rs6838639

Homo sapiens
G>A
LOC102724158 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0239 (7180/29934,GnomAD)
A=0240 (7003/29118,TOPMED)
A=0287 (1437/5008,1000G)
A=0242 (932/3854,ALSPAC)
A=0240 (889/3708,TWINSUK)
chr4:121978010 (GRCh38.p7) (4q27)
AD
GWASdb2
2   publication(s)
See rs on genome
2 Enhancers around
18 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 4NC_000004.12:g.121978010G>A
GRCh37.p13 chr 4NC_000004.11:g.122899165G>A

Gene: LOC102724158, uncharacterized LOC102724158(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC102724158 transcript variant X2XR_001741809.1:n.N/AIntron Variant
LOC102724158 transcript variant X1XR_427598.3:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.832A=0.168
1000GenomesAmericanSub694G=0.570A=0.430
1000GenomesEast AsianSub1008G=0.658A=0.342
1000GenomesEuropeSub1006G=0.764A=0.236
1000GenomesGlobalStudy-wide5008G=0.713A=0.287
1000GenomesSouth AsianSub978G=0.660A=0.340
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.758A=0.242
The Genome Aggregation DatabaseAfricanSub8708G=0.808A=0.192
The Genome Aggregation DatabaseAmericanSub838G=0.560A=0.440
The Genome Aggregation DatabaseEast AsianSub1620G=0.694A=0.306
The Genome Aggregation DatabaseEuropeSub18466G=0.752A=0.247
The Genome Aggregation DatabaseGlobalStudy-wide29934G=0.760A=0.239
The Genome Aggregation DatabaseOtherSub302G=0.760A=0.240
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.759A=0.240
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.760A=0.240
PMID Title Author Journal
21314694Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.Kendler KSAlcohol Clin Exp Res
19458352Primary biliary cirrhosis associated with HLA, IL12A, and IL12RB2 variants.Hirschfield GMN Engl J Med

P-Value

SNP ID p-value Traits Study
rs68386390.000938alcohol dependence21314694

eQTL of rs6838639 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 rs6838639 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 )
chr4122901834122902128E0712669
chr4122901834122902128E0742669


Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr4122871215122872529E067-26636
chr4122872537122873589E067-25576
chr4122871215122872529E068-26636
chr4122872537122873589E068-25576
chr4122871215122872529E069-26636
chr4122872537122873589E069-25576
chr4122872537122873589E070-25576
chr4122871215122872529E071-26636
chr4122872537122873589E071-25576
chr4122871215122872529E072-26636
chr4122872537122873589E072-25576
chr4122871215122872529E073-26636
chr4122872537122873589E073-25576
chr4122871215122872529E074-26636
chr4122872537122873589E074-25576
chr4122872537122873589E081-25576
chr4122871215122872529E082-26636
chr4122872537122873589E082-25576