rs11772608

Homo sapiens
T>C
PTPRN2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0180 (5398/29968,GnomAD)
T==0206 (6018/29118,TOPMED)
T==0224 (1123/5008,1000G)
T==0112 (433/3854,ALSPAC)
T==0104 (385/3708,TWINSUK)
chr7:158026633 (GRCh38.p7) (7q36.3)
AD
GWASdb2
1   publication(s)
See rs on genome
177 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 7NC_000007.14:g.158026633T>C
GRCh37.p13 chr 7NC_000007.13:g.157819325T>C
PTPRN2 RefSeqGeneNG_029966.1:g.566158A>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=0.343C=0.657
1000GenomesAmericanSub694T=0.190C=0.810
1000GenomesEast AsianSub1008T=0.188C=0.812
1000GenomesEuropeSub1006T=0.120C=0.880
1000GenomesGlobalStudy-wide5008T=0.224C=0.776
1000GenomesSouth AsianSub978T=0.230C=0.770
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.112C=0.888
The Genome Aggregation DatabaseAfricanSub8722T=0.311C=0.689
The Genome Aggregation DatabaseAmericanSub838T=0.190C=0.810
The Genome Aggregation DatabaseEast AsianSub1616T=0.165C=0.835
The Genome Aggregation DatabaseEuropeSub18490T=0.118C=0.882
The Genome Aggregation DatabaseGlobalStudy-wide29968T=0.180C=0.819
The Genome Aggregation DatabaseOtherSub302T=0.250C=0.750
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.206C=0.793
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.104C=0.896
PMID Title Author Journal
24277619ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.Quillen EEAm J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID p-value Traits Study
rs117726080.000723alcohol dependence24277619

eQTL of rs11772608 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 rs11772608 in Fetal Brain

Probe ID Position Gene beta p-value
cg12440927chr7:157791721PTPRN2-0.06918505223858618.6371e-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 )
chr7157807795157807900E067-11425
chr7157808000157808114E067-11211
chr7157808171157808309E067-11016
chr7157808705157810397E067-8928
chr7157808171157808309E068-11016
chr7157808705157810397E068-8928
chr7157810409157810464E068-8861
chr7157810496157810581E068-8744
chr7157817030157817080E068-2245
chr7157825544157825740E0686219
chr7157869069157869113E06849744
chr7157807795157807900E069-11425
chr7157808000157808114E069-11211
chr7157808171157808309E069-11016
chr7157808705157810397E069-8928
chr7157810409157810464E069-8861
chr7157810496157810581E069-8744
chr7157817030157817080E069-2245
chr7157790146157790221E070-29104
chr7157790507157790601E070-28724
chr7157790825157790870E070-28455
chr7157790895157790949E070-28376
chr7157791042157791119E070-28206
chr7157791159157791209E070-28116
chr7157791378157791722E070-27603
chr7157794344157794551E070-24774
chr7157794561157794681E070-24644
chr7157798374157798601E070-20724
chr7157799068157799118E070-20207
chr7157800632157800687E070-18638
chr7157801103157801225E070-18100
chr7157801306157801445E070-17880
chr7157801656157801831E070-17494
chr7157801963157802112E070-17213
chr7157802395157802537E070-16788
chr7157802730157802774E070-16551
chr7157802948157802998E070-16327
chr7157807795157807900E070-11425
chr7157810812157811356E070-7969
chr7157811747157811844E070-7481
chr7157812781157812831E070-6494
chr7157813552157813596E070-5729
chr7157813928157813983E070-5342
chr7157814080157814169E070-5156
chr7157816386157816426E070-2899
chr7157816475157816607E070-2718
chr7157816626157816690E070-2635
chr7157817030157817080E070-2245
chr7157817806157817858E070-1467
chr7157818215157818284E070-1041
chr7157818318157818368E070-957
chr7157818468157818548E070-777
chr7157818596157818690E070-635
chr7157818791157818885E070-440
chr7157818941157818991E070-334
chr7157820875157820945E0701550
chr7157821412157821564E0702087
chr7157823537157823620E0704212
chr7157824021157824071E0704696
chr7157824334157824384E0705009
chr7157825544157825740E0706219
chr7157836091157836138E07016766
chr7157836324157836446E07016999
chr7157836478157836871E07017153
chr7157837106157837181E07017781
chr7157837241157837409E07017916
chr7157842771157842821E07023446
chr7157843137157843200E07023812
chr7157843305157843399E07023980
chr7157843436157843514E07024111
chr7157844876157845140E07025551
chr7157845190157845283E07025865
chr7157845965157846097E07026640
chr7157846136157846364E07026811
chr7157846439157846489E07027114
chr7157847273157847350E07027948
chr7157865800157865970E07046475
chr7157868787157868872E07049462
chr7157868971157869040E07049646
chr7157869069157869113E07049744
chr7157808705157810397E071-8928
chr7157816386157816426E071-2899
chr7157816475157816607E071-2718
chr7157816626157816690E071-2635
chr7157817030157817080E071-2245
chr7157808705157810397E072-8928
chr7157825544157825740E0726219
chr7157868787157868872E07249462
chr7157776218157776299E073-43026
chr7157776346157776728E073-42597
chr7157808171157808309E073-11016
chr7157810647157810777E073-8548
chr7157825544157825740E0736219
chr7157856623157856683E07337298
chr7157856739157856866E07337414
chr7157867775157867836E07348450
chr7157808705157810397E074-8928
chr7157789521157789611E081-29714
chr7157789626157789701E081-29624
chr7157790146157790221E081-29104
chr7157790507157790601E081-28724
chr7157790825157790870E081-28455
chr7157790895157790949E081-28376
chr7157791042157791119E081-28206
chr7157791159157791209E081-28116
chr7157791378157791722E081-27603
chr7157794344157794551E081-24774
chr7157794561157794681E081-24644
chr7157796871157797023E081-22302
chr7157800632157800687E081-18638
chr7157801103157801225E081-18100
chr7157801306157801445E081-17880
chr7157801656157801831E081-17494
chr7157801963157802112E081-17213
chr7157802395157802537E081-16788
chr7157802730157802774E081-16551
chr7157808000157808114E081-11211
chr7157808171157808309E081-11016
chr7157808705157810397E081-8928
chr7157810409157810464E081-8861
chr7157810496157810581E081-8744
chr7157810647157810777E081-8548
chr7157810812157811356E081-7969
chr7157811747157811844E081-7481
chr7157811845157811930E081-7395
chr7157812781157812831E081-6494
chr7157813552157813596E081-5729
chr7157813928157813983E081-5342
chr7157814080157814169E081-5156
chr7157816386157816426E081-2899
chr7157816475157816607E081-2718
chr7157816626157816690E081-2635
chr7157823537157823620E0814212
chr7157824021157824071E0814696
chr7157824334157824384E0815009
chr7157835751157835801E08116426
chr7157836091157836138E08116766
chr7157836324157836446E08116999
chr7157836478157836871E08117153
chr7157837106157837181E08117781
chr7157837241157837409E08117916
chr7157843305157843399E08123980
chr7157843436157843514E08124111
chr7157844876157845140E08125551
chr7157845190157845283E08125865
chr7157845965157846097E08126640
chr7157846136157846364E08126811
chr7157846439157846489E08127114
chr7157865800157865970E08146475
chr7157866071157866152E08146746
chr7157866943157867197E08147618
chr7157867775157867836E08148450
chr7157789521157789611E082-29714
chr7157789626157789701E082-29624
chr7157790146157790221E082-29104
chr7157794344157794551E082-24774
chr7157810409157810464E082-8861
chr7157810496157810581E082-8744
chr7157810647157810777E082-8548
chr7157810812157811356E082-7969
chr7157811747157811844E082-7481
chr7157811845157811930E082-7395
chr7157825544157825740E0826219
chr7157835437157835487E08216112
chr7157835751157835801E08216426
chr7157836091157836138E08216766
chr7157836324157836446E08216999
chr7157836478157836871E08217153
chr7157843305157843399E08223980
chr7157843436157843514E08224111
chr7157844876157845140E08225551
chr7157845190157845283E08225865
chr7157845965157846097E08226640
chr7157846136157846364E08226811
chr7157861540157861605E08242215
chr7157861667157861774E08242342
chr7157868008157868068E08248683