rs488582

Homo sapiens
T>C
LOC105369545 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0142 (4254/29904,GnomAD)
T==0171 (5006/29118,TOPMED)
T==0180 (899/5008,1000G)
T==0088 (340/3854,ALSPAC)
T==0092 (341/3708,TWINSUK)
chr11:124084918 (GRCh38.p7) (11q24.2)
ND
GWASdb2
1   publication(s)
See rs on genome
15 Enhancers around
19 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 11NC_000011.10:g.124084918T>C
GRCh37.p13 chr 11NC_000011.9:g.123955625T>C

Gene: LOC105369545, uncharacterized LOC105369545(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105369545 transcriptXR_948127.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.260C=0.740
1000GenomesAmericanSub694T=0.220C=0.780
1000GenomesEast AsianSub1008T=0.210C=0.790
1000GenomesEuropeSub1006T=0.089C=0.911
1000GenomesGlobalStudy-wide5008T=0.180C=0.820
1000GenomesSouth AsianSub978T=0.110C=0.890
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.088C=0.912
The Genome Aggregation DatabaseAfricanSub8690T=0.255C=0.745
The Genome Aggregation DatabaseAmericanSub838T=0.210C=0.790
The Genome Aggregation DatabaseEast AsianSub1612T=0.235C=0.765
The Genome Aggregation DatabaseEuropeSub18462T=0.079C=0.920
The Genome Aggregation DatabaseGlobalStudy-wide29904T=0.142C=0.857
The Genome Aggregation DatabaseOtherSub302T=0.060C=0.940
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.171C=0.828
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.092C=0.908
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
rs4885820.000569nicotine dependence17158188

eQTL of rs488582 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 rs488582 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 )
chr11123940864123940941E068-14684
chr11123941055123941139E068-14486
chr11123941292123941369E068-14256
chr11123987705123987764E06832080
chr11123939453123939969E070-15656
chr11123984472123984682E07128847
chr11123984724123984968E07129099
chr11123957837123957981E0722212
chr11123940864123940941E081-14684
chr11123956096123957050E081471
chr11123961697123962118E0816072
chr11123964147123964385E0818522
chr11123964518123964693E0818893
chr11123939453123939969E082-15656
chr11123956096123957050E082471






Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr11123946528123947549E067-8076
chr11123985435123987315E06729810
chr11123946528123947549E068-8076
chr11123985435123987315E06829810
chr11123946528123947549E069-8076
chr11123985435123987315E06929810
chr11123946528123947549E070-8076
chr11123985435123987315E07029810
chr11123946528123947549E071-8076
chr11123985435123987315E07129810
chr11123946528123947549E072-8076
chr11123985435123987315E07229810
chr11123946528123947549E073-8076
chr11123985435123987315E07329810
chr11123946528123947549E074-8076
chr11123985435123987315E07429810
chr11123985435123987315E08129810
chr11123946528123947549E082-8076
chr11123985435123987315E08229810