rs13294002

Homo sapiens
T>G
LOC105376136 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0096 (2887/29974,GnomAD)
G=0085 (2474/29118,TOPMED)
G=0048 (241/5008,1000G)
G=0153 (591/3854,ALSPAC)
G=0148 (550/3708,TWINSUK)
chr9:89291224 (GRCh38.p7) (9q22.2)
AD
GWASdb2
1   publication(s)
See rs on genome
54 Enhancers around
34 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 9NC_000009.12:g.89291224T>G
GRCh37.p13 chr 9NC_000009.11:g.91906139T>G

Gene: LOC105376136, uncharacterized LOC105376136(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105376136 transcript variant X1XR_930100.2:n.N/AIntron Variant
LOC105376136 transcript variant X2XR_930101.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.993G=0.007
1000GenomesAmericanSub694T=0.950G=0.050
1000GenomesEast AsianSub1008T=0.994G=0.006
1000GenomesEuropeSub1006T=0.870G=0.130
1000GenomesGlobalStudy-wide5008T=0.952G=0.048
1000GenomesSouth AsianSub978T=0.940G=0.060
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.847G=0.153
The Genome Aggregation DatabaseAfricanSub8726T=0.971G=0.029
The Genome Aggregation DatabaseAmericanSub838T=0.940G=0.060
The Genome Aggregation DatabaseEast AsianSub1622T=0.993G=0.007
The Genome Aggregation DatabaseEuropeSub18488T=0.861G=0.138
The Genome Aggregation DatabaseGlobalStudy-wide29974T=0.903G=0.096
The Genome Aggregation DatabaseOtherSub300T=0.940G=0.060
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.915G=0.085
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.852G=0.148
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
rs132940020.000072alcoholismpha002893
rs132940020.000072alcohol dependence20201924
rs132940020.0002alcohol dependence(early age of onset)20201924

eQTL of rs13294002 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 rs13294002 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 )
chr99193229691932742E06726157
chr99193710191937212E06730962
chr99193725491937305E06731115
chr99193757591937633E06731436
chr99193879991938860E06732660
chr99193914391939183E06733004
chr99193983791939916E06733698
chr99194031191940361E06734172
chr99194037891940466E06734239
chr99194050091940550E06734361
chr99193229691932742E06826157
chr99193534491935417E06829205
chr99193548891935532E06829349
chr99193595891936011E06829819
chr99193612691936186E06829987
chr99193983791939916E06833698
chr99189617891896267E069-9872
chr99193229691932742E06926157
chr99193508691935231E06928947
chr99193534491935417E06929205
chr99193548891935532E06929349
chr99192974691929992E07023607
chr99193229691932742E07026157
chr99193725491937305E07031115
chr99193757591937633E07031436
chr99193765991937699E07031520
chr99193826791938754E07032128
chr99193879991938860E07032660
chr99193983791939916E07033698
chr99193229691932742E07126157
chr99193508691935231E07128947
chr99193826791938754E07132128
chr99193879991938860E07132660
chr99193229691932742E07326157
chr99193508691935231E07328947
chr99189617891896267E074-9872
chr99193229691932742E07426157
chr99186758391868346E081-37793
chr99187134491871398E081-34741
chr99187151591871567E081-34572
chr99193508691935231E08128947
chr99193534491935417E08129205
chr99193595891936011E08129819
chr99193612691936186E08129987
chr99193620391936278E08130064
chr99193658591936629E08130446
chr99193683791936932E08130698
chr99193710191937212E08130962
chr99193725491937305E08131115
chr99193757591937633E08131436
chr99193765991937699E08131520
chr99187151591871567E082-34572
chr99192974691929992E08223607
chr99193004791930215E08223908









Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr99192406291927592E06717923
chr99193277891934974E06726639
chr99192406291927592E06817923
chr99193277891934974E06826639
chr99192406291927592E06917923
chr99193277891934974E06926639
chr99189704091897208E070-8931
chr99189734791897471E070-8668
chr99189774291897785E070-8354
chr99192406291927592E07017923
chr99192762591927801E07021486
chr99192821491928283E07022075
chr99192849091928540E07022351
chr99193277891934974E07026639
chr99192406291927592E07117923
chr99193277891934974E07126639
chr99189734791897471E072-8668
chr99189774291897785E072-8354
chr99192406291927592E07217923
chr99193277891934974E07226639
chr99192406291927592E07317923
chr99193277891934974E07326639
chr99192406291927592E07417923
chr99193277891934974E07426639
chr99192406291927592E08117923
chr99193277891934974E08126639
chr99189704091897208E082-8931
chr99189734791897471E082-8668
chr99189774291897785E082-8354
chr99192406291927592E08217923
chr99192762591927801E08221486
chr99192821491928283E08222075
chr99192849091928540E08222351
chr99193277891934974E08226639