rs638299

Homo sapiens
A>C
LOC105369545 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A==0142 (4265/29968,GnomAD)
A==0171 (4983/29118,TOPMED)
A==0179 (896/5008,1000G)
A==0088 (340/3854,ALSPAC)
A==0092 (342/3708,TWINSUK)
chr11:124085688 (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.124085688A>C
GRCh37.p13 chr 11NC_000011.9:g.123956395A>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
1000GenomesAfricanSub1322A=0.259C=0.741
1000GenomesAmericanSub694A=0.210C=0.790
1000GenomesEast AsianSub1008A=0.210C=0.790
1000GenomesEuropeSub1006A=0.089C=0.911
1000GenomesGlobalStudy-wide5008A=0.179C=0.821
1000GenomesSouth AsianSub978A=0.110C=0.890
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.088C=0.912
The Genome Aggregation DatabaseAfricanSub8714A=0.255C=0.745
The Genome Aggregation DatabaseAmericanSub838A=0.210C=0.790
The Genome Aggregation DatabaseEast AsianSub1618A=0.235C=0.765
The Genome Aggregation DatabaseEuropeSub18498A=0.079C=0.920
The Genome Aggregation DatabaseGlobalStudy-wide29968A=0.142C=0.857
The Genome Aggregation DatabaseOtherSub300A=0.060C=0.940
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.171C=0.828
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=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
rs6382990.000185nicotine dependence17158188

eQTL of rs638299 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 rs638299 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 )
chr11123940864123940941E068-15454
chr11123941055123941139E068-15256
chr11123941292123941369E068-15026
chr11123987705123987764E06831310
chr11123939453123939969E070-16426
chr11123984472123984682E07128077
chr11123984724123984968E07128329
chr11123957837123957981E0721442
chr11123940864123940941E081-15454
chr11123956096123957050E0810
chr11123961697123962118E0815302
chr11123964147123964385E0817752
chr11123964518123964693E0818123
chr11123939453123939969E082-16426
chr11123956096123957050E0820






Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr11123946528123947549E067-8846
chr11123985435123987315E06729040
chr11123946528123947549E068-8846
chr11123985435123987315E06829040
chr11123946528123947549E069-8846
chr11123985435123987315E06929040
chr11123946528123947549E070-8846
chr11123985435123987315E07029040
chr11123946528123947549E071-8846
chr11123985435123987315E07129040
chr11123946528123947549E072-8846
chr11123985435123987315E07229040
chr11123946528123947549E073-8846
chr11123985435123987315E07329040
chr11123946528123947549E074-8846
chr11123985435123987315E07429040
chr11123985435123987315E08129040
chr11123946528123947549E082-8846
chr11123985435123987315E08229040