rs2241749

Homo sapiens
G>A
PTPRN2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0233 (6903/29548,GnomAD)
A=0273 (7965/29118,TOPMED)
A=0331 (1659/5008,1000G)
A=0094 (362/3854,ALSPAC)
A=0096 (357/3708,TWINSUK)
chr7:157950773 (GRCh38.p7) (7q36.3)
ND
GWASdb2
1   publication(s)
See rs on genome
74 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 7NC_000007.14:g.157950773G>A
GRCh37.p13 chr 7NC_000007.13:g.157743465G>A
PTPRN2 RefSeqGeneNG_029966.1:g.642018C>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
1000GenomesAfricanSub1322G=0.521A=0.479
1000GenomesAmericanSub694G=0.650A=0.350
1000GenomesEast AsianSub1008G=0.532A=0.468
1000GenomesEuropeSub1006G=0.876A=0.124
1000GenomesGlobalStudy-wide5008G=0.669A=0.331
1000GenomesSouth AsianSub978G=0.810A=0.190
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.906A=0.094
The Genome Aggregation DatabaseAfricanSub8640G=0.569A=0.431
The Genome Aggregation DatabaseAmericanSub834G=0.580A=0.420
The Genome Aggregation DatabaseEast AsianSub1620G=0.519A=0.481
The Genome Aggregation DatabaseEuropeSub18154G=0.889A=0.110
The Genome Aggregation DatabaseGlobalStudy-wide29548G=0.766A=0.233
The Genome Aggregation DatabaseOtherSub300G=0.840A=0.160
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.726A=0.273
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.904A=0.096
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
rs22417496.7E-05nicotine dependence (smoking)22377092

eQTL of rs2241749 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 rs2241749 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 )
chr7157695843157695901E067-47564
chr7157693607157693647E070-49818
chr7157693682157693732E070-49733
chr7157695843157695901E070-47564
chr7157695950157696087E070-47378
chr7157696514157696623E070-46842
chr7157696652157696796E070-46669
chr7157696825157696869E070-46596
chr7157697181157697266E070-46199
chr7157697349157697556E070-45909
chr7157697754157697851E070-45614
chr7157697948157698140E070-45325
chr7157698304157698701E070-44764
chr7157698793157698894E070-44571
chr7157699067157699117E070-44348
chr7157699120157699160E070-44305
chr7157699189157699239E070-44226
chr7157699518157699599E070-43866
chr7157722432157722536E070-20929
chr7157790146157790221E07046681
chr7157790507157790601E07047042
chr7157790825157790870E07047360
chr7157790895157790949E07047430
chr7157791042157791119E07047577
chr7157791159157791209E07047694
chr7157791378157791722E07047913
chr7157695843157695901E072-47564
chr7157695950157696087E072-47378
chr7157695843157695901E073-47564
chr7157695950157696087E073-47378
chr7157696514157696623E073-46842
chr7157696652157696796E073-46669
chr7157696825157696869E073-46596
chr7157776218157776299E07332753
chr7157776346157776728E07332881
chr7157695950157696087E081-47378
chr7157696514157696623E081-46842
chr7157696652157696796E081-46669
chr7157696825157696869E081-46596
chr7157697181157697266E081-46199
chr7157697349157697556E081-45909
chr7157697754157697851E081-45614
chr7157697948157698140E081-45325
chr7157698304157698701E081-44764
chr7157698793157698894E081-44571
chr7157699067157699117E081-44348
chr7157699120157699160E081-44305
chr7157699189157699239E081-44226
chr7157700931157701018E081-42447
chr7157721723157721994E081-21471
chr7157722432157722536E081-20929
chr7157723927157724084E081-19381
chr7157724139157724324E081-19141
chr7157763038157763088E08119573
chr7157764138157764547E08120673
chr7157789521157789611E08146056
chr7157789626157789701E08146161
chr7157790146157790221E08146681
chr7157790507157790601E08147042
chr7157790825157790870E08147360
chr7157790895157790949E08147430
chr7157791042157791119E08147577
chr7157791159157791209E08147694
chr7157791378157791722E08147913
chr7157695950157696087E082-47378
chr7157696825157696869E082-46596
chr7157697754157697851E082-45614
chr7157697948157698140E082-45325
chr7157698304157698701E082-44764
chr7157698793157698894E082-44571
chr7157721723157721994E082-21471
chr7157789521157789611E08246056
chr7157789626157789701E08246161
chr7157790146157790221E08246681