rs2164220

Homo sapiens
C>T
PTPRN2 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0108 (3243/29980,GnomAD)
T=0083 (2438/29118,TOPMED)
T=0173 (868/5008,1000G)
T=0077 (296/3854,ALSPAC)
T=0084 (313/3708,TWINSUK)
chr7:157962533 (GRCh38.p7) (7q36.3)
ND
GWASdb2
2   publication(s)
See rs on genome
52 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 7NC_000007.14:g.157962533C>T
GRCh37.p13 chr 7NC_000007.13:g.157755225C>T
PTPRN2 RefSeqGeneNG_029966.1:g.630258G>A

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=0.983T=0.017
1000GenomesAmericanSub694C=0.690T=0.310
1000GenomesEast AsianSub1008C=0.639T=0.361
1000GenomesEuropeSub1006C=0.886T=0.114
1000GenomesGlobalStudy-wide5008C=0.827T=0.173
1000GenomesSouth AsianSub978C=0.840T=0.160
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.923T=0.077
The Genome Aggregation DatabaseAfricanSub8730C=0.971T=0.029
The Genome Aggregation DatabaseAmericanSub838C=0.630T=0.370
The Genome Aggregation DatabaseEast AsianSub1616C=0.632T=0.368
The Genome Aggregation DatabaseEuropeSub18494C=0.888T=0.111
The Genome Aggregation DatabaseGlobalStudy-wide29980C=0.891T=0.108
The Genome Aggregation DatabaseOtherSub302C=0.920T=0.080
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.916T=0.083
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.916T=0.084
PMID Title Author Journal
22837378Genome-wide association studies identify CHRNA5/3 and HTR4 in the development of airflow obstruction.Wilk JBAm J Respir Crit Care Med
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
rs21642205.04E-05nicotine dependence (smoking)22377092

eQTL of rs2164220 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 rs2164220 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 )
chr7157722432157722536E070-32689
chr7157790146157790221E07034921
chr7157790507157790601E07035282
chr7157790825157790870E07035600
chr7157790895157790949E07035670
chr7157791042157791119E07035817
chr7157791159157791209E07035934
chr7157791378157791722E07036153
chr7157794344157794551E07039119
chr7157794561157794681E07039336
chr7157798374157798601E07043149
chr7157799068157799118E07043843
chr7157800632157800687E07045407
chr7157801103157801225E07045878
chr7157801306157801445E07046081
chr7157801656157801831E07046431
chr7157801963157802112E07046738
chr7157802395157802537E07047170
chr7157802730157802774E07047505
chr7157802948157802998E07047723
chr7157776218157776299E07320993
chr7157776346157776728E07321121
chr7157721723157721994E081-33231
chr7157722432157722536E081-32689
chr7157723927157724084E081-31141
chr7157724139157724324E081-30901
chr7157763038157763088E0817813
chr7157764138157764547E0818913
chr7157789521157789611E08134296
chr7157789626157789701E08134401
chr7157790146157790221E08134921
chr7157790507157790601E08135282
chr7157790825157790870E08135600
chr7157790895157790949E08135670
chr7157791042157791119E08135817
chr7157791159157791209E08135934
chr7157791378157791722E08136153
chr7157794344157794551E08139119
chr7157794561157794681E08139336
chr7157796871157797023E08141646
chr7157800632157800687E08145407
chr7157801103157801225E08145878
chr7157801306157801445E08146081
chr7157801656157801831E08146431
chr7157801963157802112E08146738
chr7157802395157802537E08147170
chr7157802730157802774E08147505
chr7157721723157721994E082-33231
chr7157789521157789611E08234296
chr7157789626157789701E08234401
chr7157790146157790221E08234921
chr7157794344157794551E08239119