rs1638755

Homo sapiens
C>T
PTPRN2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0096 (2887/29934,GnomAD)
T=0121 (3540/29118,TOPMED)
T=0149 (747/5008,1000G)
T=0024 (91/3854,ALSPAC)
T=0020 (73/3708,TWINSUK)
chr7:157760120 (GRCh38.p7) (7q36.3)
ND
GWASdb2
1   publication(s)
See rs on genome
107 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 7NC_000007.14:g.157760120C>T
GRCh37.p13 chr 7NC_000007.13:g.157552812C>T
PTPRN2 RefSeqGeneNG_029966.1:g.832671G>A
GRCh38.p7 chr 7 alt locus HSCHR7_2_CTG7NT_187563.1:g.65968C>T

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
1000GenomesAfricanSub1322C=0.766T=0.234
1000GenomesAmericanSub694C=0.800T=0.200
1000GenomesEast AsianSub1008C=0.766T=0.234
1000GenomesEuropeSub1006C=0.971T=0.029
1000GenomesGlobalStudy-wide5008C=0.851T=0.149
1000GenomesSouth AsianSub978C=0.970T=0.030
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.976T=0.024
The Genome Aggregation DatabaseAfricanSub8710C=0.793T=0.207
The Genome Aggregation DatabaseAmericanSub838C=0.770T=0.230
The Genome Aggregation DatabaseEast AsianSub1614C=0.770T=0.230
The Genome Aggregation DatabaseEuropeSub18470C=0.972T=0.027
The Genome Aggregation DatabaseGlobalStudy-wide29934C=0.903T=0.096
The Genome Aggregation DatabaseOtherSub302C=0.990T=0.010
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.878T=0.121
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.980T=0.020
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
rs16387550.000129nicotine smoking19268276

eQTL of rs1638755 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr7:157552812UBE3CENSG00000009335.13C>T2.3196e-2621205Cerebellum

meQTL of rs1638755 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 )
chr7157574527157574577E06721715
chr7157576667157576733E06723855
chr7157576774157577017E06723962
chr7157543605157543655E068-9157
chr7157543852157543943E068-8869
chr7157574648157574702E06821836
chr7157574922157575098E06822110
chr7157576774157577017E06823962
chr7157560217157560287E0697405
chr7157561817157562193E0699005
chr7157562224157562269E0699412
chr7157562290157562442E0699478
chr7157562452157562492E0699640
chr7157574527157574577E06921715
chr7157574648157574702E06921836
chr7157576774157577017E06923962
chr7157577601157577961E06924789
chr7157600033157600144E06947221
chr7157527514157527579E070-25233
chr7157527801157527891E070-24921
chr7157528113157528167E070-24645
chr7157528586157528636E070-24176
chr7157529002157529078E070-23734
chr7157530610157531206E070-21606
chr7157542982157543036E070-9776
chr7157543303157543393E070-9419
chr7157543605157543655E070-9157
chr7157543852157543943E070-8869
chr7157543985157544177E070-8635
chr7157544191157544287E070-8525
chr7157560026157560076E0707214
chr7157560217157560287E0707405
chr7157560320157560531E0707508
chr7157560616157560759E0707804
chr7157560979157561050E0708167
chr7157561505157561586E0708693
chr7157561597157561794E0708785
chr7157561817157562193E0709005
chr7157574922157575098E07022110
chr7157576667157576733E07023855
chr7157576774157577017E07023962
chr7157587024157587261E07034212
chr7157587374157587841E07034562
chr7157587863157587998E07035051
chr7157574648157574702E07121836
chr7157577601157577961E07124789
chr7157560217157560287E0727405
chr7157561597157561794E0728785
chr7157561817157562193E0729005
chr7157562224157562269E0729412
chr7157562290157562442E0729478
chr7157574527157574577E07221715
chr7157574648157574702E07221836
chr7157575521157575643E07322709
chr7157576667157576733E07323855
chr7157576774157577017E07323962
chr7157577601157577961E07424789
chr7157514627157514691E081-38121
chr7157514888157515029E081-37783
chr7157515075157515160E081-37652
chr7157515197157515332E081-37480
chr7157515659157515889E081-36923
chr7157515909157515953E081-36859
chr7157516027157516107E081-36705
chr7157516391157516583E081-36229
chr7157543605157543655E081-9157
chr7157543852157543943E081-8869
chr7157543985157544177E081-8635
chr7157544191157544287E081-8525
chr7157544322157544470E081-8342
chr7157544771157544821E081-7991
chr7157551020157551081E081-1731
chr7157551090157551170E081-1642
chr7157560217157560287E0817405
chr7157560320157560531E0817508
chr7157560616157560759E0817804
chr7157560979157561050E0818167
chr7157561505157561586E0818693
chr7157561597157561794E0818785
chr7157561817157562193E0819005
chr7157562224157562269E0819412
chr7157562290157562442E0819478
chr7157562452157562492E0819640
chr7157562750157562922E0819938
chr7157587374157587841E08134562
chr7157587863157587998E08135051
chr7157514888157515029E082-37783
chr7157515075157515160E082-37652
chr7157515197157515332E082-37480
chr7157515659157515889E082-36923
chr7157515909157515953E082-36859
chr7157516027157516107E082-36705
chr7157516391157516583E082-36229
chr7157530610157531206E082-21606
chr7157531254157531304E082-21508
chr7157543985157544177E082-8635
chr7157544191157544287E082-8525
chr7157559308157559381E0826496
chr7157560026157560076E0827214
chr7157560217157560287E0827405
chr7157560320157560531E0827508
chr7157561597157561794E0828785
chr7157561817157562193E0829005
chr7157562224157562269E0829412
chr7157562290157562442E0829478
chr7157562452157562492E0829640
chr7157562750157562922E0829938