rs2406485

Homo sapiens
T>C
LOC105377441 : Intron Variant
LOC729307 : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0271 (8108/29846,GnomAD)
T==0253 (7376/29118,TOPMED)
T==0253 (1268/5008,1000G)
T==0312 (1203/3854,ALSPAC)
T==0310 (1149/3708,TWINSUK)
chr4:137191836 (GRCh38.p7) (4q28.3)
AD
GWASdb2
1   publication(s)
See rs on genome
6 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 4NC_000004.12:g.137191836T>C
GRCh37.p13 chr 4NC_000004.11:g.138112990T>C

Gene: LOC729307, uncharacterized LOC729307(plus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
LINC02510 transcriptNR_134640.1:n.N/AUpstream Transcript Variant

Gene: LOC105377441, uncharacterized LOC105377441(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105377441 transcript variant X1XR_001741835.1:n.N/AIntron Variant
LOC105377441 transcript variant X2XR_001741836.1:n.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.157C=0.843
1000GenomesAmericanSub694T=0.390C=0.610
1000GenomesEast AsianSub1008T=0.124C=0.876
1000GenomesEuropeSub1006T=0.311C=0.689
1000GenomesGlobalStudy-wide5008T=0.253C=0.747
1000GenomesSouth AsianSub978T=0.360C=0.640
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.312C=0.688
The Genome Aggregation DatabaseAfricanSub8712T=0.192C=0.808
The Genome Aggregation DatabaseAmericanSub834T=0.380C=0.620
The Genome Aggregation DatabaseEast AsianSub1592T=0.116C=0.884
The Genome Aggregation DatabaseEuropeSub18406T=0.316C=0.683
The Genome Aggregation DatabaseGlobalStudy-wide29846T=0.271C=0.728
The Genome Aggregation DatabaseOtherSub302T=0.360C=0.640
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.253C=0.746
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.310C=0.690
PMID Title Author Journal
23743675A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.Kapoor MHum Genet

P-Value

SNP ID p-value Traits Study
rs24064855.21E-05alcohol consumption23743675

eQTL of rs2406485 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 rs2406485 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 )
chr4138127852138128346E07014862
chr4138127852138128346E07414862
chr4138134603138134662E07421613
chr4138134825138135023E07421835
chr4138127852138128346E08114862
chr4138127852138128346E08214862