rs1024895

Homo sapiens
T>C
PRICKLE2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0439 (13074/29736,GnomAD)
T==0437 (12724/29118,TOPMED)
T==0408 (2041/5008,1000G)
T==0451 (1737/3854,ALSPAC)
T==0454 (1682/3708,TWINSUK)
chr3:64125982 (GRCh38.p7) (3p14.1)
ND
GWASdb2
1   publication(s)
See rs on genome
133 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.64125982T>C
GRCh37.p13 chr 3NC_000003.11:g.64111658T>C
PRICKLE2 RefSeqGeneNG_031930.1:g.104474A>G

Gene: PRICKLE2, prickle planar cell polarity protein 2(minus strand)

Molecule type Change Amino acid[Codon] SO Term
PRICKLE2 transcriptNM_198859.3:c.N/AIntron Variant
PRICKLE2 transcript variant X1XM_011533432.2:c.N/AIntron Variant
PRICKLE2 transcript variant X2XM_011533433.2:c.N/AIntron Variant
PRICKLE2 transcript variant X3XM_011533434.2:c.N/AIntron Variant
PRICKLE2 transcript variant X4XM_011533435.2:c.N/AIntron Variant
PRICKLE2 transcript variant X5XM_011533436.2:c.N/AIntron Variant
PRICKLE2 transcript variant X6XM_011533437.2:c.N/AIntron Variant
PRICKLE2 transcript variant X8XM_011533438.2:c.N/AIntron Variant
PRICKLE2 transcript variant X10XM_011533440.2:c.N/AIntron Variant
PRICKLE2 transcript variant X7XM_017005798.1:c.N/AIntron Variant
PRICKLE2 transcript variant X9XM_017005799.1:c.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.448C=0.552
1000GenomesAmericanSub694T=0.400C=0.600
1000GenomesEast AsianSub1008T=0.424C=0.576
1000GenomesEuropeSub1006T=0.430C=0.570
1000GenomesGlobalStudy-wide5008T=0.408C=0.592
1000GenomesSouth AsianSub978T=0.320C=0.680
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.451C=0.549
The Genome Aggregation DatabaseAfricanSub8660T=0.474C=0.526
The Genome Aggregation DatabaseAmericanSub838T=0.390C=0.610
The Genome Aggregation DatabaseEast AsianSub1614T=0.418C=0.582
The Genome Aggregation DatabaseEuropeSub18322T=0.428C=0.571
The Genome Aggregation DatabaseGlobalStudy-wide29736T=0.439C=0.560
The Genome Aggregation DatabaseOtherSub302T=0.370C=0.630
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.437C=0.563
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.454C=0.546
PMID Title Author Journal
22377092ANAPC1 and SLCO3A1 are associated with nicotine dependence: meta-analysis of genome-wide association studies.Wang KSDrug Alcohol Depend

P-Value

SNP ID p-value Traits Study
rs10248952.5E-06nicotine dependence (smoking)22377092

eQTL of rs1024895 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 rs1024895 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 )
chr36409275664092848E067-18810
chr36409491564095054E067-16604
chr36409510764095551E067-16107
chr36411948664119530E0677828
chr36411976864119905E0678110
chr36412001864120068E0678360
chr36412087064120929E0679212
chr36412719064127468E06715532
chr36412907664129868E06717418
chr36413007364130147E06718415
chr36413586564137409E06724207
chr36413744464137529E06725786
chr36414673164146773E06735073
chr36414692964146979E06735271
chr36414705564147386E06735397
chr36414741764147673E06735759
chr36409408764094230E068-17428
chr36409449964094549E068-17109
chr36409491564095054E068-16604
chr36409510764095551E068-16107
chr36409562964096057E068-15601
chr36413586564137409E06824207
chr36414692964146979E06835271
chr36414705564147386E06835397
chr36414741764147673E06835759
chr36414776864147837E06836110
chr36414820064148276E06836542
chr36414834264148416E06836684
chr36414847464148524E06836816
chr36414877664148831E06837118
chr36409449964094549E069-17109
chr36409491564095054E069-16604
chr36409510764095551E069-16107
chr36409562964096057E069-15601
chr36412719064127468E06915532
chr36413586564137409E06924207
chr36413744464137529E06925786
chr36413757464138186E06925916
chr36414692964146979E06935271
chr36414705564147386E06935397
chr36414741764147673E06935759
chr36409382564093875E070-17783
chr36409408764094230E070-17428
chr36409449964094549E070-17109
chr36409491564095054E070-16604
chr36409510764095551E070-16107
chr36409562964096057E070-15601
chr36413586564137409E07024207
chr36409275664092848E071-18810
chr36409491564095054E071-16604
chr36409510764095551E071-16107
chr36409562964096057E071-15601
chr36412719064127468E07115532
chr36413586564137409E07124207
chr36413744464137529E07125786
chr36413757464138186E07125916
chr36414705564147386E07135397
chr36414741764147673E07135759
chr36414776864147837E07136110
chr36414820064148276E07136542
chr36414834264148416E07136684
chr36414847464148524E07136816
chr36414877664148831E07137118
chr36409491564095054E072-16604
chr36409510764095551E072-16107
chr36409562964096057E072-15601
chr36411886464118914E0727206
chr36411900664119202E0727348
chr36411948664119530E0727828
chr36411976864119905E0728110
chr36412001864120068E0728360
chr36412719064127468E07215532
chr36412907664129868E07217418
chr36413007364130147E07218415
chr36413018264130661E07218524
chr36413170464131754E07220046
chr36413586564137409E07224207
chr36414692964146979E07235271
chr36414705564147386E07235397
chr36414820064148276E07236542
chr36414834264148416E07236684
chr36414847464148524E07236816
chr36414877664148831E07237118
chr36408047564080671E073-30987
chr36409449964094549E073-17109
chr36409491564095054E073-16604
chr36409510764095551E073-16107
chr36411900664119202E0737348
chr36411948664119530E0737828
chr36411976864119905E0738110
chr36412001864120068E0738360
chr36412387564124044E07312217
chr36412647964126603E07314821
chr36412719064127468E07315532
chr36413007364130147E07318415
chr36413018264130661E07318524
chr36413586564137409E07324207
chr36413744464137529E07325786
chr36413757464138186E07325916
chr36414264664142706E07330988
chr36414287264143052E07331214
chr36414308664143474E07331428
chr36409491564095054E074-16604
chr36409510764095551E074-16107
chr36409562964096057E074-15601
chr36413744464137529E07425786
chr36414692964146979E07435271
chr36414705564147386E07435397
chr36414741764147673E07435759
chr36414776864147837E07436110
chr36414820064148276E07436542
chr36414834264148416E07436684
chr36406357764063727E081-47931
chr36406384964063899E081-47759
chr36406403464064187E081-47471
chr36406477564064880E081-46778
chr36406516364065406E081-46252
chr36406542964065806E081-45852
chr36406599364066102E081-45556
chr36407870264078826E081-32832
chr36407898964079287E081-32371
chr36408018464080308E081-31350
chr36412907664129868E08117418
chr36413007364130147E08118415
chr36413586564137409E08124207
chr36413757464138186E08125916
chr36416014264160282E08148484
chr36416039864160483E08148740
chr36406477564064880E082-46778
chr36406516364065406E082-46252
chr36406542964065806E082-45852
chr36406599364066102E082-45556
chr36413586564137409E08224207