rs2502521

Homo sapiens
T>C
LOC105377858 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0471 (14068/29856,GnomAD)
T==0443 (12908/29118,TOPMED)
C=0453 (2270/5008,1000G)
C=0324 (1250/3854,ALSPAC)
C=0327 (1212/3708,TWINSUK)
chr6:74699718 (GRCh38.p7) (6q13)
ND
GWASdb2
2   publication(s)
See rs on genome
0 Enhancer around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.74699718T>C
GRCh37.p13 chr 6NC_000006.11:g.75409434T>C

Gene: LOC105377858, uncharacterized LOC105377858(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105377858 transcript variant X2XR_001744201.1:n.N/AIntron Variant
LOC105377858 transcript variant X3XR_001744202.1:n.N/AIntron Variant
LOC105377858 transcript variant X1XR_942693.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.126C=0.874
1000GenomesAmericanSub694T=0.660C=0.340
1000GenomesEast AsianSub1008T=0.694C=0.306
1000GenomesEuropeSub1006T=0.652C=0.348
1000GenomesGlobalStudy-wide5008T=0.547C=0.453
1000GenomesSouth AsianSub978T=0.780C=0.220
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.676C=0.324
The Genome Aggregation DatabaseAfricanSub8712T=0.194C=0.806
The Genome Aggregation DatabaseAmericanSub832T=0.630C=0.370
The Genome Aggregation DatabaseEast AsianSub1588T=0.651C=0.349
The Genome Aggregation DatabaseEuropeSub18422T=0.670C=0.329
The Genome Aggregation DatabaseGlobalStudy-wide29856T=0.528C=0.471
The Genome Aggregation DatabaseOtherSub302T=0.630C=0.370
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.443C=0.556
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.673C=0.327
PMID Title Author Journal
17158188Novel genes identified in a high-density genome wide association study for nicotine dependence.Bierut LJHum Mol Genet
14740319Matching strategies for genetic association studies in structured populations.Hinds DAAm J Hum Genet

P-Value

SNP ID p-value Traits Study
rs25025210.000329nicotine dependence17158188

eQTL of rs2502521 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 rs2502521 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.