rs4509239

Homo sapiens
C>A / C>T
SLC25A13 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0047 (1431/29962,GnomAD)
T=0034 (1000/29118,TOPMED)
T=0041 (205/5008,1000G)
T=0042 (163/3854,ALSPAC)
T=0049 (182/3708,TWINSUK)
chr7:96264902 (GRCh38.p7) (7q21.3)
ND
GWASdb2
1   publication(s)
See rs on genome
11 Enhancers around
11 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 7NC_000007.14:g.96264902C>A
GRCh38.p7 chr 7NC_000007.14:g.96264902C>T
GRCh37.p13 chr 7NC_000007.13:g.95894214C>A
GRCh37.p13 chr 7NC_000007.13:g.95894214C>T
SLC25A13 RefSeqGeneNG_012247.1:g.62246G>T
SLC25A13 RefSeqGeneNG_012247.1:g.62246G>A

Gene: SLC25A13, solute carrier family 25 member 13(minus strand)

Molecule type Change Amino acid[Codon] SO Term
SLC25A13 transcript variant 1NM_001160210.1:c.N/AIntron Variant
SLC25A13 transcript variant 2NM_014251.2:c.N/AIntron Variant
SLC25A13 transcript variant 3NR_027662.1:n.N/AIntron Variant
SLC25A13 transcript variant X1XM_006715831.3:c.N/AIntron Variant
SLC25A13 transcript variant X3XM_011515727.2:c.N/AIntron Variant
SLC25A13 transcript variant X2XM_017011663.1:c.N/AIntron Variant
SLC25A13 transcript variant X5XM_017011664.1:c.N/AIntron Variant
SLC25A13 transcript variant X6XM_017011665.1:c.N/AIntron Variant
SLC25A13 transcript variant X4XR_001744525.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.991T=0.009
1000GenomesAmericanSub694C=0.880T=0.120
1000GenomesEast AsianSub1008C=0.987T=0.013
1000GenomesEuropeSub1006C=0.965T=0.035
1000GenomesGlobalStudy-wide5008C=0.959T=0.041
1000GenomesSouth AsianSub978C=0.940T=0.060
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.958T=0.042
The Genome Aggregation DatabaseAfricanSub8732C=0.983A=0.000
The Genome Aggregation DatabaseAmericanSub836C=0.870A=0.00,
The Genome Aggregation DatabaseEast AsianSub1618C=0.968A=0.001
The Genome Aggregation DatabaseEuropeSub18474C=0.940A=0.000
The Genome Aggregation DatabaseGlobalStudy-wide29962C=0.952A=0.000
The Genome Aggregation DatabaseOtherSub302C=0.950A=0.00,
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.965T=0.034
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.951T=0.049
PMID Title Author Journal
19268276Genome-wide association study of smoking initiation and current smoking.Vink JMAm J Hum Genet

P-Value

SNP ID p-value Traits Study
rs45092390.000798nicotine smoking19268276

eQTL of rs4509239 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 rs4509239 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 )
chr78797436187974601E06810673
chr78797463587974954E06810947
chr78797495787975033E06811269
chr78797463587974954E06910947
chr78797495787975033E06911269
chr78797680787977200E07013119
chr78797739187977441E07013703
chr78797463587974954E07110947
chr78797495787975033E07111269
chr78797508387975248E07111395
chr78797525587975396E07111567




Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr78793587687936560E067-27128
chr78793570987935833E068-27855
chr78793587687936560E068-27128
chr78793570987935833E070-27855
chr78793587687936560E070-27128
chr78793570987935833E073-27855
chr78793587687936560E073-27128
chr78793570987935833E074-27855
chr78793587687936560E074-27128
chr78793570987935833E082-27855
chr78793587687936560E082-27128