rs12640500

Homo sapiens
G>T
CCDC109B : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0199 (5974/29960,GnomAD)
T=0231 (6737/29118,TOPMED)
T=0171 (858/5008,1000G)
T=0140 (541/3854,ALSPAC)
T=0144 (535/3708,TWINSUK)
chr4:109588030 (GRCh38.p7) (4q25)
AD
GWASdb2
1   publication(s)
See rs on genome
17 Enhancers around
14 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 4NC_000004.12:g.109588030G>T
GRCh37.p13 chr 4NC_000004.11:g.110509186G>T

Gene: CCDC109B, coiled-coil domain containing 109B(plus strand)

Molecule type Change Amino acid[Codon] SO Term
MCUB transcriptNM_017918.4:c.N/AIntron Variant
MCUB transcript variant X1XM_006714246.3:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.617T=0.383
1000GenomesAmericanSub694G=0.860T=0.140
1000GenomesEast AsianSub1008G=0.909T=0.091
1000GenomesEuropeSub1006G=0.869T=0.131
1000GenomesGlobalStudy-wide5008G=0.829T=0.171
1000GenomesSouth AsianSub978G=0.970T=0.030
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.860T=0.140
The Genome Aggregation DatabaseAfricanSub8712G=0.613T=0.387
The Genome Aggregation DatabaseAmericanSub836G=0.910T=0.090
The Genome Aggregation DatabaseEast AsianSub1618G=0.902T=0.098
The Genome Aggregation DatabaseEuropeSub18494G=0.873T=0.126
The Genome Aggregation DatabaseGlobalStudy-wide29960G=0.800T=0.199
The Genome Aggregation DatabaseOtherSub300G=0.910T=0.090
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.768T=0.231
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.856T=0.144
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

P-Value

SNP ID p-value Traits Study
rs126405000.000307alcohol dependence21314694

eQTL of rs12640500 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 rs12640500 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 )
chr4110484302110484610E070-24576
chr4110495463110495517E070-13669
chr4110495577110495757E070-13429
chr4110495900110495958E070-13228
chr4110496160110496318E070-12868
chr4110496370110496496E070-12690
chr4110496709110496785E070-12401
chr4110483826110483876E081-25310
chr4110483938110484066E081-25120
chr4110495900110495958E081-13228
chr4110510250110510977E0811064
chr4110552765110553219E08143579
chr4110483938110484066E082-25120
chr4110496160110496318E082-12868
chr4110496370110496496E082-12690
chr4110497318110497370E082-11816
chr4110497666110497945E082-11241



Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr4110480758110482697E067-26489
chr4110480758110482697E068-26489
chr4110480669110480751E069-28435
chr4110480758110482697E069-26489
chr4110480669110480751E070-28435
chr4110480758110482697E070-26489
chr4110480758110482697E071-26489
chr4110480758110482697E072-26489
chr4110480669110480751E073-28435
chr4110480758110482697E073-26489
chr4110480758110482697E074-26489
chr4110480758110482697E081-26489
chr4110480669110480751E082-28435
chr4110480758110482697E082-26489