rs2889900

Homo sapiens
C>G
LINC01507 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0303 (9092/29924,GnomAD)
C==0374 (10906/29118,TOPMED)
C==0276 (1381/5008,1000G)
C==0236 (909/3854,ALSPAC)
C==0239 (887/3708,TWINSUK)
chr9:80026158 (GRCh38.p7) (9q21.31)
ND
GWASdb2
1   publication(s)
See rs on genome
14 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 9NC_000009.12:g.80026158C>G
GRCh37.p13 chr 9NC_000009.11:g.82641073C>G

Gene: LINC01507, long intergenic non-protein coding RNA 1507(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LINC01507 transcript variant 1NR_121212.1:n.N/AIntron Variant
LINC01507 transcript variant 2NR_121213.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.557G=0.443
1000GenomesAmericanSub694C=0.170G=0.830
1000GenomesEast AsianSub1008C=0.014G=0.986
1000GenomesEuropeSub1006C=0.238G=0.762
1000GenomesGlobalStudy-wide5008C=0.276G=0.724
1000GenomesSouth AsianSub978C=0.280G=0.720
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.236G=0.764
The Genome Aggregation DatabaseAfricanSub8700C=0.502G=0.498
The Genome Aggregation DatabaseAmericanSub838C=0.140G=0.860
The Genome Aggregation DatabaseEast AsianSub1612C=0.009G=0.991
The Genome Aggregation DatabaseEuropeSub18472C=0.243G=0.756
The Genome Aggregation DatabaseGlobalStudy-wide29924C=0.303G=0.696
The Genome Aggregation DatabaseOtherSub302C=0.280G=0.720
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.374G=0.625
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.239G=0.761
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
rs28899000.000568nicotine dependence17158188

eQTL of rs2889900 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 rs2889900 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 )
chr98259204782592256E068-48817
chr98259232582592510E068-48563
chr98259204782592256E070-48817
chr98259204782592256E071-48817
chr98259232582592510E071-48563
chr98259204782592256E081-48817
chr98259232582592510E081-48563
chr98259942182599661E081-41412
chr98259972282599775E081-41298
chr98259988682600149E081-40924
chr98259204782592256E082-48817
chr98259942182599661E082-41412
chr98259972282599775E082-41298
chr98259988682600149E082-40924