rs3797898

Homo sapiens
C>T
MSH3 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0161 (4838/29950,GnomAD)
T=0170 (4960/29118,TOPMED)
T=0178 (891/5008,1000G)
T=0117 (452/3854,ALSPAC)
T=0127 (472/3708,TWINSUK)
chr5:80827492 (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.80827492C>T
GRCh37.p13 chr 5NC_000005.9:g.80123311C>T
MSH3 RefSeqGeneNG_016607.1:g.178018C>T

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
1000GenomesAfricanSub1322C=0.766T=0.234
1000GenomesAmericanSub694C=0.820T=0.180
1000GenomesEast AsianSub1008C=0.763T=0.237
1000GenomesEuropeSub1006C=0.865T=0.135
1000GenomesGlobalStudy-wide5008C=0.822T=0.178
1000GenomesSouth AsianSub978C=0.920T=0.080
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.883T=0.117
The Genome Aggregation DatabaseAfricanSub8726C=0.786T=0.214
The Genome Aggregation DatabaseAmericanSub838C=0.830T=0.170
The Genome Aggregation DatabaseEast AsianSub1614C=0.740T=0.260
The Genome Aggregation DatabaseEuropeSub18470C=0.871T=0.128
The Genome Aggregation DatabaseGlobalStudy-wide29950C=0.838T=0.161
The Genome Aggregation DatabaseOtherSub302C=0.890T=0.110
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.829T=0.170
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.873T=0.127
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
rs37978980.00018alcohol dependence(Early Onset)20201924
rs37978980.00066alcohol dependence20201924

eQTL of rs3797898 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr5:80123311MSH3ENSG00000113318.9C>T2.6526e-3172340Cerebellum
Chr5:80123311MSH3ENSG00000113318.9C>T7.1973e-6172340Cerebellar_Hemisphere

meQTL of rs3797898 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 )
chr58012168680121903E068-1408
chr58012194980122055E068-1256
chr58012168680121903E071-1408
chr58012194980122055E071-1256
chr58013090980131218E0717598