rs2465810

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

PTPRB : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0171 (5144/29952,GnomAD)
G=0173 (5060/29118,TOPMED)
G=0234 (1172/5008,1000G)
G=0093 (358/3854,ALSPAC)
G=0095 (351/3708,TWINSUK)

Position: chr12:70621500 (GRCh38.p7) (12q15)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 57 Enhancers around

Promoter: 29 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.70621500A>G
GRCh37.p13 chr 12	NC_000012.11:g.71015280A>G
PTPRB RefSeqGene	NG_029940.1:g.20941T>C

Gene: PTPRB, protein tyrosine phosphatase, receptor type B(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PTPRB transcript variant 1	NM_001109754.2:c.	N/A	Intron Variant
PTPRB transcript variant 3	NM_001206971.1:c.	N/A	Genic Upstream Transcript Variant
PTPRB transcript variant 4	NM_001206972.1:c.	N/A	Genic Upstream Transcript Variant
PTPRB transcript variant 2	NM_002837.4:c.	N/A	Genic Upstream Transcript Variant
PTPRB transcript variant X1	XM_006719528.1:c.	N/A	Intron Variant
PTPRB transcript variant X2	XM_011538614.1:c.	N/A	Intron Variant
PTPRB transcript variant X3	XM_017019723.1:c.	N/A	Intron Variant
PTPRB transcript variant X4	XM_006719529.3:c.	N/A	Genic Upstream Transcript Variant
PTPRB transcript variant X4	XM_017019724.1:c.	N/A	Genic Upstream Transcript Variant
PTPRB transcript variant X5	XR_944651.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.734	G=0.266
1000Genomes	American	Sub	694	A=0.860	G=0.140
1000Genomes	East Asian	Sub	1008	A=0.656	G=0.344
1000Genomes	Europe	Sub	1006	A=0.876	G=0.124
1000Genomes	Global	Study-wide	5008	A=0.766	G=0.234
1000Genomes	South Asian	Sub	978	A=0.740	G=0.260
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.907	G=0.093
The Genome Aggregation Database	African	Sub	8716	A=0.750	G=0.250
The Genome Aggregation Database	American	Sub	838	A=0.910	G=0.090
The Genome Aggregation Database	East Asian	Sub	1618	A=0.660	G=0.340
The Genome Aggregation Database	Europe	Sub	18478	A=0.875	G=0.124
The Genome Aggregation Database	Global	Study-wide	29952	A=0.828	G=0.171
The Genome Aggregation Database	Other	Sub	302	A=0.900	G=0.100
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.826	G=0.173
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.905	G=0.095

PMID	Title	Author	Journal
19268276	Genome-wide association study of smoking initiation and current smoking.	Vink JM	Am J Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs2465810	0.000503	nicotine smoking	19268276

eQTL of rs2465810 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 rs2465810 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 )
chr12	70970197	70970251	E067	-45029
chr12	70970264	70970416	E067	-44864
chr12	70970419	70971243	E067	-44037
chr12	71057799	71058017	E067	42519
chr12	71058049	71058563	E067	42769
chr12	71058597	71058990	E067	43317
chr12	70965720	70965913	E068	-49367
chr12	70965919	70965981	E068	-49299
chr12	70966036	70966129	E068	-49151
chr12	70970197	70970251	E068	-45029
chr12	70970264	70970416	E068	-44864
chr12	70970419	70971243	E068	-44037
chr12	70983662	70983747	E068	-31533
chr12	70983776	70984335	E068	-30945
chr12	71042129	71042283	E068	26849
chr12	71042288	71042338	E068	27008
chr12	71042340	71042441	E068	27060
chr12	71042493	71042559	E068	27213
chr12	71042590	71042640	E068	27310
chr12	71042645	71042952	E068	27365
chr12	71057799	71058017	E068	42519
chr12	71058597	71058990	E068	43317
chr12	70969952	70970002	E069	-45278
chr12	70970197	70970251	E069	-45029
chr12	70970264	70970416	E069	-44864
chr12	70983776	70984335	E069	-30945
chr12	71054617	71054679	E069	39337
chr12	71054704	71054980	E069	39424
chr12	71058049	71058563	E069	42769
chr12	71059030	71059115	E069	43750
chr12	70965720	70965913	E070	-49367
chr12	70965919	70965981	E070	-49299
chr12	71031670	71031896	E070	16390
chr12	71050722	71050820	E070	35442
chr12	71050899	71050953	E070	35619
chr12	71051197	71051891	E070	35917
chr12	71054617	71054679	E070	39337
chr12	71054704	71054980	E070	39424
chr12	71060054	71060116	E070	44774
chr12	70968960	70969048	E071	-46232
chr12	70969952	70970002	E071	-45278
chr12	70970197	70970251	E071	-45029
chr12	70970264	70970416	E071	-44864
chr12	70983662	70983747	E071	-31533
chr12	70983776	70984335	E071	-30945
chr12	70992683	70992866	E071	-22414
chr12	70993441	70993670	E071	-21610
chr12	71058597	71058990	E071	43317
chr12	71059030	71059115	E071	43750
chr12	71057799	71058017	E072	42519
chr12	71058597	71058990	E072	43317
chr12	71059030	71059115	E072	43750
chr12	70970419	70971243	E073	-44037
chr12	71055507	71055981	E073	40227
chr12	71058597	71058990	E073	43317
chr12	70992683	70992866	E074	-22414
chr12	70993441	70993670	E074	-21610

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr12	71002770	71002827	E067	-12453
chr12	71002938	71003062	E067	-12218
chr12	71003082	71003365	E067	-11915
chr12	71003439	71004572	E067	-10708
chr12	71002770	71002827	E068	-12453
chr12	71002938	71003062	E068	-12218
chr12	71003082	71003365	E068	-11915
chr12	71003439	71004572	E068	-10708
chr12	71002770	71002827	E069	-12453
chr12	71002938	71003062	E069	-12218
chr12	71003082	71003365	E069	-11915
chr12	71003439	71004572	E069	-10708
chr12	71002770	71002827	E071	-12453
chr12	71002938	71003062	E071	-12218
chr12	71003082	71003365	E071	-11915
chr12	71003439	71004572	E071	-10708
chr12	71002770	71002827	E072	-12453
chr12	71002938	71003062	E072	-12218
chr12	71003082	71003365	E072	-11915
chr12	71003439	71004572	E072	-10708
chr12	71002770	71002827	E073	-12453
chr12	71002938	71003062	E073	-12218
chr12	71003082	71003365	E073	-11915
chr12	71003439	71004572	E073	-10708
chr12	71002770	71002827	E074	-12453
chr12	71002938	71003062	E074	-12218
chr12	71003082	71003365	E074	-11915
chr12	71003439	71004572	E074	-10708
chr12	71003439	71004572	E082	-10708