rs29854

Homo sapiens
T>C
CTB-12O2.1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0139 (4182/29980,GnomAD)
C=0131 (3823/29118,TOPMED)
C=0081 (407/5008,1000G)
C=0226 (871/3854,ALSPAC)
C=0220 (814/3708,TWINSUK)
chr5:152087407 (GRCh38.p7) (5q33.1)
ND
GWASdb2
1   publication(s)
See rs on genome
9 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.152087407T>C
GRCh37.p13 chr 5NC_000005.9:g.151466968T>C

Gene: CTB-12O2.1, uncharacterized LOC101927115(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LINC01933 transcriptNR_109876.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.986C=0.014
1000GenomesAmericanSub694T=0.890C=0.110
1000GenomesEast AsianSub1008T=0.998C=0.002
1000GenomesEuropeSub1006T=0.769C=0.231
1000GenomesGlobalStudy-wide5008T=0.919C=0.081
1000GenomesSouth AsianSub978T=0.920C=0.080
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.774C=0.226
The Genome Aggregation DatabaseAfricanSub8734T=0.950C=0.050
The Genome Aggregation DatabaseAmericanSub838T=0.870C=0.130
The Genome Aggregation DatabaseEast AsianSub1622T=0.999C=0.001
The Genome Aggregation DatabaseEuropeSub18484T=0.808C=0.191
The Genome Aggregation DatabaseGlobalStudy-wide29980T=0.860C=0.139
The Genome Aggregation DatabaseOtherSub302T=0.700C=0.300
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.868C=0.131
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.780C=0.220
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
rs298540.000707nicotine dependence17158188

eQTL of rs29854 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 rs29854 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 )
chr5151452261151452316E070-14652
chr5151498108151498245E07031140
chr5151498366151498494E07031398
chr5151498672151499002E07031704
chr5151516558151516610E07149590
chr5151498672151499002E08131704
chr5151451851151451964E082-15004
chr5151452261151452316E082-14652
chr5151498672151499002E08231704