rs4807016

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

PTPRS : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0314 (9401/29944,GnomAD)
A=0283 (8254/29118,TOPMED)
A=0408 (2043/5008,1000G)
A=0340 (1309/3854,ALSPAC)
A=0335 (1244/3708,TWINSUK)

Position: chr19:5258479 (GRCh38.p7) (19p13.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 199 Enhancers around

Promoter: 9 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 19	NC_000019.10:g.5258479G>A
GRCh37.p13 chr 19	NC_000019.9:g.5258490G>A
PTPRS RefSeqGene	NG_033964.1:g.87325C>T

Gene: PTPRS, protein tyrosine phosphatase, receptor type S(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PTPRS transcript variant 1	NM_002850.3:c.	N/A	Intron Variant
PTPRS transcript variant 3	NM_130853.2:c.	N/A	Intron Variant
PTPRS transcript variant 2	NM_130854.2:c.	N/A	Intron Variant
PTPRS transcript variant 4	NM_130855.2:c.	N/A	Intron Variant
PTPRS transcript variant X4	XM_005259600.2:c.	N/A	Intron Variant
PTPRS transcript variant X9	XM_005259606.2:c.	N/A	Intron Variant
PTPRS transcript variant X11	XM_005259607.2:c.	N/A	Intron Variant
PTPRS transcript variant X16	XM_005259609.1:c.	N/A	Intron Variant
PTPRS transcript variant X17	XM_005259610.1:c.	N/A	Intron Variant
PTPRS transcript variant X18	XM_011528157.2:c.	N/A	Intron Variant
PTPRS transcript variant X1	XM_017027065.1:c.	N/A	Intron Variant
PTPRS transcript variant X2	XM_017027066.1:c.	N/A	Intron Variant
PTPRS transcript variant X3	XM_017027067.1:c.	N/A	Intron Variant
PTPRS transcript variant X5	XM_017027068.1:c.	N/A	Intron Variant
PTPRS transcript variant X6	XM_017027069.1:c.	N/A	Intron Variant
PTPRS transcript variant X7	XM_017027070.1:c.	N/A	Intron Variant
PTPRS transcript variant X8	XM_017027071.1:c.	N/A	Intron Variant
PTPRS transcript variant X10	XM_017027072.1:c.	N/A	Intron Variant
PTPRS transcript variant X13	XM_017027074.1:c.	N/A	Intron Variant
PTPRS transcript variant X14	XM_017027075.1:c.	N/A	Intron Variant
PTPRS transcript variant X15	XM_017027076.1:c.	N/A	Intron Variant
PTPRS transcript variant X19	XM_011528158.2:c.	N/A	Genic Upstream Transcript Variant
PTPRS transcript variant X12	XM_017027073.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.811	A=0.189
1000Genomes	American	Sub	694	G=0.570	A=0.430
1000Genomes	East Asian	Sub	1008	G=0.236	A=0.764
1000Genomes	Europe	Sub	1006	G=0.691	A=0.309
1000Genomes	Global	Study-wide	5008	G=0.592	A=0.408
1000Genomes	South Asian	Sub	978	G=0.570	A=0.430
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.660	A=0.340
The Genome Aggregation Database	African	Sub	8726	G=0.789	A=0.211
The Genome Aggregation Database	American	Sub	838	G=0.580	A=0.420
The Genome Aggregation Database	East Asian	Sub	1614	G=0.288	A=0.712
The Genome Aggregation Database	Europe	Sub	18464	G=0.678	A=0.321
The Genome Aggregation Database	Global	Study-wide	29944	G=0.686	A=0.314
The Genome Aggregation Database	Other	Sub	302	G=0.600	A=0.400
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.716	A=0.283
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.665	A=0.335

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res
20111712	Risk of ovarian cancer and inherited variants in relapse-associated genes.	Peedicayil A	PLoS One

P-Value

SNP ID	p-value	Traits	Study
rs4807016	0.0000829	alcoholism	pha002892
rs4807016	0.000083	alcohol dependence(early age of onset)	20201924
rs4807016	0.00012	alcohol dependence	20201924

eQTL of rs4807016 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 rs4807016 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 )
chr19	5247591	5247658	E067	-10832
chr19	5248160	5248251	E067	-10239
chr19	5248396	5248442	E067	-10048
chr19	5248633	5248726	E067	-9764
chr19	5248730	5248783	E067	-9707
chr19	5249695	5249745	E067	-8745
chr19	5288108	5288365	E067	29618
chr19	5288379	5288615	E067	29889
chr19	5288623	5288768	E067	30133
chr19	5289320	5289430	E067	30830
chr19	5289674	5289946	E067	31184
chr19	5290123	5290175	E067	31633
chr19	5290486	5290584	E067	31996
chr19	5291080	5291233	E067	32590
chr19	5291352	5291456	E067	32862
chr19	5291578	5291681	E067	33088
chr19	5308158	5308326	E067	49668
chr19	5246714	5246899	E068	-11591
chr19	5247591	5247658	E068	-10832
chr19	5248160	5248251	E068	-10239
chr19	5248396	5248442	E068	-10048
chr19	5248633	5248726	E068	-9764
chr19	5248730	5248783	E068	-9707
chr19	5250247	5250406	E068	-8084
chr19	5287825	5287928	E068	29335
chr19	5288108	5288365	E068	29618
chr19	5288379	5288615	E068	29889
chr19	5288623	5288768	E068	30133
chr19	5289320	5289430	E068	30830
chr19	5289674	5289946	E068	31184
chr19	5290123	5290175	E068	31633
chr19	5291080	5291233	E068	32590
chr19	5308158	5308326	E068	49668
chr19	5246392	5246442	E069	-12048
chr19	5246714	5246899	E069	-11591
chr19	5247591	5247658	E069	-10832
chr19	5250247	5250406	E069	-8084
chr19	5250476	5250618	E069	-7872
chr19	5287552	5287789	E069	29062
chr19	5287825	5287928	E069	29335
chr19	5288108	5288365	E069	29618
chr19	5288379	5288615	E069	29889
chr19	5288623	5288768	E069	30133
chr19	5289320	5289430	E069	30830
chr19	5289674	5289946	E069	31184
chr19	5290123	5290175	E069	31633
chr19	5290486	5290584	E069	31996
chr19	5294466	5294705	E069	35976
chr19	5294736	5294832	E069	36246
chr19	5308158	5308326	E069	49668
chr19	5247591	5247658	E070	-10832
chr19	5248160	5248251	E070	-10239
chr19	5248396	5248442	E070	-10048
chr19	5248633	5248726	E070	-9764
chr19	5248730	5248783	E070	-9707
chr19	5289674	5289946	E070	31184
chr19	5290123	5290175	E070	31633
chr19	5290486	5290584	E070	31996
chr19	5290634	5291016	E070	32144
chr19	5291080	5291233	E070	32590
chr19	5291352	5291456	E070	32862
chr19	5291578	5291681	E070	33088
chr19	5294736	5294832	E070	36246
chr19	5294862	5294924	E070	36372
chr19	5294926	5295451	E070	36436
chr19	5295688	5295759	E070	37198
chr19	5306703	5306860	E070	48213
chr19	5246714	5246899	E071	-11591
chr19	5247591	5247658	E071	-10832
chr19	5248160	5248251	E071	-10239
chr19	5248396	5248442	E071	-10048
chr19	5248633	5248726	E071	-9764
chr19	5248730	5248783	E071	-9707
chr19	5250247	5250406	E071	-8084
chr19	5250476	5250618	E071	-7872
chr19	5251515	5251982	E071	-6508
chr19	5253163	5253265	E071	-5225
chr19	5253402	5253500	E071	-4990
chr19	5253544	5253765	E071	-4725
chr19	5287139	5287278	E071	28649
chr19	5287369	5287419	E071	28879
chr19	5287552	5287789	E071	29062
chr19	5287825	5287928	E071	29335
chr19	5289320	5289430	E071	30830
chr19	5308158	5308326	E071	49668
chr19	5228644	5228694	E072	-29796
chr19	5246392	5246442	E072	-12048
chr19	5246714	5246899	E072	-11591
chr19	5247591	5247658	E072	-10832
chr19	5248633	5248726	E072	-9764
chr19	5248730	5248783	E072	-9707
chr19	5250247	5250406	E072	-8084
chr19	5250476	5250618	E072	-7872
chr19	5253402	5253500	E072	-4990
chr19	5282206	5282315	E072	23716
chr19	5282350	5282400	E072	23860
chr19	5287369	5287419	E072	28879
chr19	5287552	5287789	E072	29062
chr19	5287825	5287928	E072	29335
chr19	5288108	5288365	E072	29618
chr19	5288379	5288615	E072	29889
chr19	5288623	5288768	E072	30133
chr19	5289320	5289430	E072	30830
chr19	5289674	5289946	E072	31184
chr19	5291352	5291456	E072	32862
chr19	5294466	5294705	E072	35976
chr19	5294736	5294832	E072	36246
chr19	5294862	5294924	E072	36372
chr19	5308158	5308326	E072	49668
chr19	5230070	5230185	E073	-28305
chr19	5249695	5249745	E073	-8745
chr19	5265099	5265166	E073	6609
chr19	5281542	5282148	E073	23052
chr19	5282206	5282315	E073	23716
chr19	5282350	5282400	E073	23860
chr19	5288108	5288365	E073	29618
chr19	5288379	5288615	E073	29889
chr19	5288623	5288768	E073	30133
chr19	5289320	5289430	E073	30830
chr19	5289674	5289946	E073	31184
chr19	5290123	5290175	E073	31633
chr19	5290486	5290584	E073	31996
chr19	5290634	5291016	E073	32144
chr19	5291080	5291233	E073	32590
chr19	5291352	5291456	E073	32862
chr19	5291578	5291681	E073	33088
chr19	5246392	5246442	E074	-12048
chr19	5246714	5246899	E074	-11591
chr19	5247591	5247658	E074	-10832
chr19	5248160	5248251	E074	-10239
chr19	5248396	5248442	E074	-10048
chr19	5248633	5248726	E074	-9764
chr19	5248730	5248783	E074	-9707
chr19	5288108	5288365	E074	29618
chr19	5288379	5288615	E074	29889
chr19	5288623	5288768	E074	30133
chr19	5289320	5289430	E074	30830
chr19	5289674	5289946	E074	31184
chr19	5290123	5290175	E074	31633
chr19	5290486	5290584	E074	31996
chr19	5290634	5291016	E074	32144
chr19	5291080	5291233	E074	32590
chr19	5247591	5247658	E081	-10832
chr19	5248160	5248251	E081	-10239
chr19	5248396	5248442	E081	-10048
chr19	5248633	5248726	E081	-9764
chr19	5248730	5248783	E081	-9707
chr19	5250247	5250406	E081	-8084
chr19	5250476	5250618	E081	-7872
chr19	5254839	5254899	E081	-3591
chr19	5255100	5255199	E081	-3291
chr19	5255243	5255293	E081	-3197
chr19	5255296	5255346	E081	-3144
chr19	5255475	5255564	E081	-2926
chr19	5255719	5255862	E081	-2628
chr19	5255999	5256099	E081	-2391
chr19	5256101	5256151	E081	-2339
chr19	5256872	5256922	E081	-1568
chr19	5289320	5289430	E081	30830
chr19	5289674	5289946	E081	31184
chr19	5290123	5290175	E081	31633
chr19	5290486	5290584	E081	31996
chr19	5290634	5291016	E081	32144
chr19	5291080	5291233	E081	32590
chr19	5291352	5291456	E081	32862
chr19	5291578	5291681	E081	33088
chr19	5294466	5294705	E081	35976
chr19	5294736	5294832	E081	36246
chr19	5294862	5294924	E081	36372
chr19	5294926	5295451	E081	36436
chr19	5301153	5301307	E081	42663
chr19	5301388	5301442	E081	42898
chr19	5306528	5306612	E081	48038
chr19	5306703	5306860	E081	48213
chr19	5307253	5307299	E081	48763
chr19	5307379	5307429	E081	48889
chr19	5307551	5307681	E081	49061
chr19	5307715	5307794	E081	49225
chr19	5308158	5308326	E081	49668
chr19	5248160	5248251	E082	-10239
chr19	5248396	5248442	E082	-10048
chr19	5251515	5251982	E082	-6508
chr19	5287552	5287789	E082	29062
chr19	5287825	5287928	E082	29335
chr19	5288108	5288365	E082	29618
chr19	5288379	5288615	E082	29889
chr19	5288623	5288768	E082	30133
chr19	5289320	5289430	E082	30830
chr19	5289674	5289946	E082	31184
chr19	5294736	5294832	E082	36246
chr19	5294862	5294924	E082	36372
chr19	5294926	5295451	E082	36436
chr19	5295688	5295759	E082	37198
chr19	5306528	5306612	E082	48038
chr19	5306703	5306860	E082	48213
chr19	5307253	5307299	E082	48763
chr19	5307379	5307429	E082	48889
chr19	5307551	5307681	E082	49061
chr19	5307715	5307794	E082	49225

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	5292421	5294426	E067	33931
chr19	5292421	5294426	E068	33931
chr19	5292421	5294426	E069	33931
chr19	5292421	5294426	E070	33931
chr19	5292421	5294426	E071	33931
chr19	5292421	5294426	E072	33931
chr19	5292421	5294426	E073	33931
chr19	5292421	5294426	E074	33931
chr19	5292421	5294426	E082	33931