rs597900

Homo sapiens
C>T
PKNOX2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0122 (3671/29902,GnomAD)
T=0086 (2522/29118,TOPMED)
T=0177 (885/5008,1000G)
T=0132 (507/3854,ALSPAC)
T=0139 (517/3708,TWINSUK)
chr11:125127625 (GRCh38.p7) (11q24.2)
AD
GWASdb2
1   publication(s)
See rs on genome
89 Enhancers around
24 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 11NC_000011.10:g.125127625C>T
GRCh37.p13 chr 11NC_000011.9:g.124997521C>T

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
1000GenomesAfricanSub1322C=0.986T=0.014
1000GenomesAmericanSub694C=0.820T=0.180
1000GenomesEast AsianSub1008C=0.586T=0.414
1000GenomesEuropeSub1006C=0.862T=0.138
1000GenomesGlobalStudy-wide5008C=0.823T=0.177
1000GenomesSouth AsianSub978C=0.810T=0.190
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.868T=0.132
The Genome Aggregation DatabaseAfricanSub8720C=0.966T=0.034
The Genome Aggregation DatabaseAmericanSub838C=0.810T=0.190
The Genome Aggregation DatabaseEast AsianSub1610C=0.629T=0.371
The Genome Aggregation DatabaseEuropeSub18432C=0.859T=0.140
The Genome Aggregation DatabaseGlobalStudy-wide29902C=0.877T=0.122
The Genome Aggregation DatabaseOtherSub302C=0.910T=0.090
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.913T=0.086
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.861T=0.139
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
rs5979000.00028alcohol dependence20201924

eQTL of rs597900 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 rs597900 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 )
chr11124977967124978138E067-19383
chr11124978386124978713E067-18808
chr11124980141124980216E067-17305
chr11124980222124980272E067-17249
chr11125045397125045483E06747876
chr11125045536125045668E06748015
chr11125045893125046149E06748372
chr11125046549125046646E06749028
chr11125046662125046761E06749141
chr11124980222124980272E068-17249
chr11125038615125038676E06841094
chr11125038703125041292E06841182
chr11125041398125041453E06843877
chr11125041565125041615E06844044
chr11125011461125012287E06913940
chr11125038703125041292E06941182
chr11125041398125041453E06943877
chr11125041565125041615E06944044
chr11125041642125041731E06944121
chr11125041855125041917E06944334
chr11125041953125042052E06944432
chr11125045397125045483E06947876
chr11125045536125045668E06948015
chr11125045893125046149E06948372
chr11125046207125046495E06948686
chr11125046549125046646E06949028
chr11124960889124962035E070-35486
chr11124980141124980216E070-17305
chr11124980222124980272E070-17249
chr11124999605124999675E0702084
chr11124999713124999787E0702192
chr11124999835124999964E0702314
chr11125007092125007142E0709571
chr11125007528125007578E07010007
chr11125008307125008490E07010786
chr11125008679125008763E07011158
chr11125009191125009278E07011670
chr11125010999125011129E07013478
chr11125011138125011450E07013617
chr11125011461125012287E07013940
chr11125026042125026102E07028521
chr11125026181125026231E07028660
chr11125026414125026479E07028893
chr11125026641125026714E07029120
chr11125026739125026909E07029218
chr11125026913125027167E07029392
chr11125027278125027541E07029757
chr11125027737125027809E07030216
chr11125027984125028085E07030463
chr11125028163125028245E07030642
chr11125038615125038676E07041094
chr11125038703125041292E07041182
chr11125038703125041292E07141182
chr11125038703125041292E07241182
chr11125045397125045483E07247876
chr11125045536125045668E07248015
chr11124960832124960872E073-36649
chr11124960889124962035E073-35486
chr11125038615125038676E07341094
chr11125038703125041292E07341182
chr11125041398125041453E07343877
chr11125041565125041615E07344044
chr11125041642125041731E07344121
chr11125041855125041917E07344334
chr11125041953125042052E07344432
chr11124950089124950200E074-47321
chr11125011138125011450E07413617
chr11125011461125012287E07413940
chr11125009497125009683E08111976
chr11125009715125010689E08112194
chr11125010701125010761E08113180
chr11125010763125010977E08113242
chr11125010999125011129E08113478
chr11125011138125011450E08113617
chr11125028954125028998E08131433
chr11125029339125029425E08131818
chr11125029434125029484E08131913
chr11125038615125038676E08141094
chr11125038703125041292E08141182
chr11125041398125041453E08143877
chr11125041565125041615E08144044
chr11125041642125041731E08144121
chr11124978386124978713E082-18808
chr11124978800124978874E082-18647
chr11125009497125009683E08211976
chr11125009715125010689E08212194
chr11125010701125010761E08213180
chr11125010763125010977E08213242
chr11125010999125011129E08213478










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr11124980833124982246E067-15275
chr11124994067124994391E067-3130
chr11125033136125038599E06735615
chr11124980833124982246E068-15275
chr11124994067124994391E068-3130
chr11125033136125038599E06835615
chr11124980833124982246E069-15275
chr11125033136125038599E06935615
chr11124980833124982246E070-15275
chr11125033136125038599E07035615
chr11124980833124982246E071-15275
chr11124994067124994391E071-3130
chr11125033136125038599E07135615
chr11124980833124982246E072-15275
chr11125033136125038599E07235615
chr11124980833124982246E073-15275
chr11125033136125038599E07335615
chr11124980833124982246E074-15275
chr11124994067124994391E074-3130
chr11125033136125038599E07435615
chr11124980833124982246E081-15275
chr11125033136125038599E08135615
chr11124980833124982246E082-15275
chr11125033136125038599E08235615