rs6439361

Homo sapiens
G>A
EPHA6 : Non Coding Transcript Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0279 (8351/29908,GnomAD)
A=0286 (8329/29118,TOPMED)
A=0305 (1528/5008,1000G)
A=0284 (1093/3854,ALSPAC)
A=0276 (1024/3708,TWINSUK)
chr3:97753712 (GRCh38.p7) (3q11.2)
AD
GWASdb2
1   publication(s)
See rs on genome
5 Enhancers around
10 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.97753712G>A
GRCh37.p13 chr 3NC_000003.11:g.97472556G>A

Gene: EPHA6, EPH receptor A6(plus strand)

Molecule type Change Amino acid[Codon] SO Term
EPHA6 transcript variant 1NM_001080448.2:c.N/AGenic Downstream Transcript Variant
EPHA6 transcript variant 3NM_001278300.1:c.N/AGenic Downstream Transcript Variant
EPHA6 transcript variant 4NM_001278301.1:c.N/AGenic Downstream Transcript Variant
EPHA6 transcript variant 2NM_173655.3:c.N/AGenic Downstream Transcript Variant
EPHA6 transcript variant X1XM_006713592.3:c.N/A3 Prime UTR Variant
EPHA6 transcript variant X3XM_017006210.1:c.N/A3 Prime UTR Variant
EPHA6 transcript variant X4XM_017006211.1:c.N/A3 Prime UTR Variant
EPHA6 transcript variant X5XM_017006212.1:c.N/A3 Prime UTR Variant
EPHA6 transcript variant X6XM_017006213.1:c.N/A3 Prime UTR Variant
EPHA6 transcript variant X7XM_017006214.1:c.N/A3 Prime UTR Variant
EPHA6 transcript variant X8XM_017006215.1:c.N/A3 Prime UTR Variant
EPHA6 transcript variant X9XM_017006216.1:c.N/A3 Prime UTR Variant
EPHA6 transcript variant X10XM_017006217.1:c.N/A3 Prime UTR Variant
EPHA6 transcript variant X11XM_017006218.1:c.N/A3 Prime UTR Variant
EPHA6 transcript variant X14XM_017006220.1:c.N/A3 Prime UTR Variant
EPHA6 transcript variant X15XM_017006221.1:c.N/A3 Prime UTR Variant
EPHA6 transcript variant X16XM_017006222.1:c.N/A3 Prime UTR Variant
EPHA6 transcript variant X15XM_011512705.2:c.N/AGenic Downstream Transcript Variant
EPHA6 transcript variant X16XM_011512706.2:c.N/AGenic Downstream Transcript Variant
EPHA6 transcript variant X17XM_011512707.2:c.N/AGenic Downstream Transcript Variant
EPHA6 transcript variant X13XM_017006219.1:c.N/AGenic Downstream Transcript Variant
EPHA6 transcript variant X18XM_017006223.1:c.N/AGenic Downstream Transcript Variant
EPHA6 transcript variant X2XR_001740110.1:n....XR_001740110.1:n.5249G>AG>ANon Coding Transcript Variant
EPHA6 transcript variant X12XR_924126.2:n.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.709A=0.291
1000GenomesAmericanSub694G=0.700A=0.300
1000GenomesEast AsianSub1008G=0.659A=0.341
1000GenomesEuropeSub1006G=0.717A=0.283
1000GenomesGlobalStudy-wide5008G=0.695A=0.305
1000GenomesSouth AsianSub978G=0.690A=0.310
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.716A=0.284
The Genome Aggregation DatabaseAfricanSub8704G=0.714A=0.286
The Genome Aggregation DatabaseAmericanSub836G=0.690A=0.310
The Genome Aggregation DatabaseEast AsianSub1622G=0.675A=0.325
The Genome Aggregation DatabaseEuropeSub18444G=0.728A=0.272
The Genome Aggregation DatabaseGlobalStudy-wide29908G=0.720A=0.279
The Genome Aggregation DatabaseOtherSub302G=0.800A=0.200
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.714A=0.286
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.724A=0.276
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
rs64393610.000437alcohol dependence20201924

eQTL of rs6439361 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 rs6439361 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 )
chr39743190697432039E070-40517
chr39748202597482073E0709469
chr39748202597482073E0729469
chr39742419797424494E081-48062
chr39748202597482073E0819469



Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr39748265897484606E06710102
chr39748265897484606E06810102
chr39748265897484606E06910102
chr39748265897484606E07010102
chr39748265897484606E07110102
chr39748265897484606E07210102
chr39748265897484606E07310102
chr39748265897484606E07410102
chr39748265897484606E08110102
chr39748265897484606E08210102