rs601813

Homo sapiens
A>G
PKNOX2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0159 (4772/29980,GnomAD)
G=0147 (4291/29118,TOPMED)
G=0212 (1063/5008,1000G)
G=0129 (498/3854,ALSPAC)
G=0132 (489/3708,TWINSUK)
chr11:125136457 (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.125136457A>G
GRCh37.p13 chr 11NC_000011.9:g.125006353A>G

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
1000GenomesAfricanSub1322A=0.859G=0.141
1000GenomesAmericanSub694A=0.820G=0.180
1000GenomesEast AsianSub1008A=0.565G=0.435
1000GenomesEuropeSub1006A=0.875G=0.125
1000GenomesGlobalStudy-wide5008A=0.788G=0.212
1000GenomesSouth AsianSub978A=0.810G=0.190
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.871G=0.129
The Genome Aggregation DatabaseAfricanSub8726A=0.834G=0.166
The Genome Aggregation DatabaseAmericanSub838A=0.800G=0.200
The Genome Aggregation DatabaseEast AsianSub1614A=0.579G=0.421
The Genome Aggregation DatabaseEuropeSub18500A=0.867G=0.132
The Genome Aggregation DatabaseGlobalStudy-wide29980A=0.840G=0.159
The Genome Aggregation DatabaseOtherSub302A=0.910G=0.090
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.852G=0.147
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.868G=0.132
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
rs6018130.00032alcohol dependence20201924

eQTL of rs601813 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 rs601813 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 )
chr11124977967124978138E067-28215
chr11124978386124978713E067-27640
chr11124980141124980216E067-26137
chr11124980222124980272E067-26081
chr11125045397125045483E06739044
chr11125045536125045668E06739183
chr11125045893125046149E06739540
chr11125046549125046646E06740196
chr11125046662125046761E06740309
chr11125048735125048803E06742382
chr11125048854125048935E06742501
chr11125048949125049060E06742596
chr11125049329125049384E06742976
chr11124980222124980272E068-26081
chr11125038615125038676E06832262
chr11125038703125041292E06832350
chr11125041398125041453E06835045
chr11125041565125041615E06835212
chr11125048949125049060E06842596
chr11125049329125049384E06842976
chr11125049440125049480E06843087
chr11125049491125049638E06843138
chr11125049740125050748E06843387
chr11125050754125050879E06844401
chr11125011461125012287E0695108
chr11125038703125041292E06932350
chr11125041398125041453E06935045
chr11125041565125041615E06935212
chr11125041642125041731E06935289
chr11125041855125041917E06935502
chr11125041953125042052E06935600
chr11125045397125045483E06939044
chr11125045536125045668E06939183
chr11125045893125046149E06939540
chr11125046207125046495E06939854
chr11125046549125046646E06940196
chr11125049329125049384E06942976
chr11125049440125049480E06943087
chr11125049491125049638E06943138
chr11125049740125050748E06943387
chr11124960889124962035E070-44318
chr11124980141124980216E070-26137
chr11124980222124980272E070-26081
chr11124999605124999675E070-6678
chr11124999713124999787E070-6566
chr11124999835124999964E070-6389
chr11125007092125007142E070739
chr11125007528125007578E0701175
chr11125008307125008490E0701954
chr11125008679125008763E0702326
chr11125009191125009278E0702838
chr11125010999125011129E0704646
chr11125011138125011450E0704785
chr11125011461125012287E0705108
chr11125026042125026102E07019689
chr11125026181125026231E07019828
chr11125026414125026479E07020061
chr11125026641125026714E07020288
chr11125026739125026909E07020386
chr11125026913125027167E07020560
chr11125027278125027541E07020925
chr11125027737125027809E07021384
chr11125027984125028085E07021631
chr11125028163125028245E07021810
chr11125038615125038676E07032262
chr11125038703125041292E07032350
chr11125038703125041292E07132350
chr11125049329125049384E07142976
chr11125049440125049480E07143087
chr11125049491125049638E07143138
chr11125049740125050748E07143387
chr11125050754125050879E07144401
chr11125050929125050998E07144576
chr11125051029125051134E07144676
chr11125051219125051277E07144866
chr11125051387125051439E07145034
chr11125038703125041292E07232350
chr11125045397125045483E07239044
chr11125045536125045668E07239183
chr11125048735125048803E07242382
chr11125048854125048935E07242501
chr11125048949125049060E07242596
chr11125049329125049384E07242976
chr11125049440125049480E07243087
chr11125049491125049638E07243138
chr11124960832124960872E073-45481
chr11124960889124962035E073-44318
chr11125038615125038676E07332262
chr11125038703125041292E07332350
chr11125041398125041453E07335045
chr11125041565125041615E07335212
chr11125041642125041731E07335289
chr11125041855125041917E07335502
chr11125041953125042052E07335600
chr11125048949125049060E07342596
chr11125049329125049384E07342976
chr11125049440125049480E07343087
chr11125049491125049638E07343138
chr11125050929125050998E07344576
chr11125011138125011450E0744785
chr11125011461125012287E0745108
chr11125049440125049480E07443087
chr11125049491125049638E07443138
chr11125049740125050748E07443387
chr11125009497125009683E0813144
chr11125009715125010689E0813362
chr11125010701125010761E0814348
chr11125010763125010977E0814410
chr11125010999125011129E0814646
chr11125011138125011450E0814785
chr11125028954125028998E08122601
chr11125029339125029425E08122986
chr11125029434125029484E08123081
chr11125038615125038676E08132262
chr11125038703125041292E08132350
chr11125041398125041453E08135045
chr11125041565125041615E08135212
chr11125041642125041731E08135289
chr11124978386124978713E082-27640
chr11124978800124978874E082-27479
chr11125009497125009683E0823144
chr11125009715125010689E0823362
chr11125010701125010761E0824348
chr11125010763125010977E0824410
chr11125010999125011129E0824646










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr11124980833124982246E067-24107
chr11124994067124994391E067-11962
chr11125033136125038599E06726783
chr11124980833124982246E068-24107
chr11124994067124994391E068-11962
chr11125033136125038599E06826783
chr11124980833124982246E069-24107
chr11125033136125038599E06926783
chr11124980833124982246E070-24107
chr11125033136125038599E07026783
chr11124980833124982246E071-24107
chr11124994067124994391E071-11962
chr11125033136125038599E07126783
chr11124980833124982246E072-24107
chr11125033136125038599E07226783
chr11124980833124982246E073-24107
chr11125033136125038599E07326783
chr11124980833124982246E074-24107
chr11124994067124994391E074-11962
chr11125033136125038599E07426783
chr11124980833124982246E081-24107
chr11125033136125038599E08126783
chr11124980833124982246E082-24107
chr11125033136125038599E08226783