rs10869910

Homo sapiens
C>T
VPS13A : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0188 (5640/29958,GnomAD)
T=0181 (5280/29118,TOPMED)
T=0247 (1238/5008,1000G)
T=0207 (799/3854,ALSPAC)
T=0204 (758/3708,TWINSUK)
chr9:77209086 (GRCh38.p7) (9q21.2)
ND
GWASdb2
1   publication(s)
See rs on genome
1 Enhancer around
11 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 9NC_000009.12:g.77209086C>T
GRCh37.p13 chr 9NC_000009.11:g.79824002C>T
VPS13A RefSeqGeneNG_008931.1:g.36642C>T

Gene: VPS13A, vacuolar protein sorting 13 homolog A(plus strand)

Molecule type Change Amino acid[Codon] SO Term
VPS13A transcript variant CNM_001018037.1:c.N/AIntron Variant
VPS13A transcript variant DNM_001018038.2:c.N/AIntron Variant
VPS13A transcript variant BNM_015186.3:c.N/AIntron Variant
VPS13A transcript variant ANM_033305.2:c.N/AIntron Variant
VPS13A transcript variant X1XR_001746259.1:n.N/AIntron Variant
VPS13A transcript variant X2XR_001746260.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.925T=0.075
1000GenomesAmericanSub694C=0.700T=0.300
1000GenomesEast AsianSub1008C=0.592T=0.408
1000GenomesEuropeSub1006C=0.796T=0.204
1000GenomesGlobalStudy-wide5008C=0.753T=0.247
1000GenomesSouth AsianSub978C=0.680T=0.320
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.793T=0.207
The Genome Aggregation DatabaseAfricanSub8728C=0.899T=0.101
The Genome Aggregation DatabaseAmericanSub836C=0.670T=0.330
The Genome Aggregation DatabaseEast AsianSub1614C=0.602T=0.398
The Genome Aggregation DatabaseEuropeSub18478C=0.795T=0.204
The Genome Aggregation DatabaseGlobalStudy-wide29958C=0.811T=0.188
The Genome Aggregation DatabaseOtherSub302C=0.790T=0.210
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.818T=0.181
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.796T=0.204
PMID Title Author Journal
17158188Novel genes identified in a high-density genome wide association study for nicotine dependence.Bierut LJHum Mol Genet

P-Value

SNP ID p-value Traits Study
rs108699100.000491nicotine dependence17158188

eQTL of rs10869910 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 rs10869910 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 )
chr97979091279791398E082-32604

Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr97979142879794327E067-29675
chr97978299579783133E068-40869
chr97979142879794327E068-29675
chr97979142879794327E069-29675
chr97979142879794327E070-29675
chr97979142879794327E071-29675
chr97979142879794327E072-29675
chr97979142879794327E073-29675
chr97979142879794327E074-29675
chr97979142879794327E081-29675
chr97979142879794327E082-29675