rs6895889

Homo sapiens
G>T
GAPT : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0332 (9953/29934,GnomAD)
T=0344 (10033/29118,TOPMED)
T=0337 (1300/3854,ALSPAC)
T=0320 (1187/3708,TWINSUK)
chr5:58490716 (GRCh38.p7) (5q11.2)
AD
GWASdb2
1   publication(s)
See rs on genome
11 Enhancers around
77 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.58490716G>T
GRCh37.p13 chr 5NC_000005.9:g.57786543G>T

Gene: GAPT, GRB2-binding adaptor protein, transmembrane(plus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
GAPT transcript variant 1NM_001304428.1:c.N/AUpstream Transcript Variant
GAPT transcript variant 2NM_001304429.1:c.N/AUpstream Transcript Variant
GAPT transcript variant 3NM_001304431.1:c.N/AUpstream Transcript Variant
GAPT transcript variant 4NM_152687.3:c.N/AUpstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.663T=0.337
The Genome Aggregation DatabaseAfricanSub8708G=0.642T=0.358
The Genome Aggregation DatabaseAmericanSub836G=0.790T=0.210
The Genome Aggregation DatabaseEast AsianSub1614G=0.818T=0.182
The Genome Aggregation DatabaseEuropeSub18476G=0.661T=0.338
The Genome Aggregation DatabaseGlobalStudy-wide29934G=0.667T=0.332
The Genome Aggregation DatabaseOtherSub300G=0.640T=0.360
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.655T=0.344
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.680T=0.320
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
rs68958890.000597alcohol dependence20201924

eQTL of rs6895889 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 rs6895889 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 )
chr55776280157763073E068-23470
chr55778619557786288E070-255
chr55778636157786567E0700
chr55778667157786734E070128
chr55779936757799498E07012824
chr55779956757799732E07013024
chr55781988957819990E07033346
chr55782051657820697E07033973
chr55775794557758819E071-27724
chr55778636157786567E0740
chr55778667157786734E074128




Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr55775093057751281E067-35262
chr55775136957751454E067-35089
chr55775145757751571E067-34972
chr55775184357752176E067-34367
chr55775225557752535E067-34008
chr55775300857753544E067-32999
chr55775370757753757E067-32786
chr55775396657754024E067-32519
chr55775404257754220E067-32323
chr55775427257754480E067-32063
chr55775448957757094E067-29449
chr55775001757750122E068-36421
chr55775184357752176E068-34367
chr55775225557752535E068-34008
chr55775370757753757E068-32786
chr55775396657754024E068-32519
chr55775404257754220E068-32323
chr55775427257754480E068-32063
chr55775448957757094E068-29449
chr55775093057751281E069-35262
chr55775184357752176E069-34367
chr55775225557752535E069-34008
chr55775300857753544E069-32999
chr55775370757753757E069-32786
chr55775396657754024E069-32519
chr55775404257754220E069-32323
chr55775427257754480E069-32063
chr55775448957757094E069-29449
chr55775300857753544E070-32999
chr55775370757753757E070-32786
chr55775396657754024E070-32519
chr55775404257754220E070-32323
chr55775427257754480E070-32063
chr55775448957757094E070-29449
chr55775136957751454E071-35089
chr55775184357752176E071-34367
chr55775225557752535E071-34008
chr55775300857753544E071-32999
chr55775370757753757E071-32786
chr55775396657754024E071-32519
chr55775404257754220E071-32323
chr55775427257754480E071-32063
chr55775448957757094E071-29449
chr55775001757750122E072-36421
chr55775093057751281E072-35262
chr55775136957751454E072-35089
chr55775145757751571E072-34972
chr55775184357752176E072-34367
chr55775225557752535E072-34008
chr55775300857753544E072-32999
chr55775370757753757E072-32786
chr55775396657754024E072-32519
chr55775404257754220E072-32323
chr55775427257754480E072-32063
chr55775448957757094E072-29449
chr55775001757750122E073-36421
chr55775093057751281E073-35262
chr55775136957751454E073-35089
chr55775145757751571E073-34972
chr55775184357752176E073-34367
chr55775225557752535E073-34008
chr55775370757753757E073-32786
chr55775396657754024E073-32519
chr55775404257754220E073-32323
chr55775427257754480E073-32063
chr55775448957757094E073-29449
chr55775448957757094E074-29449
chr55775093057751281E081-35262
chr55775396657754024E081-32519
chr55775404257754220E081-32323
chr55775427257754480E081-32063
chr55775448957757094E081-29449
chr55775370757753757E082-32786
chr55775396657754024E082-32519
chr55775404257754220E082-32323
chr55775427257754480E082-32063
chr55775448957757094E082-29449