rs2829729

Homo sapiens
T>C
LINC00158 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0070 (2109/29972,GnomAD)
C=0041 (1207/29118,TOPMED)
C=0122 (613/5008,1000G)
C=0079 (303/3854,ALSPAC)
C=0079 (293/3708,TWINSUK)
chr21:25397616 (GRCh38.p7) (21q21.2)
ND
GWASdb2
1   publication(s)
See rs on genome
0 Enhancer around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 21NC_000021.9:g.25397616T>C
GRCh37.p13 chr 21NC_000021.8:g.26769928T>C

Gene: LINC00158, long intergenic non-protein coding RNA 158(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LINC00158 transcriptNR_024027.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.995C=0.005
1000GenomesAmericanSub694T=0.980C=0.020
1000GenomesEast AsianSub1008T=0.661C=0.339
1000GenomesEuropeSub1006T=0.917C=0.083
1000GenomesGlobalStudy-wide5008T=0.878C=0.122
1000GenomesSouth AsianSub978T=0.830C=0.170
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.921C=0.079
The Genome Aggregation DatabaseAfricanSub8722T=0.983C=0.017
The Genome Aggregation DatabaseAmericanSub838T=0.960C=0.040
The Genome Aggregation DatabaseEast AsianSub1616T=0.666C=0.334
The Genome Aggregation DatabaseEuropeSub18494T=0.925C=0.074
The Genome Aggregation DatabaseGlobalStudy-wide29972T=0.929C=0.070
The Genome Aggregation DatabaseOtherSub302T=0.990C=0.010
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.958C=0.041
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.921C=0.079
PMID Title Author Journal
22377092ANAPC1 and SLCO3A1 are associated with nicotine dependence: meta-analysis of genome-wide association studies.Wang KSDrug Alcohol Depend

P-Value

SNP ID p-value Traits Study
rs28297293.41E-05nicotine dependence (smoking)22377092

eQTL of rs2829729 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 rs2829729 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.