rs830010

Homo sapiens
C>A
PRICKLE2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0414 (12384/29906,GnomAD)
C==0433 (12630/29118,TOPMED)
C==0407 (2036/5008,1000G)
C==0394 (1519/3854,ALSPAC)
C==0388 (1438/3708,TWINSUK)
chr3:64123061 (GRCh38.p7) (3p14.1)
ND
GWASdb2
1   publication(s)
See rs on genome
131 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.64123061C>A
GRCh37.p13 chr 3NC_000003.11:g.64108737C>A
PRICKLE2 RefSeqGeneNG_031930.1:g.107395G>T

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
1000GenomesAfricanSub1322C=0.514A=0.486
1000GenomesAmericanSub694C=0.390A=0.610
1000GenomesEast AsianSub1008C=0.411A=0.589
1000GenomesEuropeSub1006C=0.389A=0.611
1000GenomesGlobalStudy-wide5008C=0.407A=0.593
1000GenomesSouth AsianSub978C=0.290A=0.710
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.394A=0.606
The Genome Aggregation DatabaseAfricanSub8714C=0.517A=0.483
The Genome Aggregation DatabaseAmericanSub836C=0.370A=0.630
The Genome Aggregation DatabaseEast AsianSub1604C=0.412A=0.588
The Genome Aggregation DatabaseEuropeSub18450C=0.369A=0.630
The Genome Aggregation DatabaseGlobalStudy-wide29906C=0.414A=0.585
The Genome Aggregation DatabaseOtherSub302C=0.300A=0.700
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.433A=0.566
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.388A=0.612
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
rs8300109.79E-05nicotine dependence (smoking)22377092

eQTL of rs830010 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 rs830010 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 )
chr36409275664092848E067-15889
chr36409491564095054E067-13683
chr36409510764095551E067-13186
chr36411948664119530E06710749
chr36411976864119905E06711031
chr36412001864120068E06711281
chr36412087064120929E06712133
chr36412719064127468E06718453
chr36412907664129868E06720339
chr36413007364130147E06721336
chr36413586564137409E06727128
chr36413744464137529E06728707
chr36414673164146773E06737994
chr36414692964146979E06738192
chr36414705564147386E06738318
chr36414741764147673E06738680
chr36409408764094230E068-14507
chr36409449964094549E068-14188
chr36409491564095054E068-13683
chr36409510764095551E068-13186
chr36409562964096057E068-12680
chr36413586564137409E06827128
chr36414692964146979E06838192
chr36414705564147386E06838318
chr36414741764147673E06838680
chr36414776864147837E06839031
chr36414820064148276E06839463
chr36414834264148416E06839605
chr36414847464148524E06839737
chr36414877664148831E06840039
chr36409449964094549E069-14188
chr36409491564095054E069-13683
chr36409510764095551E069-13186
chr36409562964096057E069-12680
chr36412719064127468E06918453
chr36413586564137409E06927128
chr36413744464137529E06928707
chr36413757464138186E06928837
chr36414692964146979E06938192
chr36414705564147386E06938318
chr36414741764147673E06938680
chr36409382564093875E070-14862
chr36409408764094230E070-14507
chr36409449964094549E070-14188
chr36409491564095054E070-13683
chr36409510764095551E070-13186
chr36409562964096057E070-12680
chr36413586564137409E07027128
chr36409275664092848E071-15889
chr36409491564095054E071-13683
chr36409510764095551E071-13186
chr36409562964096057E071-12680
chr36412719064127468E07118453
chr36413586564137409E07127128
chr36413744464137529E07128707
chr36413757464138186E07128837
chr36414705564147386E07138318
chr36414741764147673E07138680
chr36414776864147837E07139031
chr36414820064148276E07139463
chr36414834264148416E07139605
chr36414847464148524E07139737
chr36414877664148831E07140039
chr36409491564095054E072-13683
chr36409510764095551E072-13186
chr36409562964096057E072-12680
chr36411886464118914E07210127
chr36411900664119202E07210269
chr36411948664119530E07210749
chr36411976864119905E07211031
chr36412001864120068E07211281
chr36412719064127468E07218453
chr36412907664129868E07220339
chr36413007364130147E07221336
chr36413018264130661E07221445
chr36413170464131754E07222967
chr36413586564137409E07227128
chr36414692964146979E07238192
chr36414705564147386E07238318
chr36414820064148276E07239463
chr36414834264148416E07239605
chr36414847464148524E07239737
chr36414877664148831E07240039
chr36408047564080671E073-28066
chr36409449964094549E073-14188
chr36409491564095054E073-13683
chr36409510764095551E073-13186
chr36411900664119202E07310269
chr36411948664119530E07310749
chr36411976864119905E07311031
chr36412001864120068E07311281
chr36412387564124044E07315138
chr36412647964126603E07317742
chr36412719064127468E07318453
chr36413007364130147E07321336
chr36413018264130661E07321445
chr36413586564137409E07327128
chr36413744464137529E07328707
chr36413757464138186E07328837
chr36414264664142706E07333909
chr36414287264143052E07334135
chr36414308664143474E07334349
chr36409491564095054E074-13683
chr36409510764095551E074-13186
chr36409562964096057E074-12680
chr36413744464137529E07428707
chr36414692964146979E07438192
chr36414705564147386E07438318
chr36414741764147673E07438680
chr36414776864147837E07439031
chr36414820064148276E07439463
chr36414834264148416E07439605
chr36406357764063727E081-45010
chr36406384964063899E081-44838
chr36406403464064187E081-44550
chr36406477564064880E081-43857
chr36406516364065406E081-43331
chr36406542964065806E081-42931
chr36406599364066102E081-42635
chr36407870264078826E081-29911
chr36407898964079287E081-29450
chr36408018464080308E081-28429
chr36412907664129868E08120339
chr36413007364130147E08121336
chr36413586564137409E08127128
chr36413757464138186E08128837
chr36406477564064880E082-43857
chr36406516364065406E082-43331
chr36406542964065806E082-42931
chr36406599364066102E082-42635
chr36413586564137409E08227128