rs253922

Homo sapiens
C>T
PDZD2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0378 (11323/29936,GnomAD)
C==0401 (11675/29118,TOPMED)
C==0354 (1773/5008,1000G)
C==0419 (1616/3854,ALSPAC)
C==0429 (1592/3708,TWINSUK)
chr5:31723153 (GRCh38.p7) (5p13.3)
ND
GWASdb2
1   publication(s)
See rs on genome
150 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 5NC_000005.10:g.31723153C>T
GRCh37.p13 chr 5NC_000005.9:g.31723260C>T
PDZD2 RefSeqGeneNG_033962.2:g.88744C>T

Gene: PDZD2, PDZ domain containing 2(plus strand)

Molecule type Change Amino acid[Codon] SO Term
PDZD2 transcriptNM_178140.3:c.N/AIntron Variant
PDZD2 transcript variant X2XM_005248269.4:c.N/AIntron Variant
PDZD2 transcript variant X1XM_011513992.2:c.N/AIntron Variant
PDZD2 transcript variant X3XM_011513993.2:c.N/AIntron Variant
PDZD2 transcript variant X4XM_011513994.2:c.N/AIntron Variant
PDZD2 transcript variant X5XM_011513995.2:c.N/AIntron Variant
PDZD2 transcript variant X6XM_011513996.2:c.N/AIntron Variant
PDZD2 transcript variant X10XM_017009246.1:c.N/AIntron Variant
PDZD2 transcript variant X8XM_005248271.1:c.N/AGenic Upstream Transcript Variant
PDZD2 transcript variant X7XM_005248272.3:c.N/AGenic Upstream Transcript Variant
PDZD2 transcript variant X11XM_006714460.2:c.N/AGenic Upstream Transcript Variant
PDZD2 transcript variant X9XM_017009245.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.372T=0.628
1000GenomesAmericanSub694C=0.340T=0.660
1000GenomesEast AsianSub1008C=0.242T=0.758
1000GenomesEuropeSub1006C=0.447T=0.553
1000GenomesGlobalStudy-wide5008C=0.354T=0.646
1000GenomesSouth AsianSub978C=0.360T=0.640
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.419T=0.581
The Genome Aggregation DatabaseAfricanSub8710C=0.379T=0.621
The Genome Aggregation DatabaseAmericanSub838C=0.290T=0.710
The Genome Aggregation DatabaseEast AsianSub1614C=0.201T=0.799
The Genome Aggregation DatabaseEuropeSub18472C=0.396T=0.603
The Genome Aggregation DatabaseGlobalStudy-wide29936C=0.378T=0.621
The Genome Aggregation DatabaseOtherSub302C=0.440T=0.560
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.401T=0.599
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.429T=0.571
PMID Title Author Journal
17158188Novel genes identified in a high-density genome wide association study for nicotine dependence.Bierut LJHum Mol Genet

P-Value

SNP ID p-value Traits Study
rs2539220.000303nicotine dependence17158188

eQTL of rs253922 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 rs253922 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 )
chr53168065931680967E067-42293
chr53170182431702417E067-20843
chr53173329431733391E06710034
chr53173416431734215E06710904
chr53173766531737715E06714405
chr53174163131741998E06718371
chr53174215531742210E06718895
chr53175486931755087E06731609
chr53175512731755293E06731867
chr53175533231755372E06732072
chr53175773531757931E06734475
chr53175795331758177E06734693
chr53168065931680967E068-42293
chr53170161631701687E068-21573
chr53171133331711373E068-11887
chr53171165131711718E068-11542
chr53171774031718044E068-5216
chr53173230931732452E0689049
chr53173271631732777E0689456
chr53173329431733391E06810034
chr53173508831735128E06811828
chr53174072731741107E06817467
chr53174128431741523E06818024
chr53174163131741998E06818371
chr53174215531742210E06818895
chr53175416731754367E06830907
chr53175453531754612E06831275
chr53175467031754721E06831410
chr53175486931755087E06831609
chr53175512731755293E06831867
chr53175533231755372E06832072
chr53175594931756078E06832689
chr53175611731756235E06832857
chr53175795331758177E06834693
chr53176901731769170E06845757
chr53176934131769422E06846081
chr53176969631769767E06846436
chr53176981231769885E06846552
chr53177013031770270E06846870
chr53177032331770617E06847063
chr53177063231770709E06847372
chr53177076831770838E06847508
chr53177109231771172E06847832
chr53177127731771416E06848017
chr53170161631701687E069-21573
chr53170182431702417E069-20843
chr53173230931732452E0699049
chr53173271631732777E0699456
chr53173329431733391E06910034
chr53173340531734091E06910145
chr53173416431734215E06910904
chr53174163131741998E06918371
chr53174215531742210E06918895
chr53175416731754367E06930907
chr53175453531754612E06931275
chr53175467031754721E06931410
chr53175486931755087E06931609
chr53175512731755293E06931867
chr53175773531757931E06934475
chr53175795331758177E06934693
chr53176981231769885E06946552
chr53177013031770270E06946870
chr53177032331770617E06947063
chr53177063231770709E06947372
chr53177076831770838E06947508
chr53173340531734091E07010145
chr53175416731754367E07030907
chr53175453531754612E07031275
chr53175467031754721E07031410
chr53175486931755087E07031609
chr53175512731755293E07031867
chr53175533231755372E07032072
chr53170182431702417E071-20843
chr53171774031718044E071-5216
chr53173212531732250E0718865
chr53173230931732452E0719049
chr53173271631732777E0719456
chr53173340531734091E07110145
chr53173416431734215E07110904
chr53174163131741998E07118371
chr53174215531742210E07118895
chr53175388231754129E07130622
chr53175416731754367E07130907
chr53175453531754612E07131275
chr53175467031754721E07131410
chr53175486931755087E07131609
chr53175512731755293E07131867
chr53175533231755372E07132072
chr53175795331758177E07134693
chr53176981231769885E07146552
chr53177013031770270E07146870
chr53177032331770617E07147063
chr53177063231770709E07147372
chr53177076831770838E07147508
chr53173212531732250E0728865
chr53173230931732452E0729049
chr53173416431734215E07210904
chr53174163131741998E07218371
chr53175453531754612E07231275
chr53175467031754721E07231410
chr53175486931755087E07231609
chr53175512731755293E07231867
chr53175533231755372E07232072
chr53175594931756078E07232689
chr53175611731756235E07232857
chr53177013031770270E07246870
chr53177032331770617E07247063
chr53168065931680967E073-42293
chr53169274031693220E073-30040
chr53173230931732452E0739049
chr53173271631732777E0739456
chr53173329431733391E07310034
chr53173416431734215E07310904
chr53175486931755087E07331609
chr53175512731755293E07331867
chr53175533231755372E07332072
chr53175594931756078E07332689
chr53175611731756235E07332857
chr53176981231769885E07346552
chr53177013031770270E07346870
chr53177032331770617E07347063
chr53177063231770709E07347372
chr53177076831770838E07347508
chr53177109231771172E07347832
chr53177127731771416E07348017
chr53177154631771939E07348286
chr53168065931680967E074-42293
chr53170161631701687E074-21573
chr53170182431702417E074-20843
chr53171115731711211E074-12049
chr53171133331711373E074-11887
chr53171165131711718E074-11542
chr53173329431733391E07410034
chr53173340531734091E07410145
chr53173416431734215E07410904
chr53176893531768991E07445675
chr53176981231769885E07446552
chr53177013031770270E07446870
chr53177032331770617E07447063
chr53177063231770709E07447372
chr53177076831770838E07447508
chr53168313031683286E081-39974
chr53170182431702417E081-20843
chr53173271631732777E0819456
chr53173329431733391E08110034
chr53173340531734091E08110145
chr53173416431734215E08110904
chr53174857331748940E08125313
chr53173340531734091E08210145
chr53174900031749151E08225740