rs11145410

Homo sapiens
G>A
VPS13A : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0163 (4888/29902,GnomAD)
A=0150 (4376/29118,TOPMED)
A=0207 (1036/5008,1000G)
A=0201 (775/3854,ALSPAC)
A=0199 (737/3708,TWINSUK)
chr9:77397484 (GRCh38.p7) (9q21.2)
ND
GWASdb2
1   publication(s)
See rs on genome
20 Enhancers around
2 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 9NC_000009.12:g.77397484G>A
GRCh37.p13 chr 9NC_000009.11:g.80012400G>A
VPS13A RefSeqGeneNG_008931.1:g.225040G>A

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 ANM_033305.2:c.N/AIntron Variant
VPS13A transcript variant DNM_001018038.2:c.N/AGenic Downstream Transcript Variant
VPS13A transcript variant BNM_015186.3:c.N/AGenic Downstream Transcript 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
1000GenomesAfricanSub1322G=0.977A=0.023
1000GenomesAmericanSub694G=0.710A=0.290
1000GenomesEast AsianSub1008G=0.689A=0.311
1000GenomesEuropeSub1006G=0.804A=0.196
1000GenomesGlobalStudy-wide5008G=0.793A=0.207
1000GenomesSouth AsianSub978G=0.700A=0.300
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.799A=0.201
The Genome Aggregation DatabaseAfricanSub8716G=0.954A=0.046
The Genome Aggregation DatabaseAmericanSub834G=0.670A=0.330
The Genome Aggregation DatabaseEast AsianSub1612G=0.663A=0.337
The Genome Aggregation DatabaseEuropeSub18438G=0.804A=0.195
The Genome Aggregation DatabaseGlobalStudy-wide29902G=0.836A=0.163
The Genome Aggregation DatabaseOtherSub302G=0.790A=0.210
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.849A=0.150
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.801A=0.199
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
rs111454100.000786nicotine dependence17158188

eQTL of rs11145410 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 rs11145410 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 )
chr98005466280055632E06742262
chr98004226180042341E06929861
chr98004234780042567E06929947
chr98004258380042663E06930183
chr98005466280055632E06942262
chr98005032680050456E07037926
chr98005064180050948E07038241
chr98005096380051121E07038563
chr98005133980051389E07038939
chr98005142580051485E07039025
chr98005149580051577E07039095
chr98005446780054540E07142067
chr98005466280055632E07242262
chr98004258380042663E07330183
chr98004277380042823E07330373
chr98004710780047157E07334707
chr98004950980049568E07337109
chr98004974380049839E07337343
chr98004950980049568E08137109
chr98005466280055632E08142262







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr98002292980023011E07410529
chr98002322080023274E07410820