rs1379842

Homo sapiens
C>A / C>T
EPHA6 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0262 (7843/29908,GnomAD)
A=0337 (9822/29118,TOPMED)
A=0298 (1494/5008,1000G)
A=0097 (373/3854,ALSPAC)
A=0100 (372/3708,TWINSUK)
chr3:97482906 (GRCh38.p7) (3q11.2)
AD
GWASdb2
1   publication(s)
See rs on genome
0 Enhancer around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.97482906C>A
GRCh38.p7 chr 3NC_000003.12:g.97482906C>T
GRCh37.p13 chr 3NC_000003.11:g.97201750C>A
GRCh37.p13 chr 3NC_000003.11:g.97201750C>T

Gene: EPHA6, EPH receptor A6(plus strand)

Molecule type Change Amino acid[Codon] SO Term
EPHA6 transcript variant 1NM_001080448.2:c.N/AIntron Variant
EPHA6 transcript variant 3NM_001278300.1:c.N/AIntron Variant
EPHA6 transcript variant 2NM_173655.3:c.N/AIntron Variant
EPHA6 transcript variant 4NM_001278301.1:c.N/AGenic Downstream Transcript Variant
EPHA6 transcript variant X1XM_006713592.3:c.N/AIntron Variant
EPHA6 transcript variant X3XM_017006210.1:c.N/AIntron Variant
EPHA6 transcript variant X4XM_017006211.1:c.N/AIntron Variant
EPHA6 transcript variant X5XM_017006212.1:c.N/AIntron Variant
EPHA6 transcript variant X6XM_017006213.1:c.N/AIntron Variant
EPHA6 transcript variant X7XM_017006214.1:c.N/AIntron Variant
EPHA6 transcript variant X8XM_017006215.1:c.N/AIntron Variant
EPHA6 transcript variant X9XM_017006216.1:c.N/AIntron Variant
EPHA6 transcript variant X10XM_017006217.1:c.N/AIntron Variant
EPHA6 transcript variant X11XM_017006218.1:c.N/AIntron Variant
EPHA6 transcript variant X14XM_017006220.1:c.N/AIntron Variant
EPHA6 transcript variant X15XM_017006221.1:c.N/AIntron Variant
EPHA6 transcript variant X16XM_017006222.1:c.N/AIntron Variant
EPHA6 transcript variant X18XM_017006223.1:c.N/AIntron 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 X2XR_001740110.1:n.N/AIntron Variant
EPHA6 transcript variant X12XR_924126.2:n.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.281A=0.719
1000GenomesAmericanSub694C=0.680A=0.320
1000GenomesEast AsianSub1008C=0.886A=0.114
1000GenomesEuropeSub1006C=0.908A=0.092
1000GenomesGlobalStudy-wide5008C=0.702A=0.298
1000GenomesSouth AsianSub978C=0.880A=0.120
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.903A=0.097
The Genome Aggregation DatabaseAfricanSub8702C=0.373T=0.000
The Genome Aggregation DatabaseAmericanSub834C=0.630T=0.00,
The Genome Aggregation DatabaseEast AsianSub1608C=0.881T=0.000
The Genome Aggregation DatabaseEuropeSub18462C=0.899T=0.000
The Genome Aggregation DatabaseGlobalStudy-wide29908C=0.737T=0.000
The Genome Aggregation DatabaseOtherSub302C=0.920T=0.00,
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.662A=0.337
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.900A=0.100
PMID Title Author Journal
24277619ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.Quillen EEAm J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID p-value Traits Study
rs13798420.000915alcohol consumption (maxi-drinks)24277619

eQTL of rs1379842 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 rs1379842 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.