rs6589804

Homo sapiens
G>A
POU2F3 : Intron Variant
LOC105369531 : Non Coding Transcript Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0118 (3560/29968,GnomAD)
A=0145 (4242/29118,TOPMED)
A=0107 (537/5008,1000G)
A=0070 (268/3854,ALSPAC)
A=0080 (295/3708,TWINSUK)
chr11:120290932 (GRCh38.p7) (11q23.3)
ND
GWASdb2
1   publication(s)
See rs on genome
76 Enhancers around
25 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 11NC_000011.10:g.120290932G>A
GRCh37.p13 chr 11NC_000011.9:g.120161641G>A
POU2F3 RefSeqGeneNG_030035.1:g.59293G>A

Gene: POU2F3, POU class 2 homeobox 3(plus strand)

Molecule type Change Amino acid[Codon] SO Term
POU2F3 transcript variant 2NM_001244682.1:c.N/AIntron Variant
POU2F3 transcript variant 1NM_014352.3:c.N/AIntron Variant
POU2F3 transcript variant X1XM_011542739.2:c.N/AIntron Variant
POU2F3 transcript variant X2XM_011542740.2:c.N/AIntron Variant
POU2F3 transcript variant X3XM_011542741.2:c.N/AIntron Variant
POU2F3 transcript variant X4XM_011542742.2:c.N/AIntron Variant
POU2F3 transcript variant X6XM_011542743.2:c.N/AIntron Variant
POU2F3 transcript variant X7XM_017017487.1:c.N/AIntron Variant
POU2F3 transcript variant X6XR_947818.1:n.N/AIntron Variant

Gene: LOC105369531, uncharacterized LOC105369531(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105369531 transcript variant X1XR_001748417.1:n....XR_001748417.1:n.836C>TC>TNon Coding Transcript Variant
LOC105369531 transcript variant X2XR_948102.2:n.836C>TC>TNon Coding Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.720A=0.280
1000GenomesAmericanSub694G=0.900A=0.100
1000GenomesEast AsianSub1008G=0.999A=0.001
1000GenomesEuropeSub1006G=0.913A=0.087
1000GenomesGlobalStudy-wide5008G=0.893A=0.107
1000GenomesSouth AsianSub978G=0.990A=0.010
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.930A=0.070
The Genome Aggregation DatabaseAfricanSub8702G=0.761A=0.239
The Genome Aggregation DatabaseAmericanSub838G=0.950A=0.050
The Genome Aggregation DatabaseEast AsianSub1622G=1.000A=0.000
The Genome Aggregation DatabaseEuropeSub18504G=0.923A=0.076
The Genome Aggregation DatabaseGlobalStudy-wide29968G=0.881A=0.118
The Genome Aggregation DatabaseOtherSub302G=0.930A=0.070
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.854A=0.145
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.920A=0.080
PMID Title Author Journal
19268276Genome-wide association study of smoking initiation and current smoking.Vink JMAm J Hum Genet

P-Value

SNP ID p-value Traits Study
rs65898040.000927nicotine smoking19268276

eQTL of rs6589804 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 rs6589804 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 )
chr11120187477120188459E06725836
chr11120188493120188583E06726852
chr11120198287120198388E06736646
chr11120199638120199813E06737997
chr11120187270120187403E06825629
chr11120187477120188459E06825836
chr11120188493120188583E06826852
chr11120198287120198388E06836646
chr11120199232120199339E06837591
chr11120199378120199502E06837737
chr11120187270120187403E06925629
chr11120187477120188459E06925836
chr11120124956120125018E070-36623
chr11120125198120125386E070-36255
chr11120126811120126957E070-34684
chr11120132130120132329E070-29312
chr11120132448120132526E070-29115
chr11120132534120132604E070-29037
chr11120132624120132703E070-28938
chr11120132772120132880E070-28761
chr11120132947120132997E070-28644
chr11120198287120198388E07036646
chr11120187477120188459E07125836
chr11120199232120199339E07137591
chr11120199378120199502E07137737
chr11120199638120199813E07137997
chr11120204595120204807E07142954
chr11120204901120204979E07143260
chr11120205104120205275E07143463
chr11120205279120205370E07143638
chr11120205382120205426E07143741
chr11120187060120187223E07225419
chr11120187270120187403E07225629
chr11120187477120188459E07225836
chr11120188493120188583E07226852
chr11120198287120198388E07236646
chr11120199232120199339E07237591
chr11120199378120199502E07237737
chr11120199638120199813E07237997
chr11120187477120188459E07325836
chr11120198287120198388E07336646
chr11120199232120199339E07337591
chr11120199378120199502E07337737
chr11120199638120199813E07337997
chr11120187477120188459E07425836
chr11120198287120198388E07436646
chr11120198486120198547E07436845
chr11120199232120199339E07437591
chr11120199378120199502E07437737
chr11120205279120205370E07443638
chr11120111827120111877E081-49764
chr11120111891120111951E081-49690
chr11120111963120112047E081-49594
chr11120112125120112344E081-49297
chr11120116020120116216E081-45425
chr11120116316120116624E081-45017
chr11120116928120117067E081-44574
chr11120120645120120876E081-40765
chr11120120941120121116E081-40525
chr11120121965120122013E081-39628
chr11120122130120122188E081-39453
chr11120122370120122492E081-39149
chr11120123220120123630E081-38011
chr11120123783120123949E081-37692
chr11120125198120125386E081-36255
chr11120126811120126957E081-34684
chr11120126988120127511E081-34130
chr11120198287120198388E08136646
chr11120199232120199339E08137591
chr11120199378120199502E08137737
chr11120199638120199813E08137997
chr11120116928120117067E082-44574
chr11120177010120177088E08215369
chr11120178035120178102E08216394
chr11120187477120188459E08225836
chr11120198287120198388E08236646










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr11120205601120209660E06743960
chr11120209798120209887E06748157
chr11120195442120198223E06833801
chr11120205601120209660E06843960
chr11120209798120209887E06848157
chr11120195442120198223E06933801
chr11120205601120209660E06943960
chr11120209798120209887E06948157
chr11120205601120209660E07043960
chr11120209798120209887E07048157
chr11120195442120198223E07133801
chr11120205601120209660E07143960
chr11120209798120209887E07148157
chr11120195442120198223E07233801
chr11120205601120209660E07243960
chr11120209798120209887E07248157
chr11120195442120198223E07333801
chr11120205601120209660E07343960
chr11120209798120209887E07348157
chr11120195442120198223E07433801
chr11120205601120209660E07443960
chr11120205601120209660E08143960
chr11120195442120198223E08233801
chr11120205601120209660E08243960
chr11120209798120209887E08248157