rs11764539

Homo sapiens
T>C
PTPRN2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0249 (7337/29466,GnomAD)
C=0231 (6741/29118,TOPMED)
C=0231 (1155/5008,1000G)
C=0254 (979/3854,ALSPAC)
C=0268 (995/3708,TWINSUK)
chr7:157666180 (GRCh38.p7) (7q36.3)
ND
GWASdb2
1   publication(s)
See rs on genome
113 Enhancers around
18 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 7NC_000007.14:g.157666180T>C
GRCh37.p13 chr 7NC_000007.13:g.157458872T>C
PTPRN2 RefSeqGeneNG_029966.1:g.926611A>G

Gene: PTPRN2, protein tyrosine phosphatase, receptor type N2(minus strand)

Molecule type Change Amino acid[Codon] SO Term
PTPRN2 transcript variant 4NM_001308267.1:c.N/AIntron Variant
PTPRN2 transcript variant 5NM_001308268.1:c.N/AIntron Variant
PTPRN2 transcript variant 1NM_002847.4:c.N/AIntron Variant
PTPRN2 transcript variant 2NM_130842.3:c.N/AIntron Variant
PTPRN2 transcript variant 3NM_130843.3:c.N/AIntron Variant
PTPRN2 transcript variant X3XM_011516446.1:c.N/AIntron Variant
PTPRN2 transcript variant X1XM_017012475.1:c.N/AIntron Variant
PTPRN2 transcript variant X2XM_017012476.1:c.N/AIntron Variant
PTPRN2 transcript variant X4XM_011516447.2:c.N/AGenic Downstream Transcript Variant
PTPRN2 transcript variant X5XM_011516448.2:c.N/AGenic Downstream Transcript Variant
PTPRN2 transcript variant X6XM_011516449.2:c.N/AGenic Downstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.802C=0.198
1000GenomesAmericanSub694T=0.680C=0.320
1000GenomesEast AsianSub1008T=0.756C=0.244
1000GenomesEuropeSub1006T=0.762C=0.238
1000GenomesGlobalStudy-wide5008T=0.769C=0.231
1000GenomesSouth AsianSub978T=0.810C=0.190
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.746C=0.254
The Genome Aggregation DatabaseAfricanSub8648T=0.777C=0.223
The Genome Aggregation DatabaseAmericanSub828T=0.720C=0.280
The Genome Aggregation DatabaseEast AsianSub1610T=0.766C=0.234
The Genome Aggregation DatabaseEuropeSub18080T=0.738C=0.261
The Genome Aggregation DatabaseGlobalStudy-wide29466T=0.751C=0.249
The Genome Aggregation DatabaseOtherSub300T=0.770C=0.230
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.768C=0.231
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.732C=0.268
PMID Title Author Journal
19268276Genome-wide association study of smoking initiation and current smoking.Vink JMAm J Hum Genet

P-Value

SNP ID p-value Traits Study
rs117645390.00087nicotine smoking19268276

eQTL of rs11764539 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 rs11764539 in Fetal Brain

Probe ID Position Gene beta p-value
cg27113326chr7:157454068PTPRN2-0.09185230020761462.0201e-10
cg05766510chr7:157454062PTPRN2-0.07000261194284351.1260e-9

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 )
chr7157423164157423358E067-35514
chr7157423526157423641E067-35231
chr7157423747157423820E067-35052
chr7157408976157409139E068-49733
chr7157423526157423641E068-35231
chr7157423747157423820E068-35052
chr7157430646157430740E068-28132
chr7157451160157451210E068-7662
chr7157451224157451302E068-7570
chr7157451345157451423E068-7449
chr7157451450157451511E068-7361
chr7157451628157451760E068-7112
chr7157455031157455081E068-3791
chr7157455138157455188E068-3684
chr7157455238157455348E068-3524
chr7157455410157455454E068-3418
chr7157455521157455578E068-3294
chr7157455621157455719E068-3153
chr7157455986157456415E068-2457
chr7157456509157456569E068-2303
chr7157462808157464486E0683936
chr7157464542157464616E0685670
chr7157465257157465307E0686385
chr7157465310157465416E0686438
chr7157468333157468383E0689461
chr7157468596157468719E0689724
chr7157469751157469948E06810879
chr7157469976157470080E06811104
chr7157470110157470175E06811238
chr7157471156157471206E06812284
chr7157471244157471448E06812372
chr7157471470157471624E06812598
chr7157408976157409139E069-49733
chr7157409145157409376E069-49496
chr7157430015157430278E069-28594
chr7157430308157430592E069-28280
chr7157430646157430740E069-28132
chr7157455410157455454E069-3418
chr7157455521157455578E069-3294
chr7157455621157455719E069-3153
chr7157455986157456415E069-2457
chr7157456750157456860E069-2012
chr7157456906157456956E069-1916
chr7157422530157422596E070-36276
chr7157423164157423358E070-35514
chr7157423526157423641E070-35231
chr7157423747157423820E070-35052
chr7157426599157426649E070-32223
chr7157427851157427901E070-30971
chr7157427969157428077E070-30795
chr7157428531157428595E070-30277
chr7157430646157430740E070-28132
chr7157431473157431562E070-27310
chr7157431575157431669E070-27203
chr7157454149157454264E070-4608
chr7157454388157454438E070-4434
chr7157455986157456415E070-2457
chr7157456509157456569E070-2303
chr7157456750157456860E070-2012
chr7157456906157456956E070-1916
chr7157457530157457631E070-1241
chr7157460687157460755E0701815
chr7157460844157461249E0701972
chr7157461361157461499E0702489
chr7157461601157461729E0702729
chr7157461754157461858E0702882
chr7157461902157461973E0703030
chr7157462136157462587E0703264
chr7157465257157465307E0706385
chr7157465310157465416E0706438
chr7157468596157468719E0709724
chr7157455621157455719E071-3153
chr7157455986157456415E071-2457
chr7157408976157409139E072-49733
chr7157409145157409376E072-49496
chr7157409496157409540E072-49332
chr7157410314157410364E072-48508
chr7157455621157455719E072-3153
chr7157455986157456415E072-2457
chr7157456509157456569E072-2303
chr7157456750157456860E072-2012
chr7157456906157456956E072-1916
chr7157408976157409139E073-49733
chr7157409145157409376E073-49496
chr7157409496157409540E073-49332
chr7157430015157430278E073-28594
chr7157430308157430592E073-28280
chr7157430646157430740E073-28132
chr7157455621157455719E073-3153
chr7157467739157467789E0738867
chr7157468333157468383E0739461
chr7157468596157468719E0739724
chr7157430015157430278E074-28594
chr7157430308157430592E074-28280
chr7157430646157430740E074-28132
chr7157430015157430278E081-28594
chr7157430308157430592E081-28280
chr7157430646157430740E081-28132
chr7157450561157450740E081-8132
chr7157450831157450995E081-7877
chr7157451018157451116E081-7756
chr7157451160157451210E081-7662
chr7157461754157461858E0812882
chr7157461902157461973E0813030
chr7157462136157462587E0813264
chr7157462808157464486E0813936
chr7157472473157472548E08113601
chr7157472591157472660E08113719
chr7157472850157472896E08113978
chr7157430646157430740E082-28132
chr7157431473157431562E082-27310
chr7157455986157456415E082-2457
chr7157456509157456569E082-2303










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr7157482817157482996E06723945
chr7157483011157484953E06724139
chr7157423074157423127E068-35745
chr7157482817157482996E06823945
chr7157483011157484953E06824139
chr7157483011157484953E06924139
chr7157477314157477452E07018442
chr7157477481157478076E07018609
chr7157482817157482996E07023945
chr7157483011157484953E07024139
chr7157483011157484953E07124139
chr7157483011157484953E07224139
chr7157482817157482996E07323945
chr7157483011157484953E07324139
chr7157482817157482996E07423945
chr7157483011157484953E07424139
chr7157477314157477452E08218442
chr7157477481157478076E08218609