rs585977

Homo sapiens
G>A
PKNOX2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0221 (6612/29912,GnomAD)
A=0189 (5503/29118,TOPMED)
A=0300 (1500/5008,1000G)
A=0196 (757/3854,ALSPAC)
A=0206 (762/3708,TWINSUK)
chr11:125131947 (GRCh38.p7) (11q24.2)
AD
GWASdb2
1   publication(s)
See rs on genome
125 Enhancers around
24 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 11NC_000011.10:g.125131947G>A
GRCh37.p13 chr 11NC_000011.9:g.125001843G>A

Gene: PKNOX2, PBX/knotted 1 homeobox 2(plus strand)

Molecule type Change Amino acid[Codon] SO Term
PKNOX2 transcriptNM_022062.2:c.N/AGenic Upstream Transcript Variant
PKNOX2 transcript variant X2XM_017018110.1:c.N/AIntron Variant
PKNOX2 transcript variant X5XM_005271642.2:c.N/AGenic Upstream Transcript Variant
PKNOX2 transcript variant X5XM_005271643.2:c.N/AGenic Upstream Transcript Variant
PKNOX2 transcript variant X12XM_006718894.2:c.N/AGenic Upstream Transcript Variant
PKNOX2 transcript variant X2XM_011542944.2:c.N/AGenic Upstream Transcript Variant
PKNOX2 transcript variant X6XM_011542945.2:c.N/AGenic Upstream Transcript Variant
PKNOX2 transcript variant X11XM_011542946.1:c.N/AGenic Upstream Transcript Variant
PKNOX2 transcript variant X13XM_011542947.2:c.N/AGenic Upstream Transcript Variant
PKNOX2 transcript variant X14XM_017018111.1:c.N/AGenic Upstream Transcript Variant
PKNOX2 transcript variant X10XM_017018112.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.836A=0.164
1000GenomesAmericanSub694G=0.790A=0.210
1000GenomesEast AsianSub1008G=0.383A=0.617
1000GenomesEuropeSub1006G=0.789A=0.211
1000GenomesGlobalStudy-wide5008G=0.700A=0.300
1000GenomesSouth AsianSub978G=0.690A=0.310
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.804A=0.196
The Genome Aggregation DatabaseAfricanSub8708G=0.815A=0.185
The Genome Aggregation DatabaseAmericanSub836G=0.770A=0.230
The Genome Aggregation DatabaseEast AsianSub1612G=0.379A=0.621
The Genome Aggregation DatabaseEuropeSub18454G=0.795A=0.204
The Genome Aggregation DatabaseGlobalStudy-wide29912G=0.779A=0.221
The Genome Aggregation DatabaseOtherSub302G=0.880A=0.120
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.811A=0.189
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.794A=0.206
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs5859770.0000615alcoholismpha002892
rs5859770.000062alcohol dependence20201924

eQTL of rs585977 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 rs585977 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 )
chr11124977967124978138E067-23705
chr11124978386124978713E067-23130
chr11124980141124980216E067-21627
chr11124980222124980272E067-21571
chr11125045397125045483E06743554
chr11125045536125045668E06743693
chr11125045893125046149E06744050
chr11125046549125046646E06744706
chr11125046662125046761E06744819
chr11125048735125048803E06746892
chr11125048854125048935E06747011
chr11125048949125049060E06747106
chr11125049329125049384E06747486
chr11124980222124980272E068-21571
chr11125038615125038676E06836772
chr11125038703125041292E06836860
chr11125041398125041453E06839555
chr11125041565125041615E06839722
chr11125048949125049060E06847106
chr11125049329125049384E06847486
chr11125049440125049480E06847597
chr11125049491125049638E06847648
chr11125049740125050748E06847897
chr11125050754125050879E06848911
chr11125011461125012287E0699618
chr11125038703125041292E06936860
chr11125041398125041453E06939555
chr11125041565125041615E06939722
chr11125041642125041731E06939799
chr11125041855125041917E06940012
chr11125041953125042052E06940110
chr11125045397125045483E06943554
chr11125045536125045668E06943693
chr11125045893125046149E06944050
chr11125046207125046495E06944364
chr11125046549125046646E06944706
chr11125049329125049384E06947486
chr11125049440125049480E06947597
chr11125049491125049638E06947648
chr11125049740125050748E06947897
chr11124960889124962035E070-39808
chr11124980141124980216E070-21627
chr11124980222124980272E070-21571
chr11124999605124999675E070-2168
chr11124999713124999787E070-2056
chr11124999835124999964E070-1879
chr11125007092125007142E0705249
chr11125007528125007578E0705685
chr11125008307125008490E0706464
chr11125008679125008763E0706836
chr11125009191125009278E0707348
chr11125010999125011129E0709156
chr11125011138125011450E0709295
chr11125011461125012287E0709618
chr11125026042125026102E07024199
chr11125026181125026231E07024338
chr11125026414125026479E07024571
chr11125026641125026714E07024798
chr11125026739125026909E07024896
chr11125026913125027167E07025070
chr11125027278125027541E07025435
chr11125027737125027809E07025894
chr11125027984125028085E07026141
chr11125028163125028245E07026320
chr11125038615125038676E07036772
chr11125038703125041292E07036860
chr11125038703125041292E07136860
chr11125049329125049384E07147486
chr11125049440125049480E07147597
chr11125049491125049638E07147648
chr11125049740125050748E07147897
chr11125050754125050879E07148911
chr11125050929125050998E07149086
chr11125051029125051134E07149186
chr11125051219125051277E07149376
chr11125051387125051439E07149544
chr11125038703125041292E07236860
chr11125045397125045483E07243554
chr11125045536125045668E07243693
chr11125048735125048803E07246892
chr11125048854125048935E07247011
chr11125048949125049060E07247106
chr11125049329125049384E07247486
chr11125049440125049480E07247597
chr11125049491125049638E07247648
chr11124960832124960872E073-40971
chr11124960889124962035E073-39808
chr11125038615125038676E07336772
chr11125038703125041292E07336860
chr11125041398125041453E07339555
chr11125041565125041615E07339722
chr11125041642125041731E07339799
chr11125041855125041917E07340012
chr11125041953125042052E07340110
chr11125048949125049060E07347106
chr11125049329125049384E07347486
chr11125049440125049480E07347597
chr11125049491125049638E07347648
chr11125050929125050998E07349086
chr11125011138125011450E0749295
chr11125011461125012287E0749618
chr11125049440125049480E07447597
chr11125049491125049638E07447648
chr11125049740125050748E07447897
chr11125009497125009683E0817654
chr11125009715125010689E0817872
chr11125010701125010761E0818858
chr11125010763125010977E0818920
chr11125010999125011129E0819156
chr11125011138125011450E0819295
chr11125028954125028998E08127111
chr11125029339125029425E08127496
chr11125029434125029484E08127591
chr11125038615125038676E08136772
chr11125038703125041292E08136860
chr11125041398125041453E08139555
chr11125041565125041615E08139722
chr11125041642125041731E08139799
chr11124978386124978713E082-23130
chr11124978800124978874E082-22969
chr11125009497125009683E0827654
chr11125009715125010689E0827872
chr11125010701125010761E0828858
chr11125010763125010977E0828920
chr11125010999125011129E0829156










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr11124980833124982246E067-19597
chr11124994067124994391E067-7452
chr11125033136125038599E06731293
chr11124980833124982246E068-19597
chr11124994067124994391E068-7452
chr11125033136125038599E06831293
chr11124980833124982246E069-19597
chr11125033136125038599E06931293
chr11124980833124982246E070-19597
chr11125033136125038599E07031293
chr11124980833124982246E071-19597
chr11124994067124994391E071-7452
chr11125033136125038599E07131293
chr11124980833124982246E072-19597
chr11125033136125038599E07231293
chr11124980833124982246E073-19597
chr11125033136125038599E07331293
chr11124980833124982246E074-19597
chr11124994067124994391E074-7452
chr11125033136125038599E07431293
chr11124980833124982246E081-19597
chr11125033136125038599E08131293
chr11124980833124982246E082-19597
chr11125033136125038599E08231293