rs1490504

Homo sapiens
G>A / G>C
LOC105377161 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0113 (3408/29934,GnomAD)
C=0106 (3100/29116,TOPMED)
C=0180 (901/5008,1000G)
chr3:72601204 (GRCh38.p7) (3p13)
ND
GWASdb2
1   publication(s)
See rs on genome
14 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.72601204G>A
GRCh38.p7 chr 3NC_000003.12:g.72601204G>C
GRCh37.p13 chr 3NC_000003.11:g.72650355G>A
GRCh37.p13 chr 3NC_000003.11:g.72650355G>C
GRCh38.p7 chr 3 fix patch HG126_PATCHNW_011332691.1:g.276113G>A
GRCh38.p7 chr 3 fix patch HG126_PATCHNW_011332691.1:g.276113G>C

Gene: LOC105377161, uncharacterized LOC105377161(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105377161 transcriptXR_940962.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.937C=0.063
1000GenomesAmericanSub694G=0.880C=0.120
1000GenomesEast AsianSub1008G=0.657C=0.343
1000GenomesEuropeSub1006G=0.872C=0.128
1000GenomesGlobalStudy-wide5008G=0.820C=0.180
1000GenomesSouth AsianSub978G=0.740C=0.260
The Genome Aggregation DatabaseAfricanSub8718G=0.930C=0.065
The Genome Aggregation DatabaseAmericanSub834G=0.860C=0.14,
The Genome Aggregation DatabaseEast AsianSub1614G=0.634C=0.366
The Genome Aggregation DatabaseEuropeSub18466G=0.888C=0.111
The Genome Aggregation DatabaseGlobalStudy-wide29934G=0.884C=0.113
The Genome Aggregation DatabaseOtherSub302G=0.770C=0.23,
Trans-Omics for Precision MedicineGlobalStudy-wide29116G=0.893C=0.106
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
rs14905040.000599nicotine dependence17158188

eQTL of rs1490504 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 rs1490504 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 )
chr36819080468190860E07023683
chr36819138868192149E07024267
chr36817051768170754E0813396
chr36817143168171481E0814310
chr36818034168180392E08113220
chr36818338568183607E08116264
chr36818364568183813E08116524
chr36818509368185201E08117972
chr36818563668185938E08118515
chr36819080468190860E08123683
chr36819138868192149E08124267
chr36819318168193343E08126060
chr36819771568197857E08130594
chr36818078568180856E08213664