168680121903E06812428
chr58012194980122055E06812691
chr58012168680121903E07112428
chr58012194980122055E07112691
chr58013090980131218E07121651