rs12284594

Homo sapiens
A>G / A>T
PKNOX2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
G=0241 (7236/29920,GnomAD)
G=0252 (7358/29118,TOPMED)
G=0305 (1525/5008,1000G)
G=0174 (672/3854,ALSPAC)
G=0180 (667/3708,TWINSUK)
chr11:125309957 (GRCh38.p7) (11q24.2)
AD
GWASdb2
6   publication(s)
See rs on genome
79 Enhancers around
11 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 11NC_000011.10:g.125309957A>G
GRCh38.p7 chr 11NC_000011.10:g.125309957A>T
GRCh37.p13 chr 11NC_000011.9:g.125179853A>G
GRCh37.p13 chr 11NC_000011.9:g.125179853A>T

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

Molecule type Change Amino acid[Codon] SO Term
PKNOX2 transcriptNM_022062.2:c.N/AIntron Variant
PKNOX2 transcript variant X5XM_005271642.2:c.N/AIntron Variant
PKNOX2 transcript variant X12XM_006718894.2:c.N/AIntron Variant
PKNOX2 transcript variant X2XM_011542944.2:c.N/AIntron Variant
PKNOX2 transcript variant X6XM_011542945.2:c.N/AIntron Variant
PKNOX2 transcript variant X11XM_011542946.1:c.N/AIntron Variant
PKNOX2 transcript variant X13XM_011542947.2:c.N/AIntron Variant
PKNOX2 transcript variant X2XM_017018110.1:c.N/AIntron Variant
PKNOX2 transcript variant X14XM_017018111.1:c.N/AIntron Variant
PKNOX2 transcript variant X5XM_005271643.2: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=0.631G=0.369
1000GenomesAmericanSub694A=0.900G=0.100
1000GenomesEast AsianSub1008A=0.482G=0.518
1000GenomesEuropeSub1006A=0.826G=0.174
1000GenomesGlobalStudy-wide5008A=0.695G=0.305
1000GenomesSouth AsianSub978A=0.720G=0.280
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.826G=0.174
The Genome Aggregation DatabaseAfricanSub8706A=0.677G=0.322
The Genome Aggregation DatabaseAmericanSub838A=0.900G=0.10,
The Genome Aggregation DatabaseEast AsianSub1608A=0.484G=0.516
The Genome Aggregation DatabaseEuropeSub18466A=0.811G=0.188
The Genome Aggregation DatabaseGlobalStudy-wide29920A=0.757G=0.241
The Genome Aggregation DatabaseOtherSub302A=0.860G=0.14,
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.747G=0.252
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.820G=0.180
PMID Title Author Journal
26044620Gene network analysis shows immune-signaling and ERK1/2 as novel genetic markers for multiple addiction phenotypes: alcohol, smoking and opioid addiction.Reyes-Gibby CCBMC Syst Biol
21703634A meta-analysis of two genome-wide association studies identifies 3 new loci for alcohol dependence.Wang KSJ Psychiatr Res
21956439Genome-wide association study of alcohol dependence implicates KIAA0040 on chromosome 1q.Zuo LNeuropsychopharmacology
20202923A genome-wide association study of alcohol dependence.Bierut LJProc Natl Acad Sci U S A
21298047The nuclear transcription factor PKNOX2 is a candidate gene for substance dependence in European-origin women.Chen XPLoS One
23691092Associations of prenatal nicotine exposure and the dopamine related genes ANKK1 and DRD2 to verbal language.Eicher JDPLoS One

P-Value

SNP ID p-value Traits Study
rs122845940.00000653alcohol dependence21703634
rs122845940.00000812alcohol dependence20202923
rs122845940.00097alcohol dependence21956439

eQTL of rs12284594 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 rs12284594 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 )
chr111092051110922760E067-35516
chr111096301310963317E0674737
chr111096346410963523E0675188
chr111096356810963669E0675292
chr111099541110995621E06737135
chr111099726310997528E06738987
chr111099768010997868E06739404
chr111092051110922760E068-35516
chr111096301310963317E0684737
chr111096346410963523E0685188
chr111096356810963669E0685292
chr111092028210920484E069-37792
chr111092051110922760E069-35516
chr111095498610955057E069-3219
chr111096301310963317E0694737
chr111096346410963523E0695188
chr111096356810963669E0695292
chr111099541110995621E06937135
chr111099726310997528E06938987
chr111092051110922760E070-35516
chr111095423910954312E070-3964
chr111095438210954451E070-3825
chr111095451810954950E070-3326
chr111095498610955057E070-3219
chr111099343510993485E07035159
chr111099358010993654E07035304
chr111099371010993839E07035434
chr111099399810994048E07035722
chr111099435410994404E07036078
chr111099463710994815E07036361
chr111099496010995340E07036684
chr111099541110995621E07037135
chr111099644210996700E07038166
chr111099670510996792E07038429
chr111099726310997528E07038987
chr111099768010997868E07039404
chr111092051110922760E071-35516
chr111095498610955057E071-3219
chr111096301310963317E0714737
chr111096346410963523E0715188
chr111096356810963669E0715292
chr111099726310997528E07138987
chr111092051110922760E072-35516
chr111096301310963317E0724737
chr111096346410963523E0725188
chr111096356810963669E0725292
chr111099435410994404E07236078
chr111099463710994815E07236361
chr111099496010995340E07236684
chr111099541110995621E07237135
chr111092051110922760E073-35516
chr111099541110995621E07337135
chr111092051110922760E074-35516
chr111096301310963317E0744737
chr111096346410963523E0745188
chr111096356810963669E0745292
chr111092051110922760E081-35516
chr111093512810935275E081-23001
chr111093530310935566E081-22710
chr111094771810947778E081-10498
chr111094794310949540E081-8736
chr111095165410951719E081-6557
chr111095423910954312E081-3964
chr111095438210954451E081-3825
chr111095451810954950E081-3326
chr111095498610955057E081-3219
chr111099670510996792E08138429
chr111094794310949540E082-8736
chr111095423910954312E082-3964
chr111095438210954451E082-3825
chr111095451810954950E082-3326
chr111095498610955057E082-3219
chr111099343510993485E08235159
chr111099358010993654E08235304
chr111099371010993839E08235434
chr111099399810994048E08235722
chr111099435410994404E08236078
chr111099463710994815E08236361
chr111099496010995340E08236684










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr111095185910954165E067-4111
chr111095185910954165E068-4111
chr111095185910954165E069-4111
chr111095185910954165E070-4111
chr111095185910954165E071-4111
chr111095185910954165E072-4111
chr111095508210956456E072-1820
chr111095185910954165E073-4111
chr111095185910954165E074-4111
chr111095185910954165E081-4111
chr111095185910954165E082-4111