rs4365239

Homo sapiens
C>T
NOX5 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0117 (3512/29948,GnomAD)
T=0137 (4011/29118,TOPMED)
T=0170 (850/5008,1000G)
T=0061 (237/3854,ALSPAC)
T=0056 (207/3708,TWINSUK)
chr15:68952341 (GRCh38.p7) (15q23)
ND
GWASdb2
1   publication(s)
See rs on genome
4 Enhancers around
6 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 15NC_000015.10:g.68952341C>T
GRCh37.p13 chr 15NC_000015.9:g.69244680C>T
NOX5 RefSeqGeneNG_030464.1:g.26842C>T

Gene: NOX5, NADPH oxidase, EF-hand calcium binding domain 5(plus strand)

Molecule type Change Amino acid[Codon] SO Term
NOX5 transcript variant 3NM_001184780.1:c.N/AIntron Variant
NOX5 transcript variant 2NM_001184779.1:c.N/AGenic Upstream Transcript Variant
NOX5 transcript variant 1NM_024505.3:c.N/AGenic Upstream Transcript Variant
NOX5 transcript variant 4NR_033671.2:n.N/AIntron Variant
NOX5 transcript variant 5NR_033672.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.708T=0.292
1000GenomesAmericanSub694C=0.940T=0.060
1000GenomesEast AsianSub1008C=0.765T=0.235
1000GenomesEuropeSub1006C=0.938T=0.062
1000GenomesGlobalStudy-wide5008C=0.830T=0.170
1000GenomesSouth AsianSub978C=0.870T=0.130
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.939T=0.061
The Genome Aggregation DatabaseAfricanSub8704C=0.779T=0.221
The Genome Aggregation DatabaseAmericanSub838C=0.930T=0.070
The Genome Aggregation DatabaseEast AsianSub1616C=0.785T=0.215
The Genome Aggregation DatabaseEuropeSub18488C=0.937T=0.063
The Genome Aggregation DatabaseGlobalStudy-wide29948C=0.882T=0.117
The Genome Aggregation DatabaseOtherSub302C=0.940T=0.060
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.862T=0.137
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.944T=0.056
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
rs43652393.26E-06alcohol and nictotine co-dependence20158304

eQTL of rs4365239 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 rs4365239 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 )
chr156926483669264935E07020156
chr156926493769265067E07020257
chr156926520569265339E07020525
chr156924367269243749E081-931


Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr156922245869222588E070-22092
chr156922261969223271E070-21409
chr156922261969223271E071-21409
chr156922261969223271E074-21409
chr156922245869222588E082-22092
chr156922261969223271E082-21409