rs3806373

Homo sapiens
T>C
VTCN1 : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0222 (6637/29894,GnomAD)
C=0278 (8122/29118,TOPMED)
C=0254 (1272/5008,1000G)
C=0135 (521/3854,ALSPAC)
C=0153 (566/3708,TWINSUK)
chr1:117211437 (GRCh38.p7) (1p12)
AD
GWASdb2
1   publication(s)
See rs on genome
22 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.117211437T>C
GRCh37.p13 chr 1NC_000001.10:g.117754059T>C

Gene: VTCN1, V-set domain containing T cell activation inhibitor 1(minus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
VTCN1 transcript variant 3NM_001253850.1:c.N/AUpstream Transcript Variant
VTCN1 transcript variant 1NM_024626.3:c.N/AUpstream Transcript Variant
VTCN1 transcript variant 2NM_001253849.1:c.N/AN/A
VTCN1 transcript variant 4NR_045603.1:n.N/AUpstream Transcript Variant
VTCN1 transcript variant 5NR_045604.1:n.N/AUpstream Transcript Variant
VTCN1 transcript variant X2XM_017002335.1:c.N/AUpstream Transcript Variant
VTCN1 transcript variant X1XM_011542143.2:c.N/AN/A

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.504C=0.496
1000GenomesAmericanSub694T=0.770C=0.230
1000GenomesEast AsianSub1008T=0.862C=0.138
1000GenomesEuropeSub1006T=0.842C=0.158
1000GenomesGlobalStudy-wide5008T=0.746C=0.254
1000GenomesSouth AsianSub978T=0.840C=0.160
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.865C=0.135
The Genome Aggregation DatabaseAfricanSub8686T=0.556C=0.444
The Genome Aggregation DatabaseAmericanSub836T=0.770C=0.230
The Genome Aggregation DatabaseEast AsianSub1608T=0.875C=0.125
The Genome Aggregation DatabaseEuropeSub18462T=0.873C=0.127
The Genome Aggregation DatabaseGlobalStudy-wide29894T=0.778C=0.222
The Genome Aggregation DatabaseOtherSub302T=0.880C=0.120
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.721C=0.278
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.847C=0.153
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
rs38063730.000438alcohol dependence20201924

eQTL of rs3806373 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 rs3806373 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 )
chr1117714306117715174E068-38885
chr1117774413117774453E06820354
chr1117774568117774950E06820509
chr1117714306117715174E069-38885
chr1117719132117719313E069-34746
chr1117719356117719460E069-34599
chr1117714306117715174E070-38885
chr1117714306117715174E071-38885
chr1117774413117774453E07120354
chr1117774568117774950E07120509
chr1117780443117780603E07126384
chr1117780771117780883E07126712
chr1117714306117715174E072-38885
chr1117722923117723005E074-31054
chr1117723124117723376E074-30683
chr1117714306117715174E081-38885
chr1117724975117725335E081-28724
chr1117704597117704930E082-49129
chr1117714306117715174E082-38885
chr1117722923117723005E082-31054
chr1117723124117723376E082-30683
chr1117724116117724645E082-29414