rs9996730

Homo sapiens
G>T
CCDC109B : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G==0285 (8528/29870,GnomAD)
G==0267 (7788/29118,TOPMED)
G==0306 (1533/5008,1000G)
G==0347 (1336/3854,ALSPAC)
G==0341 (1265/3708,TWINSUK)
chr4:109648939 (GRCh38.p7) (4q25)
ND
GWASdb2
1   publication(s)
See rs on genome
16 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 4NC_000004.12:g.109648939G>T
GRCh37.p13 chr 4NC_000004.11:g.110570095G>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=0.136T=0.864
1000GenomesAmericanSub694G=0.400T=0.600
1000GenomesEast AsianSub1008G=0.481T=0.519
1000GenomesEuropeSub1006G=0.345T=0.655
1000GenomesGlobalStudy-wide5008G=0.306T=0.694
1000GenomesSouth AsianSub978G=0.250T=0.750
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.347T=0.653
The Genome Aggregation DatabaseAfricanSub8700G=0.163T=0.837
The Genome Aggregation DatabaseAmericanSub836G=0.420T=0.580
The Genome Aggregation DatabaseEast AsianSub1610G=0.462T=0.538
The Genome Aggregation DatabaseEuropeSub18422G=0.319T=0.680
The Genome Aggregation DatabaseGlobalStudy-wide29870G=0.285T=0.714
The Genome Aggregation DatabaseOtherSub302G=0.430T=0.570
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.267T=0.732
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.341T=0.659
PMID Title Author Journal
20158304A genomewide association study of nicotine and alcohol dependence in Australian and Dutch populations.Lind PATwin Res Hum Genet

P-Value

SNP ID p-value Traits Study
rs99967308.82E-05alcohol and nictotine co-dependence20158304

eQTL of rs9996730 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr4:110570095CASP6ENSG00000138794.5G>T6.8229e-8-54644Cerebellum
Chr4:110570095CASP6ENSG00000138794.5G>T5.0521e-7-54644Cerebellar_Hemisphere
Chr4:110570095PLA2G12AENSG00000123739.6G>T4.8449e-6-81138Brain_Spinal_cord_cervical
Chr4:110570095PLA2G12AENSG00000123739.6G>T1.3741e-4-81138Anterior_cingulate_cortex

meQTL of rs9996730 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 )
chr4110583927110584261E06813832
chr4110584708110584758E06814613
chr4110583927110584261E06913832
chr4110584708110584758E06914613
chr4110583927110584261E07013832
chr4110584708110584758E07014613
chr4110587312110587500E07017217
chr4110584708110584758E07114613
chr4110583927110584261E07213832
chr4110583927110584261E07413832
chr4110589348110589558E07419253
chr4110552765110553219E081-16876
chr4110583927110584261E08113832
chr4110584708110584758E08114613
chr4110587312110587500E08117217
chr4110587312110587500E08217217