rs7801395

Homo sapiens
T>C
PTPRN2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0463 (13874/29924,GnomAD)
C=0442 (12873/29118,TOPMED)
T==0436 (2181/5008,1000G)
C=0485 (1869/3854,ALSPAC)
C=0477 (1767/3708,TWINSUK)
chr7:158497735 (GRCh38.p7) (7q36.3)
ND
GWASdb2
1   publication(s)
See rs on genome
288 Enhancers around
2 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 7NC_000007.14:g.158497735T>C
GRCh37.p13 chr 7NC_000007.13:g.158290427T>C
PTPRN2 RefSeqGeneNG_029966.1:g.95056A>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 X4XM_011516447.2:c.N/AIntron Variant
PTPRN2 transcript variant X5XM_011516448.2:c.N/AIntron Variant
PTPRN2 transcript variant X6XM_011516449.2:c.N/AIntron Variant
PTPRN2 transcript variant X2XM_017012476.1:c.N/AIntron Variant
PTPRN2 transcript variant X1XM_017012475.1:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.567C=0.433
1000GenomesAmericanSub694T=0.460C=0.540
1000GenomesEast AsianSub1008T=0.304C=0.696
1000GenomesEuropeSub1006T=0.510C=0.490
1000GenomesGlobalStudy-wide5008T=0.436C=0.564
1000GenomesSouth AsianSub978T=0.300C=0.700
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.515C=0.485
The Genome Aggregation DatabaseAfricanSub8724T=0.550C=0.450
The Genome Aggregation DatabaseAmericanSub836T=0.510C=0.490
The Genome Aggregation DatabaseEast AsianSub1620T=0.296C=0.704
The Genome Aggregation DatabaseEuropeSub18442T=0.550C=0.449
The Genome Aggregation DatabaseGlobalStudy-wide29924T=0.536C=0.463
The Genome Aggregation DatabaseOtherSub302T=0.630C=0.370
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.557C=0.442
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.523C=0.477
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
rs78013950.000558nicotine smoking19268276

eQTL of rs7801395 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 rs7801395 in Fetal Brain

Probe ID Position Gene beta p-value
cg09705243chr16:30786672-0.003629865357745344.5634e-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 )
chr7158263014158263120E067-27307
chr7158265577158265692E067-24735
chr7158265703158266469E067-23958
chr7158331833158331873E06741406
chr7158332140158332272E06741713
chr7158251464158251519E068-38908
chr7158252361158252445E068-37982
chr7158264788158264948E068-25479
chr7158265260158265533E068-24894
chr7158265577158265692E068-24735
chr7158265703158266469E068-23958
chr7158266589158266890E068-23537
chr7158267016158267066E068-23361
chr7158271793158271843E068-18584
chr7158272406158272498E068-17929
chr7158272798158272861E068-17566
chr7158272926158272976E068-17451
chr7158284569158284650E068-5777
chr7158284913158284981E068-5446
chr7158284986158285306E068-5121
chr7158287211158287261E068-3166
chr7158287281158287398E068-3029
chr7158290724158290856E068297
chr7158291217158291553E068790
chr7158291556158291804E0681129
chr7158291941158292019E0681514
chr7158302120158302203E06811693
chr7158312116158312272E06821689
chr7158323795158323835E06833368
chr7158323850158324012E06833423
chr7158325832158325872E06835405
chr7158333913158334198E06843486
chr7158334216158334621E06843789
chr7158261568158261678E069-28749
chr7158284569158284650E069-5777
chr7158284913158284981E069-5446
chr7158284986158285306E069-5121
chr7158285545158285597E069-4830
chr7158285639158285679E069-4748
chr7158287211158287261E069-3166
chr7158287281158287398E069-3029
chr7158287636158287838E069-2589
chr7158287847158288011E069-2416
chr7158288077158288906E069-1521
chr7158313489158313558E06923062
chr7158313666158313778E06923239
chr7158240443158240497E070-49930
chr7158260165158260425E070-30002
chr7158260482158260618E070-29809
chr7158260662158260973E070-29454
chr7158260990158261190E070-29237
chr7158261304158261384E070-29043
chr7158261568158261678E070-28749
chr7158262221158262308E070-28119
chr7158265260158265533E070-24894
chr7158265577158265692E070-24735
chr7158265703158266469E070-23958
chr7158266589158266890E070-23537
chr7158280384158280541E070-9886
chr7158281430158281610E070-8817
chr7158284913158284981E070-5446
chr7158284986158285306E070-5121
chr7158286660158286756E070-3671
chr7158286915158287200E070-3227
chr7158287211158287261E070-3166
chr7158287281158287398E070-3029
chr7158287636158287838E070-2589
chr7158288916158288994E070-1433
chr7158291556158291804E0701129
chr7158291941158292019E0701514
chr7158293036158293237E0702609
chr7158293275158293718E0702848
chr7158294162158294253E0703735
chr7158294360158294413E0703933
chr7158323396158323448E07032969
chr7158323630158323786E07033203
chr7158323795158323835E07033368
chr7158323850158324012E07033423
chr7158333616158333674E07043189
chr7158333913158334198E07043486
chr7158334216158334621E07043789
chr7158288077158288906E071-1521
chr7158293275158293718E0712848
chr7158254921158254971E072-35456
chr7158255059158255190E072-35237
chr7158256083158256133E072-34294
chr7158261568158261678E072-28749
chr7158284569158284650E072-5777
chr7158284913158284981E072-5446
chr7158286915158287200E072-3227
chr7158287211158287261E072-3166
chr7158287281158287398E072-3029
chr7158287636158287838E072-2589
chr7158287847158288011E072-2416
chr7158288077158288906E072-1521
chr7158288916158288994E072-1433
chr7158311315158311365E07220888
chr7158313489158313558E07223062
chr7158313666158313778E07223239
chr7158284569158284650E073-5777
chr7158284913158284981E073-5446
chr7158284986158285306E073-5121
chr7158285545158285597E073-4830
chr7158286660158286756E073-3671
chr7158286915158287200E073-3227
chr7158287211158287261E073-3166
chr7158287281158287398E073-3029
chr7158287636158287838E073-2589
chr7158287847158288011E073-2416
chr7158288077158288906E073-1521
chr7158293036158293237E0732609
chr7158293275158293718E0732848
chr7158300436158300775E07310009
chr7158300950158301000E07310523
chr7158313489158313558E07323062
chr7158313666158313778E07323239
chr7158333913158334198E07343486
chr7158334216158334621E07343789
chr7158261568158261678E074-28749
chr7158284913158284981E074-5446
chr7158240443158240497E081-49930
chr7158240663158240736E081-49691
chr7158246572158246675E081-43752
chr7158254921158254971E081-35456
chr7158255059158255190E081-35237
chr7158260165158260425E081-30002
chr7158260482158260618E081-29809
chr7158260662158260973E081-29454
chr7158260990158261190E081-29237
chr7158261304158261384E081-29043
chr7158261568158261678E081-28749
chr7158263014158263120E081-27307
chr7158263134158263317E081-27110
chr7158263852158264072E081-26355
chr7158264788158264948E081-25479
chr7158265260158265533E081-24894
chr7158265577158265692E081-24735
chr7158265703158266469E081-23958
chr7158266589158266890E081-23537
chr7158267016158267066E081-23361
chr7158268055158268105E081-22322
chr7158268454158268504E081-21923
chr7158268626158268671E081-21756
chr7158269069158269701E081-20726
chr7158269812158269912E081-20515
chr7158271167158271240E081-19187
chr7158271294158271344E081-19083
chr7158271793158271843E081-18584
chr7158271889158272042E081-18385
chr7158272075158272254E081-18173
chr7158272321158272388E081-18039
chr7158272406158272498E081-17929
chr7158272798158272861E081-17566
chr7158272926158272976E081-17451
chr7158273027158273077E081-17350
chr7158278364158278424E081-12003
chr7158279162158279212E081-11215
chr7158279230158279274E081-11153
chr7158279409158279476E081-10951
chr7158279516158279566E081-10861
chr7158279681158279731E081-10696
chr7158280384158280541E081-9886
chr7158281430158281610E081-8817
chr7158284569158284650E081-5777
chr7158284913158284981E081-5446
chr7158284986158285306E081-5121
chr7158285545158285597E081-4830
chr7158285639158285679E081-4748
chr7158285937158285987E081-4440
chr7158286660158286756E081-3671
chr7158286915158287200E081-3227
chr7158287211158287261E081-3166
chr7158287281158287398E081-3029
chr7158287636158287838E081-2589
chr7158287847158288011E081-2416
chr7158288077158288906E081-1521
chr7158288916158288994E081-1433
chr7158289208158289266E081-1161
chr7158290100158290281E081-146
chr7158290522158290602E08195
chr7158290724158290856E081297
chr7158290896158290936E081469
chr7158291012158291056E081585
chr7158291217158291553E081790
chr7158291556158291804E0811129
chr7158291941158292019E0811514
chr7158292833158292905E0812406
chr7158293036158293237E0812609
chr7158293275158293718E0812848
chr7158294162158294253E0813735
chr7158294360158294413E0813933
chr7158294521158294608E0814094
chr7158294673158294915E0814246
chr7158310658158310739E08120231
chr7158311068158311118E08120641
chr7158311315158311365E08120888
chr7158311751158311917E08121324
chr7158311975158312061E08121548
chr7158312116158312272E08121689
chr7158312359158312968E08121932
chr7158313489158313558E08123062
chr7158313666158313778E08123239
chr7158318868158318923E08128441
chr7158318938158319079E08128511
chr7158320824158320923E08130397
chr7158322258158322308E08131831
chr7158322504158322554E08132077
chr7158323215158323345E08132788
chr7158323396158323448E08132969
chr7158323630158323786E08133203
chr7158323795158323835E08133368
chr7158323850158324012E08133423
chr7158324528158324624E08134101
chr7158324721158324771E08134294
chr7158324930158325179E08134503
chr7158325289158325547E08134862
chr7158325559158325609E08135132
chr7158325619158325706E08135192
chr7158325832158325872E08135405
chr7158327182158327244E08136755
chr7158328306158328395E08137879
chr7158333616158333674E08143189
chr7158333913158334198E08143486
chr7158334216158334621E08143789
chr7158334633158334729E08144206
chr7158335277158335372E08144850
chr7158335893158335943E08145466
chr7158336235158336383E08145808
chr7158336490158336530E08146063
chr7158336648158336718E08146221
chr7158337947158338057E08147520
chr7158338086158338241E08147659
chr7158340147158340278E08149720
chr7158240443158240497E082-49930
chr7158240663158240736E082-49691
chr7158260165158260425E082-30002
chr7158260482158260618E082-29809
chr7158260662158260973E082-29454
chr7158260990158261190E082-29237
chr7158261304158261384E082-29043
chr7158261568158261678E082-28749
chr7158265260158265533E082-24894
chr7158265577158265692E082-24735
chr7158266589158266890E082-23537
chr7158267016158267066E082-23361
chr7158268055158268105E082-22322
chr7158269812158269912E082-20515
chr7158280384158280541E082-9886
chr7158284986158285306E082-5121
chr7158285545158285597E082-4830
chr7158285639158285679E082-4748
chr7158285937158285987E082-4440
chr7158286660158286756E082-3671
chr7158286915158287200E082-3227
chr7158287211158287261E082-3166
chr7158287281158287398E082-3029
chr7158287636158287838E082-2589
chr7158292833158292905E0822406
chr7158293036158293237E0822609
chr7158293275158293718E0822848
chr7158294162158294253E0823735
chr7158294360158294413E0823933
chr7158294521158294608E0824094
chr7158294673158294915E0824246
chr7158302120158302203E08211693
chr7158311751158311917E08221324
chr7158311975158312061E08221548
chr7158312116158312272E08221689
chr7158312359158312968E08221932
chr7158313489158313558E08223062
chr7158313666158313778E08223239
chr7158317647158317707E08227220
chr7158317946158318048E08227519
chr7158318050158318123E08227623
chr7158318277158318329E08227850
chr7158318490158318530E08228063
chr7158318670158318730E08228243
chr7158318868158318923E08228441
chr7158318938158319079E08228511
chr7158322504158322554E08232077
chr7158323215158323345E08232788
chr7158323396158323448E08232969
chr7158323630158323786E08233203
chr7158323795158323835E08233368
chr7158323850158324012E08233423
chr7158333913158334198E08243486
chr7158335893158335943E08245466
chr7158336235158336383E08245808










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr7158253204158253298E072-37129
chr7158253204158253298E073-37129