rs11582876

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

PTPRF : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0044 (1291/29118,TOPMED)
T=0054 (1371/25068,GnomAD)
T=0078 (391/5008,1000G)

Position: chr1:43597156 (GRCh38.p7) (1p34.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 362 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.43597156C>T
GRCh37.p13 chr 1	NC_000001.10:g.44062827C>T

Gene: PTPRF, protein tyrosine phosphatase, receptor type F(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PTPRF transcript variant 1	NM_002840.3:c.	N/A	Intron Variant
PTPRF transcript variant 2	NM_130440.2:c.	N/A	Intron Variant
PTPRF transcript variant X1	XM_005271079.3:c.	N/A	Intron Variant
PTPRF transcript variant X6	XM_005271080.3:c.	N/A	Intron Variant
PTPRF transcript variant X10	XM_005271081.3:c.	N/A	Intron Variant
PTPRF transcript variant X17	XM_005271082.3:c.	N/A	Intron Variant
PTPRF transcript variant X4	XM_006710795.3:c.	N/A	Intron Variant
PTPRF transcript variant X7	XM_006710796.3:c.	N/A	Intron Variant
PTPRF transcript variant X9	XM_006710797.3:c.	N/A	Intron Variant
PTPRF transcript variant X11	XM_006710798.3:c.	N/A	Intron Variant
PTPRF transcript variant X12	XM_006710799.3:c.	N/A	Intron Variant
PTPRF transcript variant X13	XM_006710800.3:c.	N/A	Intron Variant
PTPRF transcript variant X18	XM_006710801.3:c.	N/A	Intron Variant
PTPRF transcript variant X2	XM_011541871.2:c.	N/A	Intron Variant
PTPRF transcript variant X3	XM_011541872.2:c.	N/A	Intron Variant
PTPRF transcript variant X5	XM_011541873.2:c.	N/A	Intron Variant
PTPRF transcript variant X8	XM_017001942.1:c.	N/A	Intron Variant
PTPRF transcript variant X14	XM_017001943.1:c.	N/A	Intron Variant
PTPRF transcript variant X15	XM_017001944.1:c.	N/A	Intron Variant
PTPRF transcript variant X16	XM_017001945.1:c.	N/A	Intron Variant
PTPRF transcript variant X19	XM_017001946.1:c.	N/A	Intron Variant
PTPRF transcript variant X20	XM_017001947.1:c.	N/A	Intron Variant
PTPRF transcript variant X21	XM_017001948.1:c.	N/A	Intron Variant
PTPRF transcript variant X20	XM_017001949.1:c.	N/A	Intron Variant
PTPRF transcript variant X23	XM_017001950.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.993	T=0.007
1000Genomes	American	Sub	694	C=0.880	T=0.120
1000Genomes	East Asian	Sub	1008	C=0.848	T=0.152
1000Genomes	Europe	Sub	1006	C=0.946	T=0.054
1000Genomes	Global	Study-wide	5008	C=0.922	T=0.078
1000Genomes	South Asian	Sub	978	C=0.900	T=0.100
The Genome Aggregation Database	African	Sub	6866	C=0.987	T=0.013
The Genome Aggregation Database	American	Sub	800	C=0.860	T=0.140
The Genome Aggregation Database	East Asian	Sub	1352	C=0.778	T=0.222
The Genome Aggregation Database	Europe	Sub	15776	C=0.945	T=0.054
The Genome Aggregation Database	Global	Study-wide	25068	C=0.945	T=0.054
The Genome Aggregation Database	Other	Sub	274	C=0.990	T=0.010
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.955	T=0.044

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs11582876	0.000675	alcohol dependence	21314694

eQTL of rs11582876 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 rs11582876 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 )
chr1	44012854	44012939	E067	-49888
chr1	44013184	44013234	E067	-49593
chr1	44013344	44013400	E067	-49427
chr1	44013437	44013553	E067	-49274
chr1	44013688	44013738	E067	-49089
chr1	44013982	44014503	E067	-48324
chr1	44014536	44014607	E067	-48220
chr1	44014673	44014723	E067	-48104
chr1	44017176	44017321	E067	-45506
chr1	44017848	44017935	E067	-44892
chr1	44018172	44018899	E067	-43928
chr1	44019146	44019196	E067	-43631
chr1	44019882	44019933	E067	-42894
chr1	44020080	44020173	E067	-42654
chr1	44020187	44020455	E067	-42372
chr1	44024847	44024951	E067	-37876
chr1	44025008	44025102	E067	-37725
chr1	44025213	44025372	E067	-37455
chr1	44029253	44029375	E067	-33452
chr1	44029431	44029524	E067	-33303
chr1	44029606	44030495	E067	-32332
chr1	44030601	44030861	E067	-31966
chr1	44032247	44032326	E067	-30501
chr1	44032399	44032661	E067	-30166
chr1	44036099	44036173	E067	-26654
chr1	44036180	44036257	E067	-26570
chr1	44036395	44036742	E067	-26085
chr1	44037025	44037075	E067	-25752
chr1	44038308	44038530	E067	-24297
chr1	44038690	44038861	E067	-23966
chr1	44038937	44039048	E067	-23779
chr1	44039223	44039320	E067	-23507
chr1	44043521	44043561	E067	-19266
chr1	44043642	44043738	E067	-19089
chr1	44043768	44043986	E067	-18841
chr1	44044106	44044158	E067	-18669
chr1	44044310	44044482	E067	-18345
chr1	44047816	44048271	E067	-14556
chr1	44067709	44067749	E067	4882
chr1	44012854	44012939	E068	-49888
chr1	44013184	44013234	E068	-49593
chr1	44013344	44013400	E068	-49427
chr1	44013437	44013553	E068	-49274
chr1	44013688	44013738	E068	-49089
chr1	44013982	44014503	E068	-48324
chr1	44014536	44014607	E068	-48220
chr1	44014673	44014723	E068	-48104
chr1	44017848	44017935	E068	-44892
chr1	44018172	44018899	E068	-43928
chr1	44019146	44019196	E068	-43631
chr1	44019882	44019933	E068	-42894
chr1	44020080	44020173	E068	-42654
chr1	44022621	44022754	E068	-40073
chr1	44029253	44029375	E068	-33452
chr1	44029431	44029524	E068	-33303
chr1	44029606	44030495	E068	-32332
chr1	44030601	44030861	E068	-31966
chr1	44032247	44032326	E068	-30501
chr1	44032399	44032661	E068	-30166
chr1	44036099	44036173	E068	-26654
chr1	44036180	44036257	E068	-26570
chr1	44036395	44036742	E068	-26085
chr1	44037025	44037075	E068	-25752
chr1	44037588	44037644	E068	-25183
chr1	44037830	44038114	E068	-24713
chr1	44038308	44038530	E068	-24297
chr1	44038690	44038861	E068	-23966
chr1	44038937	44039048	E068	-23779
chr1	44039223	44039320	E068	-23507
chr1	44043521	44043561	E068	-19266
chr1	44043642	44043738	E068	-19089
chr1	44043768	44043986	E068	-18841
chr1	44044106	44044158	E068	-18669
chr1	44105853	44105940	E068	43026
chr1	44106086	44106212	E068	43259
chr1	44012854	44012939	E069	-49888
chr1	44013184	44013234	E069	-49593
chr1	44013344	44013400	E069	-49427
chr1	44013437	44013553	E069	-49274
chr1	44013688	44013738	E069	-49089
chr1	44013982	44014503	E069	-48324
chr1	44014536	44014607	E069	-48220
chr1	44014673	44014723	E069	-48104
chr1	44016556	44016632	E069	-46195
chr1	44016660	44016751	E069	-46076
chr1	44016890	44017051	E069	-45776
chr1	44017176	44017321	E069	-45506
chr1	44017848	44017935	E069	-44892
chr1	44018172	44018899	E069	-43928
chr1	44019146	44019196	E069	-43631
chr1	44019882	44019933	E069	-42894
chr1	44020080	44020173	E069	-42654
chr1	44020187	44020455	E069	-42372
chr1	44022621	44022754	E069	-40073
chr1	44022957	44023027	E069	-39800
chr1	44023331	44024684	E069	-38143
chr1	44024847	44024951	E069	-37876
chr1	44025008	44025102	E069	-37725
chr1	44025213	44025372	E069	-37455
chr1	44025515	44025688	E069	-37139
chr1	44025739	44025793	E069	-37034
chr1	44025899	44025994	E069	-36833
chr1	44029253	44029375	E069	-33452
chr1	44029431	44029524	E069	-33303
chr1	44029606	44030495	E069	-32332
chr1	44030601	44030861	E069	-31966
chr1	44032399	44032661	E069	-30166
chr1	44034418	44034520	E069	-28307
chr1	44034579	44034654	E069	-28173
chr1	44034725	44034769	E069	-28058
chr1	44034924	44035148	E069	-27679
chr1	44035399	44035490	E069	-27337
chr1	44036099	44036173	E069	-26654
chr1	44036180	44036257	E069	-26570
chr1	44036395	44036742	E069	-26085
chr1	44037025	44037075	E069	-25752
chr1	44037588	44037644	E069	-25183
chr1	44037830	44038114	E069	-24713
chr1	44038308	44038530	E069	-24297
chr1	44038690	44038861	E069	-23966
chr1	44038937	44039048	E069	-23779
chr1	44039223	44039320	E069	-23507
chr1	44043521	44043561	E069	-19266
chr1	44043642	44043738	E069	-19089
chr1	44043768	44043986	E069	-18841
chr1	44044106	44044158	E069	-18669
chr1	44068575	44069079	E069	5748
chr1	44012854	44012939	E070	-49888
chr1	44013184	44013234	E070	-49593
chr1	44013344	44013400	E070	-49427
chr1	44023331	44024684	E070	-38143
chr1	44024847	44024951	E070	-37876
chr1	44025008	44025102	E070	-37725
chr1	44029253	44029375	E070	-33452
chr1	44029431	44029524	E070	-33303
chr1	44029606	44030495	E070	-32332
chr1	44032247	44032326	E070	-30501
chr1	44032399	44032661	E070	-30166
chr1	44036395	44036742	E070	-26085
chr1	44038308	44038530	E070	-24297
chr1	44038690	44038861	E070	-23966
chr1	44038937	44039048	E070	-23779
chr1	44049299	44049361	E070	-13466
chr1	44049520	44049683	E070	-13144
chr1	44050074	44050124	E070	-12703
chr1	44050619	44050673	E070	-12154
chr1	44051069	44051119	E070	-11708
chr1	44051327	44051560	E070	-11267
chr1	44012854	44012939	E071	-49888
chr1	44013184	44013234	E071	-49593
chr1	44013344	44013400	E071	-49427
chr1	44013437	44013553	E071	-49274
chr1	44013688	44013738	E071	-49089
chr1	44013982	44014503	E071	-48324
chr1	44014536	44014607	E071	-48220
chr1	44014673	44014723	E071	-48104
chr1	44015051	44015296	E071	-47531
chr1	44016890	44017051	E071	-45776
chr1	44017176	44017321	E071	-45506
chr1	44017848	44017935	E071	-44892
chr1	44018172	44018899	E071	-43928
chr1	44019146	44019196	E071	-43631
chr1	44019882	44019933	E071	-42894
chr1	44020080	44020173	E071	-42654
chr1	44023331	44024684	E071	-38143
chr1	44024847	44024951	E071	-37876
chr1	44025008	44025102	E071	-37725
chr1	44025213	44025372	E071	-37455
chr1	44029253	44029375	E071	-33452
chr1	44029431	44029524	E071	-33303
chr1	44029606	44030495	E071	-32332
chr1	44030601	44030861	E071	-31966
chr1	44032399	44032661	E071	-30166
chr1	44034579	44034654	E071	-28173
chr1	44034725	44034769	E071	-28058
chr1	44034924	44035148	E071	-27679
chr1	44035399	44035490	E071	-27337
chr1	44036099	44036173	E071	-26654
chr1	44036180	44036257	E071	-26570
chr1	44036395	44036742	E071	-26085
chr1	44037025	44037075	E071	-25752
chr1	44037588	44037644	E071	-25183
chr1	44037830	44038114	E071	-24713
chr1	44038308	44038530	E071	-24297
chr1	44038690	44038861	E071	-23966
chr1	44038937	44039048	E071	-23779
chr1	44039223	44039320	E071	-23507
chr1	44043521	44043561	E071	-19266
chr1	44046460	44046614	E071	-16213
chr1	44047816	44048271	E071	-14556
chr1	44067191	44067323	E071	4364
chr1	44067709	44067749	E071	4882
chr1	44068575	44069079	E071	5748
chr1	44012854	44012939	E072	-49888
chr1	44013184	44013234	E072	-49593
chr1	44013344	44013400	E072	-49427
chr1	44013437	44013553	E072	-49274
chr1	44013688	44013738	E072	-49089
chr1	44013982	44014503	E072	-48324
chr1	44014536	44014607	E072	-48220
chr1	44014673	44014723	E072	-48104
chr1	44015051	44015296	E072	-47531
chr1	44016890	44017051	E072	-45776
chr1	44017176	44017321	E072	-45506
chr1	44017848	44017935	E072	-44892
chr1	44018172	44018899	E072	-43928
chr1	44019146	44019196	E072	-43631
chr1	44019882	44019933	E072	-42894
chr1	44020080	44020173	E072	-42654
chr1	44020187	44020455	E072	-42372
chr1	44022351	44022482	E072	-40345
chr1	44022621	44022754	E072	-40073
chr1	44023331	44024684	E072	-38143
chr1	44025213	44025372	E072	-37455
chr1	44025515	44025688	E072	-37139
chr1	44025739	44025793	E072	-37034
chr1	44025899	44025994	E072	-36833
chr1	44029253	44029375	E072	-33452
chr1	44029431	44029524	E072	-33303
chr1	44029606	44030495	E072	-32332
chr1	44032247	44032326	E072	-30501
chr1	44032399	44032661	E072	-30166
chr1	44034418	44034520	E072	-28307
chr1	44034579	44034654	E072	-28173
chr1	44034725	44034769	E072	-28058
chr1	44034924	44035148	E072	-27679
chr1	44035399	44035490	E072	-27337
chr1	44036099	44036173	E072	-26654
chr1	44036180	44036257	E072	-26570
chr1	44036395	44036742	E072	-26085
chr1	44037025	44037075	E072	-25752
chr1	44037588	44037644	E072	-25183
chr1	44037830	44038114	E072	-24713
chr1	44038308	44038530	E072	-24297
chr1	44038690	44038861	E072	-23966
chr1	44038937	44039048	E072	-23779
chr1	44039223	44039320	E072	-23507
chr1	44043521	44043561	E072	-19266
chr1	44043642	44043738	E072	-19089
chr1	44043768	44043986	E072	-18841
chr1	44047816	44048271	E072	-14556
chr1	44067191	44067323	E072	4364
chr1	44067709	44067749	E072	4882
chr1	44068575	44069079	E072	5748
chr1	44088177	44088681	E072	25350
chr1	44012854	44012939	E073	-49888
chr1	44013184	44013234	E073	-49593
chr1	44013344	44013400	E073	-49427
chr1	44013437	44013553	E073	-49274
chr1	44013688	44013738	E073	-49089
chr1	44013982	44014503	E073	-48324
chr1	44018172	44018899	E073	-43928
chr1	44019146	44019196	E073	-43631
chr1	44019882	44019933	E073	-42894
chr1	44020080	44020173	E073	-42654
chr1	44020187	44020455	E073	-42372
chr1	44023331	44024684	E073	-38143
chr1	44025515	44025688	E073	-37139
chr1	44025739	44025793	E073	-37034
chr1	44025899	44025994	E073	-36833
chr1	44029253	44029375	E073	-33452
chr1	44029431	44029524	E073	-33303
chr1	44029606	44030495	E073	-32332
chr1	44030601	44030861	E073	-31966
chr1	44032399	44032661	E073	-30166
chr1	44035399	44035490	E073	-27337
chr1	44036099	44036173	E073	-26654
chr1	44036180	44036257	E073	-26570
chr1	44036395	44036742	E073	-26085
chr1	44037025	44037075	E073	-25752
chr1	44037588	44037644	E073	-25183
chr1	44037830	44038114	E073	-24713
chr1	44038308	44038530	E073	-24297
chr1	44038690	44038861	E073	-23966
chr1	44038937	44039048	E073	-23779
chr1	44039223	44039320	E073	-23507
chr1	44051069	44051119	E073	-11708
chr1	44051327	44051560	E073	-11267
chr1	44012854	44012939	E074	-49888
chr1	44013184	44013234	E074	-49593
chr1	44013344	44013400	E074	-49427
chr1	44013437	44013553	E074	-49274
chr1	44013688	44013738	E074	-49089
chr1	44013982	44014503	E074	-48324
chr1	44014536	44014607	E074	-48220
chr1	44014673	44014723	E074	-48104
chr1	44016890	44017051	E074	-45776
chr1	44017176	44017321	E074	-45506
chr1	44017848	44017935	E074	-44892
chr1	44018172	44018899	E074	-43928
chr1	44019882	44019933	E074	-42894
chr1	44020080	44020173	E074	-42654
chr1	44020187	44020455	E074	-42372
chr1	44022621	44022754	E074	-40073
chr1	44022957	44023027	E074	-39800
chr1	44024847	44024951	E074	-37876
chr1	44025008	44025102	E074	-37725
chr1	44029253	44029375	E074	-33452
chr1	44029431	44029524	E074	-33303
chr1	44029606	44030495	E074	-32332
chr1	44030601	44030861	E074	-31966
chr1	44032093	44032153	E074	-30674
chr1	44032247	44032326	E074	-30501
chr1	44032399	44032661	E074	-30166
chr1	44034725	44034769	E074	-28058
chr1	44034924	44035148	E074	-27679
chr1	44035399	44035490	E074	-27337
chr1	44036099	44036173	E074	-26654
chr1	44036180	44036257	E074	-26570
chr1	44036395	44036742	E074	-26085
chr1	44037830	44038114	E074	-24713
chr1	44038308	44038530	E074	-24297
chr1	44038690	44038861	E074	-23966
chr1	44038937	44039048	E074	-23779
chr1	44039223	44039320	E074	-23507
chr1	44043521	44043561	E074	-19266
chr1	44046460	44046614	E074	-16213
chr1	44067191	44067323	E074	4364
chr1	44067709	44067749	E074	4882
chr1	44068575	44069079	E074	5748
chr1	44105853	44105940	E074	43026
chr1	44106086	44106212	E074	43259
chr1	44023331	44024684	E081	-38143
chr1	44024847	44024951	E081	-37876
chr1	44025213	44025372	E081	-37455
chr1	44025515	44025688	E081	-37139
chr1	44025739	44025793	E081	-37034
chr1	44025899	44025994	E081	-36833
chr1	44029253	44029375	E081	-33452
chr1	44029431	44029524	E081	-33303
chr1	44029606	44030495	E081	-32332
chr1	44030601	44030861	E081	-31966
chr1	44032093	44032153	E081	-30674
chr1	44032247	44032326	E081	-30501
chr1	44032399	44032661	E081	-30166
chr1	44036099	44036173	E081	-26654
chr1	44036180	44036257	E081	-26570
chr1	44036395	44036742	E081	-26085
chr1	44038308	44038530	E081	-24297
chr1	44038690	44038861	E081	-23966
chr1	44038937	44039048	E081	-23779
chr1	44039223	44039320	E081	-23507
chr1	44023331	44024684	E082	-38143
chr1	44024847	44024951	E082	-37876
chr1	44025008	44025102	E082	-37725
chr1	44025213	44025372	E082	-37455
chr1	44025515	44025688	E082	-37139
chr1	44025739	44025793	E082	-37034
chr1	44029431	44029524	E082	-33303
chr1	44029606	44030495	E082	-32332
chr1	44032247	44032326	E082	-30501
chr1	44032399	44032661	E082	-30166
chr1	44036099	44036173	E082	-26654
chr1	44036180	44036257	E082	-26570
chr1	44036395	44036742	E082	-26085
chr1	44037025	44037075	E082	-25752
chr1	44037588	44037644	E082	-25183
chr1	44037830	44038114	E082	-24713
chr1	44038308	44038530	E082	-24297
chr1	44038690	44038861	E082	-23966
chr1	44038937	44039048	E082	-23779
chr1	44039223	44039320	E082	-23507