rs3961460

Homo sapiens
T>C
LOC105374165 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0242 (7256/29916,GnomAD)
C=0312 (9093/29118,TOPMED)
C=0274 (1372/5008,1000G)
C=0166 (639/3854,ALSPAC)
C=0169 (625/3708,TWINSUK)
chr3:153598435 (GRCh38.p7) (3q25.2)
AD
GWASdb2
1   publication(s)
See rs on genome
12 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.153598435T>C
GRCh37.p13 chr 3NC_000003.11:g.153316224T>C

Gene: LOC105374165, uncharacterized LOC105374165(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105374165 transcript variant X1XR_001740976.1:n.N/AIntron Variant
LOC105374165 transcript variant X2XR_924594.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.501C=0.499
1000GenomesAmericanSub694T=0.690C=0.310
1000GenomesEast AsianSub1008T=0.923C=0.077
1000GenomesEuropeSub1006T=0.822C=0.178
1000GenomesGlobalStudy-wide5008T=0.726C=0.274
1000GenomesSouth AsianSub978T=0.750C=0.250
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.834C=0.166
The Genome Aggregation DatabaseAfricanSub8708T=0.573C=0.427
The Genome Aggregation DatabaseAmericanSub834T=0.710C=0.290
The Genome Aggregation DatabaseEast AsianSub1608T=0.905C=0.095
The Genome Aggregation DatabaseEuropeSub18464T=0.832C=0.167
The Genome Aggregation DatabaseGlobalStudy-wide29916T=0.757C=0.242
The Genome Aggregation DatabaseOtherSub302T=0.830C=0.170
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.687C=0.312
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.831C=0.169
PMID Title Author Journal
21529783A quantitative-trait genome-wide association study of alcoholism risk in the community: findings and implications.Heath ACBiol Psychiatry

P-Value

SNP ID p-value Traits Study
rs39614601.2E-05alcoholism (heaviness of drinking)21529783

eQTL of rs3961460 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 rs3961460 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 )
chr3153323302153323831E0817078
chr3153348504153348654E08132280
chr3153348682153348732E08132458
chr3153348972153349308E08132748
chr3153357917153358143E08141693
chr3153358301153358418E08142077
chr3153348504153348654E08232280
chr3153348682153348732E08232458
chr3153348972153349308E08232748
chr3153357917153358143E08241693
chr3153358301153358418E08242077
chr3153358459153359034E08242235