rs1096170

Homo sapiens
C>T
PRICKLE2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0479 (14212/29652,GnomAD)
T=0499 (14539/29118,TOPMED)
C==0467 (2338/5008,1000G)
C==0464 (1790/3854,ALSPAC)
C==0462 (1714/3708,TWINSUK)
chr3:64118712 (GRCh38.p7) (3p14.1)
ND
GWASdb2
1   publication(s)
See rs on genome
132 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.64118712C>T
GRCh37.p13 chr 3NC_000003.11:g.64104388C>T
PRICKLE2 RefSeqGeneNG_031930.1:g.111744G>A

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=0.598T=0.402
1000GenomesAmericanSub694C=0.430T=0.570
1000GenomesEast AsianSub1008C=0.435T=0.565
1000GenomesEuropeSub1006C=0.446T=0.554
1000GenomesGlobalStudy-wide5008C=0.467T=0.533
1000GenomesSouth AsianSub978C=0.370T=0.630
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.464T=0.536
The Genome Aggregation DatabaseAfricanSub8598C=0.594T=0.406
The Genome Aggregation DatabaseAmericanSub830C=0.420T=0.580
The Genome Aggregation DatabaseEast AsianSub1590C=0.432T=0.568
The Genome Aggregation DatabaseEuropeSub18334C=0.433T=0.566
The Genome Aggregation DatabaseGlobalStudy-wide29652C=0.479T=0.520
The Genome Aggregation DatabaseOtherSub300C=0.410T=0.590
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.500T=0.499
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.462T=0.538
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
rs10961705.18E-05nicotine dependence (smoking)22377092

eQTL of rs1096170 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 rs1096170 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 )
chr36409275664092848E067-11540
chr36409491564095054E067-9334
chr36409510764095551E067-8837
chr36411948664119530E06715098
chr36411976864119905E06715380
chr36412001864120068E06715630
chr36412087064120929E06716482
chr36412719064127468E06722802
chr36412907664129868E06724688
chr36413007364130147E06725685
chr36413586564137409E06731477
chr36413744464137529E06733056
chr36414673164146773E06742343
chr36414692964146979E06742541
chr36414705564147386E06742667
chr36414741764147673E06743029
chr36409408764094230E068-10158
chr36409449964094549E068-9839
chr36409491564095054E068-9334
chr36409510764095551E068-8837
chr36409562964096057E068-8331
chr36413586564137409E06831477
chr36414692964146979E06842541
chr36414705564147386E06842667
chr36414741764147673E06843029
chr36414776864147837E06843380
chr36414820064148276E06843812
chr36414834264148416E06843954
chr36414847464148524E06844086
chr36414877664148831E06844388
chr36409449964094549E069-9839
chr36409491564095054E069-9334
chr36409510764095551E069-8837
chr36409562964096057E069-8331
chr36412719064127468E06922802
chr36413586564137409E06931477
chr36413744464137529E06933056
chr36413757464138186E06933186
chr36414692964146979E06942541
chr36414705564147386E06942667
chr36414741764147673E06943029
chr36409382564093875E070-10513
chr36409408764094230E070-10158
chr36409449964094549E070-9839
chr36409491564095054E070-9334
chr36409510764095551E070-8837
chr36409562964096057E070-8331
chr36413586564137409E07031477
chr36409275664092848E071-11540
chr36409491564095054E071-9334
chr36409510764095551E071-8837
chr36409562964096057E071-8331
chr36412719064127468E07122802
chr36413586564137409E07131477
chr36413744464137529E07133056
chr36413757464138186E07133186
chr36414705564147386E07142667
chr36414741764147673E07143029
chr36414776864147837E07143380
chr36414820064148276E07143812
chr36414834264148416E07143954
chr36414847464148524E07144086
chr36414877664148831E07144388
chr36409491564095054E072-9334
chr36409510764095551E072-8837
chr36409562964096057E072-8331
chr36411886464118914E07214476
chr36411900664119202E07214618
chr36411948664119530E07215098
chr36411976864119905E07215380
chr36412001864120068E07215630
chr36412719064127468E07222802
chr36412907664129868E07224688
chr36413007364130147E07225685
chr36413018264130661E07225794
chr36413170464131754E07227316
chr36413586564137409E07231477
chr36414692964146979E07242541
chr36414705564147386E07242667
chr36414820064148276E07243812
chr36414834264148416E07243954
chr36414847464148524E07244086
chr36414877664148831E07244388
chr36408047564080671E073-23717
chr36409449964094549E073-9839
chr36409491564095054E073-9334
chr36409510764095551E073-8837
chr36411900664119202E07314618
chr36411948664119530E07315098
chr36411976864119905E07315380
chr36412001864120068E07315630
chr36412387564124044E07319487
chr36412647964126603E07322091
chr36412719064127468E07322802
chr36413007364130147E07325685
chr36413018264130661E07325794
chr36413586564137409E07331477
chr36413744464137529E07333056
chr36413757464138186E07333186
chr36414264664142706E07338258
chr36414287264143052E07338484
chr36414308664143474E07338698
chr36409491564095054E074-9334
chr36409510764095551E074-8837
chr36409562964096057E074-8331
chr36413744464137529E07433056
chr36414692964146979E07442541
chr36414705564147386E07442667
chr36414741764147673E07443029
chr36414776864147837E07443380
chr36414820064148276E07443812
chr36414834264148416E07443954
chr36405787964058115E081-46273
chr36406357764063727E081-40661
chr36406384964063899E081-40489
chr36406403464064187E081-40201
chr36406477564064880E081-39508
chr36406516364065406E081-38982
chr36406542964065806E081-38582
chr36406599364066102E081-38286
chr36407870264078826E081-25562
chr36407898964079287E081-25101
chr36408018464080308E081-24080
chr36412907664129868E08124688
chr36413007364130147E08125685
chr36413586564137409E08131477
chr36413757464138186E08133186
chr36406477564064880E082-39508
chr36406516364065406E082-38982
chr36406542964065806E082-38582
chr36406599364066102E082-38286
chr36413586564137409E08231477