rs4142654

Homo sapiens
A>G
POU2F3 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0090 (2709/29980,GnomAD)
G=0050 (1472/29118,TOPMED)
G=0210 (1052/5008,1000G)
G=0063 (244/3854,ALSPAC)
G=0071 (264/3708,TWINSUK)
chr11:120296348 (GRCh38.p7) (11q23.3)
AD
GWASdb2
1   publication(s)
See rs on genome
98 Enhancers around
25 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 11NC_000011.10:g.120296348A>G
GRCh37.p13 chr 11NC_000011.9:g.120167057A>G
POU2F3 RefSeqGeneNG_030035.1:g.64709A>G

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

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.992G=0.008
1000GenomesAmericanSub694A=0.930G=0.070
1000GenomesEast AsianSub1008A=0.346G=0.654
1000GenomesEuropeSub1006A=0.921G=0.079
1000GenomesGlobalStudy-wide5008A=0.790G=0.210
1000GenomesSouth AsianSub978A=0.740G=0.260
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.937G=0.063
The Genome Aggregation DatabaseAfricanSub8722A=0.984G=0.016
The Genome Aggregation DatabaseAmericanSub836A=0.960G=0.040
The Genome Aggregation DatabaseEast AsianSub1622A=0.311G=0.689
The Genome Aggregation DatabaseEuropeSub18498A=0.924G=0.075
The Genome Aggregation DatabaseGlobalStudy-wide29980A=0.909G=0.090
The Genome Aggregation DatabaseOtherSub302A=0.940G=0.060
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.949G=0.050
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.929G=0.071
PMID Title Author Journal
21314694Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.Kendler KSAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs41426540.000576alcohol dependence21314694

eQTL of rs4142654 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 rs4142654 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 )
chr11120187477120188459E06720420
chr11120188493120188583E06721436
chr11120198287120198388E06731230
chr11120199638120199813E06732581
chr11120212989120213379E06745932
chr11120214910120215005E06747853
chr11120215015120215718E06747958
chr11120187270120187403E06820213
chr11120187477120188459E06820420
chr11120188493120188583E06821436
chr11120198287120198388E06831230
chr11120199232120199339E06832175
chr11120199378120199502E06832321
chr11120211320120211792E06844263
chr11120212118120212233E06845061
chr11120212287120212333E06845230
chr11120214696120214818E06847639
chr11120214910120215005E06847853
chr11120215015120215718E06847958
chr11120215748120215815E06848691
chr11120187270120187403E06920213
chr11120187477120188459E06920420
chr11120211320120211792E06944263
chr11120215748120215815E06948691
chr11120215868120215950E06948811
chr11120124956120125018E070-42039
chr11120125198120125386E070-41671
chr11120126811120126957E070-40100
chr11120132130120132329E070-34728
chr11120132448120132526E070-34531
chr11120132534120132604E070-34453
chr11120132624120132703E070-34354
chr11120132772120132880E070-34177
chr11120132947120132997E070-34060
chr11120198287120198388E07031230
chr11120187477120188459E07120420
chr11120199232120199339E07132175
chr11120199378120199502E07132321
chr11120199638120199813E07132581
chr11120204595120204807E07137538
chr11120204901120204979E07137844
chr11120205104120205275E07138047
chr11120205279120205370E07138222
chr11120205382120205426E07138325
chr11120213862120213906E07146805
chr11120214252120214542E07147195
chr11120214696120214818E07147639
chr11120214910120215005E07147853
chr11120215015120215718E07147958
chr11120215748120215815E07148691
chr11120215868120215950E07148811
chr11120187060120187223E07220003
chr11120187270120187403E07220213
chr11120187477120188459E07220420
chr11120188493120188583E07221436
chr11120198287120198388E07231230
chr11120199232120199339E07232175
chr11120199378120199502E07232321
chr11120199638120199813E07232581
chr11120211320120211792E07244263
chr11120215748120215815E07248691
chr11120215868120215950E07248811
chr11120187477120188459E07320420
chr11120198287120198388E07331230
chr11120199232120199339E07332175
chr11120199378120199502E07332321
chr11120199638120199813E07332581
chr11120214910120215005E07347853
chr11120215015120215718E07347958
chr11120187477120188459E07420420
chr11120198287120198388E07431230
chr11120198486120198547E07431429
chr11120199232120199339E07432175
chr11120199378120199502E07432321
chr11120205279120205370E07438222
chr11120214910120215005E07447853
chr11120215015120215718E07447958
chr11120215748120215815E07448691
chr11120215868120215950E07448811
chr11120216707120216757E07449650
chr11120120645120120876E081-46181
chr11120120941120121116E081-45941
chr11120121965120122013E081-45044
chr11120122130120122188E081-44869
chr11120122370120122492E081-44565
chr11120123220120123630E081-43427
chr11120123783120123949E081-43108
chr11120125198120125386E081-41671
chr11120126811120126957E081-40100
chr11120126988120127511E081-39546
chr11120198287120198388E08131230
chr11120199232120199339E08132175
chr11120199378120199502E08132321
chr11120199638120199813E08132581
chr11120177010120177088E0829953
chr11120178035120178102E08210978
chr11120187477120188459E08220420
chr11120198287120198388E08231230










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr11120205601120209660E06738544
chr11120209798120209887E06742741
chr11120195442120198223E06828385
chr11120205601120209660E06838544
chr11120209798120209887E06842741
chr11120195442120198223E06928385
chr11120205601120209660E06938544
chr11120209798120209887E06942741
chr11120205601120209660E07038544
chr11120209798120209887E07042741
chr11120195442120198223E07128385
chr11120205601120209660E07138544
chr11120209798120209887E07142741
chr11120195442120198223E07228385
chr11120205601120209660E07238544
chr11120209798120209887E07242741
chr11120195442120198223E07328385
chr11120205601120209660E07338544
chr11120209798120209887E07342741
chr11120195442120198223E07428385
chr11120205601120209660E07438544
chr11120205601120209660E08138544
chr11120195442120198223E08228385
chr11120205601120209660E08238544
chr11120209798120209887E08242741