rs2230681

Homo sapiens
T>C
PSMD9 : Missense Variant
HPD : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0144 (12356/85626,ExAC)
T==0165 (4948/29944,GnomAD)
T==0153 (4478/29118,TOPMED)
C=0140 (1818/12988,GO-ESP)
T==0166 (833/5008,1000G)
T==0120 (463/3854,ALSPAC)
T==0121 (448/3708,TWINSUK)
chr12:121888906 (GRCh38.p7) (12q24.31)
ND
GWASdb2
3   publication(s)
See rs on genome
82 Enhancers around
27 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 12NC_000012.12:g.121888906T>C
GRCh37.p13 chr 12NC_000012.11:g.122326812T>C
HPD RefSeqGeneNG_016461.1:g.4706A>G

Gene: HPD, 4-hydroxyphenylpyruvate dioxygenase(minus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
HPD transcript variant 2NM_001171993.1:c.N/AUpstream Transcript Variant
HPD transcript variant 1NM_002150.2:c.N/AN/A

Gene: PSMD9, proteasome 26S subunit, non-ATPase 9(plus strand)

Molecule type Change Amino acid[Codon] SO Term
PSMD9 transcript variant 1NM_002813.6:c.50T>CV [GTC]> A [GCC]Coding Sequence Variant
26S proteasome non-ATPase regulatory subunit 9 isoform 1NP_002804.2:p.Val...NP_002804.2:p.Val17AlaV [Val]> A [Ala]Missense Variant
PSMD9 transcript variant 2NM_001261400.2:c....NM_001261400.2:c.50T>CV [GTC]> A [GCC]Coding Sequence Variant
26S proteasome non-ATPase regulatory subunit 9 isoform 2NP_001248329.1:p....NP_001248329.1:p.Val17AlaV [Val]> A [Ala]Missense Variant
PSMD9 transcript variant 3NR_048555.2:n.176T>CT>CNon Coding Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.187C=0.813
1000GenomesAmericanSub694T=0.270C=0.730
1000GenomesEast AsianSub1008T=0.125C=0.875
1000GenomesEuropeSub1006T=0.127C=0.873
1000GenomesGlobalStudy-wide5008T=0.166C=0.834
1000GenomesSouth AsianSub978T=0.150C=0.850
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.120C=0.880
The Exome Aggregation ConsortiumAmericanSub14016T=0.198C=0.801
The Exome Aggregation ConsortiumAsianSub19754T=0.148C=0.851
The Exome Aggregation ConsortiumEuropeSub51256T=0.128C=0.872
The Exome Aggregation ConsortiumGlobalStudy-wide85626T=0.144C=0.855
The Exome Aggregation ConsortiumOtherSub600T=0.140C=0.860
The Genome Aggregation DatabaseAfricanSub8718T=0.169C=0.831
The Genome Aggregation DatabaseAmericanSub836T=0.280C=0.720
The Genome Aggregation DatabaseEast AsianSub1622T=0.132C=0.868
The Genome Aggregation DatabaseEuropeSub18466T=0.161C=0.838
The Genome Aggregation DatabaseGlobalStudy-wide29944T=0.165C=0.834
The Genome Aggregation DatabaseOtherSub302T=0.140C=0.860
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.153C=0.846
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.121C=0.879
PMID Title Author Journal
20158304A genomewide association study of nicotine and alcohol dependence in Australian and Dutch populations.Lind PATwin Res Hum Genet
24490108Genetics of proteasome diseases.Gomes AVScientifica (Cairo)
18389087Rarity of Somatic Mutation and Frequency of Normal Sequence Variation Detected in Sporadic Colon Adenocarcinoma Using High-Throughput cDNA Sequencing.Kan TBioinform Biol Insights

P-Value

SNP ID p-value Traits Study
rs22306811.36E-05alcohol and nictotine co-dependence20158304

eQTL of rs2230681 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 rs2230681 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 )
chr12122299557122300175E067-26637
chr12122310401122311032E067-15780
chr12122325819122325907E067-905
chr12122325908122325962E067-850
chr12122328127122328223E0671315
chr12122328538122328578E0671726
chr12122331174122331684E0674362
chr12122331699122332409E0674887
chr12122357143122357239E06730331
chr12122357273122357389E06730461
chr12122357394122357504E06730582
chr12122296777122297615E068-29197
chr12122325819122325907E068-905
chr12122325908122325962E068-850
chr12122328127122328223E0681315
chr12122328538122328578E0681726
chr12122331699122332409E0684887
chr12122355365122355721E06828553
chr12122279256122279321E069-47491
chr12122279322122279372E069-47440
chr12122279415122279572E069-47240
chr12122328127122328223E0691315
chr12122328538122328578E0691726
chr12122331090122331167E0694278
chr12122331174122331684E0694362
chr12122331699122332409E0694887
chr12122332542122332840E0695730
chr12122332981122333081E0696169
chr12122355227122355283E06928415
chr12122355365122355721E06928553
chr12122355808122355871E06928996
chr12122357143122357239E06930331
chr12122357273122357389E06930461
chr12122310401122311032E071-15780
chr12122325612122325681E071-1131
chr12122328127122328223E0711315
chr12122328538122328578E0711726
chr12122330978122331028E0714166
chr12122331090122331167E0714278
chr12122331174122331684E0714362
chr12122331699122332409E0714887
chr12122335851122335896E0719039
chr12122355808122355871E07128996
chr12122362503122363673E07135691
chr12122279256122279321E072-47491
chr12122279322122279372E072-47440
chr12122279415122279572E072-47240
chr12122310401122311032E072-15780
chr12122325819122325907E072-905
chr12122325908122325962E072-850
chr12122328127122328223E0721315
chr12122328538122328578E0721726
chr12122355365122355721E07228553
chr12122310401122311032E073-15780
chr12122325819122325907E073-905
chr12122325908122325962E073-850
chr12122328127122328223E0731315
chr12122331174122331684E0734362
chr12122355365122355721E07328553
chr12122355808122355871E07328996
chr12122279256122279321E074-47491
chr12122279322122279372E074-47440
chr12122279415122279572E074-47240
chr12122325612122325681E074-1131
chr12122328127122328223E0741315
chr12122330978122331028E0744166
chr12122331090122331167E0744278
chr12122331174122331684E0744362
chr12122331699122332409E0744887
chr12122355227122355283E07428415
chr12122355365122355721E07428553
chr12122355808122355871E07428996
chr12122303929122304000E081-22812
chr12122304705122304798E081-22014
chr12122304883122304933E081-21879
chr12122305129122305199E081-21613
chr12122310401122311032E081-15780
chr12122328127122328223E0811315
chr12122362503122363673E08135691
chr12122310401122311032E082-15780
chr12122328127122328223E0821315
chr12122328538122328578E0821726









Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr12122277021122278279E067-48533
chr12122326017122327830E0670
chr12122355909122356997E06729097
chr12122277021122278279E068-48533
chr12122326017122327830E0680
chr12122355909122356997E06829097
chr12122277021122278279E069-48533
chr12122326017122327830E0690
chr12122355909122356997E06929097
chr12122326017122327830E0700
chr12122355909122356997E07029097
chr12122277021122278279E071-48533
chr12122326017122327830E0710
chr12122355909122356997E07129097
chr12122277021122278279E072-48533
chr12122326017122327830E0720
chr12122355909122356997E07229097
chr12122277021122278279E073-48533
chr12122326017122327830E0730
chr12122355909122356997E07329097
chr12122277021122278279E074-48533
chr12122326017122327830E0740
chr12122355909122356997E07429097
chr12122326017122327830E0810
chr12122277021122278279E082-48533
chr12122326017122327830E0820
chr12122355909122356997E08229097