rs1052067

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

PMF1 : Missense Variant
PMF1-BGLAP : Missense Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0234 (28391/121098,ExAC)
A=0236 (7082/29906,GnomAD)
A=0206 (5999/29118,TOPMED)
G==0236 (3076/13006,GO-ESP)
A=0194 (970/5008,1000G)
A=0281 (1084/3854,ALSPAC)
A=0292 (1083/3708,TWINSUK)

Position: chr1:156236330 (GRCh38.p7) (1q22)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 263 Enhancers around

Promoter: 30 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.156236330G>A
GRCh37.p13 chr 1	NC_000001.10:g.156206121G>A

Gene: PMF1, polyamine-modulated factor 1(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PMF1 transcript variant 3	NM_001199653.1:c.	N/A	Intron Variant
PMF1 transcript variant 2	NM_007221.3:c.411G>A	M [ATG]> I [ATA]	Coding Sequence Variant
polyamine-modulated factor 1 isoform 2	NP_009152.2:p.Met...NP_009152.2:p.Met137Ile	M [Met]> I [Ile]	Missense Variant
PMF1 transcript variant 1	NM_001199654.1:c....NM_001199654.1:c.417G>A	M [ATG]> I [ATA]	Coding Sequence Variant
polyamine-modulated factor 1 isoform 1	NP_001186583.1:p....NP_001186583.1:p.Met139Ile	M [Met]> I [Ile]	Missense Variant

Gene: PMF1-BGLAP, PMF1-BGLAP readthrough(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PMF1-BGLAP transcript variant 1	NM_001199661.1:c.	N/A	Intron Variant
PMF1-BGLAP transcript variant 3	NM_001199663.1:c.	N/A	Intron Variant
PMF1-BGLAP transcript variant 4	NM_001199664.1:c....NM_001199664.1:c.204G>A	M [ATG]> I [ATA]	Coding Sequence Variant
PMF1-BGLAP protein isoform 4	NP_001186593.1:p....NP_001186593.1:p.Met68Ile	M [Met]> I [Ile]	Missense Variant
PMF1-BGLAP transcript variant 2	NM_001199662.1:c....NM_001199662.1:c.411G>A	M [ATG]> I [ATA]	Coding Sequence Variant
PMF1-BGLAP protein isoform 2	NP_001186591.1:p....NP_001186591.1:p.Met137Ile	M [Met]> I [Ile]	Missense Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.887	A=0.113
1000Genomes	American	Sub	694	G=0.780	A=0.220
1000Genomes	East Asian	Sub	1008	G=0.793	A=0.207
1000Genomes	Europe	Sub	1006	G=0.723	A=0.277
1000Genomes	Global	Study-wide	5008	G=0.806	A=0.194
1000Genomes	South Asian	Sub	978	G=0.810	A=0.190
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.719	A=0.281
The Exome Aggregation Consortium	American	Sub	21926	G=0.849	A=0.150
The Exome Aggregation Consortium	Asian	Sub	25120	G=0.819	A=0.180
The Exome Aggregation Consortium	Europe	Sub	73148	G=0.722	A=0.278
The Exome Aggregation Consortium	Global	Study-wide	121098	G=0.765	A=0.234
The Exome Aggregation Consortium	Other	Sub	904	G=0.750	A=0.250
The Genome Aggregation Database	African	Sub	8716	G=0.846	A=0.154
The Genome Aggregation Database	American	Sub	838	G=0.810	A=0.190
The Genome Aggregation Database	East Asian	Sub	1618	G=0.840	A=0.160
The Genome Aggregation Database	Europe	Sub	18432	G=0.716	A=0.283
The Genome Aggregation Database	Global	Study-wide	29906	G=0.763	A=0.236
The Genome Aggregation Database	Other	Sub	302	G=0.700	A=0.300
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.794	A=0.206
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.708	A=0.292

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs1052067	0.0000512	alcoholism	pha002891
rs1052067	0.0000512	alcohol dependence	20201924

eQTL of rs1052067 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:156206121	SEMA4A	ENSG00000196189.8	G>A	7.4717e-4	88964	Cerebellar_Hemisphere

meQTL of rs1052067 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	156164805	156164861	E067	-41260
chr1	156165186	156165316	E067	-40805
chr1	156165576	156165682	E067	-40439
chr1	156165780	156165896	E067	-40225
chr1	156165904	156165954	E067	-40167
chr1	156166378	156166489	E067	-39632
chr1	156168597	156168934	E067	-37187
chr1	156168978	156169028	E067	-37093
chr1	156192638	156192819	E067	-13302
chr1	156192839	156193265	E067	-12856
chr1	156215879	156216550	E067	9758
chr1	156216598	156216712	E067	10477
chr1	156216826	156217359	E067	10705
chr1	156217774	156218184	E067	11653
chr1	156218186	156218257	E067	12065
chr1	156218302	156218376	E067	12181
chr1	156218870	156218929	E067	12749
chr1	156218946	156219026	E067	12825
chr1	156221288	156221710	E067	15167
chr1	156227502	156227552	E067	21381
chr1	156227644	156227739	E067	21523
chr1	156229737	156229849	E067	23616
chr1	156229999	156230049	E067	23878
chr1	156230109	156230188	E067	23988
chr1	156230320	156230422	E067	24199
chr1	156230660	156231038	E067	24539
chr1	156250866	156250920	E067	44745
chr1	156164805	156164861	E068	-41260
chr1	156165186	156165316	E068	-40805
chr1	156165576	156165682	E068	-40439
chr1	156165780	156165896	E068	-40225
chr1	156165904	156165954	E068	-40167
chr1	156166378	156166489	E068	-39632
chr1	156211377	156211578	E068	5256
chr1	156212018	156212130	E068	5897
chr1	156212198	156212265	E068	6077
chr1	156212295	156212382	E068	6174
chr1	156218186	156218257	E068	12065
chr1	156218302	156218376	E068	12181
chr1	156218870	156218929	E068	12749
chr1	156218946	156219026	E068	12825
chr1	156220212	156220318	E068	14091
chr1	156220575	156220662	E068	14454
chr1	156221288	156221710	E068	15167
chr1	156227073	156227446	E068	20952
chr1	156227502	156227552	E068	21381
chr1	156227644	156227739	E068	21523
chr1	156229737	156229849	E068	23616
chr1	156229999	156230049	E068	23878
chr1	156230109	156230188	E068	23988
chr1	156230320	156230422	E068	24199
chr1	156230660	156231038	E068	24539
chr1	156231123	156231174	E068	25002
chr1	156253847	156254168	E068	47726
chr1	156164805	156164861	E069	-41260
chr1	156165186	156165316	E069	-40805
chr1	156165780	156165896	E069	-40225
chr1	156165904	156165954	E069	-40167
chr1	156166378	156166489	E069	-39632
chr1	156171802	156171856	E069	-34265
chr1	156192839	156193265	E069	-12856
chr1	156211377	156211578	E069	5256
chr1	156212018	156212130	E069	5897
chr1	156212198	156212265	E069	6077
chr1	156212295	156212382	E069	6174
chr1	156212583	156212652	E069	6462
chr1	156212827	156212931	E069	6706
chr1	156213594	156213683	E069	7473
chr1	156214739	156214807	E069	8618
chr1	156214836	156214890	E069	8715
chr1	156215879	156216550	E069	9758
chr1	156218186	156218257	E069	12065
chr1	156218302	156218376	E069	12181
chr1	156218870	156218929	E069	12749
chr1	156218946	156219026	E069	12825
chr1	156220212	156220318	E069	14091
chr1	156220575	156220662	E069	14454
chr1	156221288	156221710	E069	15167
chr1	156227073	156227446	E069	20952
chr1	156227502	156227552	E069	21381
chr1	156227644	156227739	E069	21523
chr1	156229737	156229849	E069	23616
chr1	156229999	156230049	E069	23878
chr1	156230109	156230188	E069	23988
chr1	156230320	156230422	E069	24199
chr1	156230660	156231038	E069	24539
chr1	156231123	156231174	E069	25002
chr1	156232396	156232582	E069	26275
chr1	156232800	156233082	E069	26679
chr1	156250866	156250920	E069	44745
chr1	156253847	156254168	E069	47726
chr1	156164805	156164861	E070	-41260
chr1	156165186	156165316	E070	-40805
chr1	156165576	156165682	E070	-40439
chr1	156165780	156165896	E070	-40225
chr1	156165904	156165954	E070	-40167
chr1	156166378	156166489	E070	-39632
chr1	156214739	156214807	E070	8618
chr1	156214836	156214890	E070	8715
chr1	156217774	156218184	E070	11653
chr1	156218186	156218257	E070	12065
chr1	156218302	156218376	E070	12181
chr1	156218870	156218929	E070	12749
chr1	156250720	156250764	E070	44599
chr1	156250866	156250920	E070	44745
chr1	156164805	156164861	E071	-41260
chr1	156165186	156165316	E071	-40805
chr1	156165576	156165682	E071	-40439
chr1	156165780	156165896	E071	-40225
chr1	156165904	156165954	E071	-40167
chr1	156166378	156166489	E071	-39632
chr1	156192638	156192819	E071	-13302
chr1	156192839	156193265	E071	-12856
chr1	156195169	156195620	E071	-10501
chr1	156211377	156211578	E071	5256
chr1	156212018	156212130	E071	5897
chr1	156212198	156212265	E071	6077
chr1	156212295	156212382	E071	6174
chr1	156212583	156212652	E071	6462
chr1	156212827	156212931	E071	6706
chr1	156213594	156213683	E071	7473
chr1	156214025	156214136	E071	7904
chr1	156214836	156214890	E071	8715
chr1	156218302	156218376	E071	12181
chr1	156218870	156218929	E071	12749
chr1	156218946	156219026	E071	12825
chr1	156220212	156220318	E071	14091
chr1	156220575	156220662	E071	14454
chr1	156221288	156221710	E071	15167
chr1	156222713	156222820	E071	16592
chr1	156227073	156227446	E071	20952
chr1	156227502	156227552	E071	21381
chr1	156227644	156227739	E071	21523
chr1	156228562	156229095	E071	22441
chr1	156229737	156229849	E071	23616
chr1	156229999	156230049	E071	23878
chr1	156230109	156230188	E071	23988
chr1	156230320	156230422	E071	24199
chr1	156230660	156231038	E071	24539
chr1	156231123	156231174	E071	25002
chr1	156232396	156232582	E071	26275
chr1	156232800	156233082	E071	26679
chr1	156253847	156254168	E071	47726
chr1	156164805	156164861	E072	-41260
chr1	156165186	156165316	E072	-40805
chr1	156165576	156165682	E072	-40439
chr1	156165780	156165896	E072	-40225
chr1	156165904	156165954	E072	-40167
chr1	156166378	156166489	E072	-39632
chr1	156192638	156192819	E072	-13302
chr1	156192839	156193265	E072	-12856
chr1	156210821	156210944	E072	4700
chr1	156213594	156213683	E072	7473
chr1	156214739	156214807	E072	8618
chr1	156214836	156214890	E072	8715
chr1	156215879	156216550	E072	9758
chr1	156218186	156218257	E072	12065
chr1	156218302	156218376	E072	12181
chr1	156218870	156218929	E072	12749
chr1	156218946	156219026	E072	12825
chr1	156220212	156220318	E072	14091
chr1	156220575	156220662	E072	14454
chr1	156221288	156221710	E072	15167
chr1	156227073	156227446	E072	20952
chr1	156227502	156227552	E072	21381
chr1	156227644	156227739	E072	21523
chr1	156228562	156229095	E072	22441
chr1	156229737	156229849	E072	23616
chr1	156229999	156230049	E072	23878
chr1	156230109	156230188	E072	23988
chr1	156230320	156230422	E072	24199
chr1	156230660	156231038	E072	24539
chr1	156231123	156231174	E072	25002
chr1	156232800	156233082	E072	26679
chr1	156250720	156250764	E072	44599
chr1	156250866	156250920	E072	44745
chr1	156253847	156254168	E072	47726
chr1	156254207	156254342	E072	48086
chr1	156164805	156164861	E073	-41260
chr1	156165186	156165316	E073	-40805
chr1	156165576	156165682	E073	-40439
chr1	156165780	156165896	E073	-40225
chr1	156165904	156165954	E073	-40167
chr1	156166378	156166489	E073	-39632
chr1	156192839	156193265	E073	-12856
chr1	156212018	156212130	E073	5897
chr1	156212198	156212265	E073	6077
chr1	156212295	156212382	E073	6174
chr1	156214739	156214807	E073	8618
chr1	156214836	156214890	E073	8715
chr1	156215879	156216550	E073	9758
chr1	156218186	156218257	E073	12065
chr1	156218302	156218376	E073	12181
chr1	156218870	156218929	E073	12749
chr1	156218946	156219026	E073	12825
chr1	156220212	156220318	E073	14091
chr1	156220575	156220662	E073	14454
chr1	156221288	156221710	E073	15167
chr1	156222713	156222820	E073	16592
chr1	156222845	156222885	E073	16724
chr1	156227502	156227552	E073	21381
chr1	156227644	156227739	E073	21523
chr1	156228562	156229095	E073	22441
chr1	156229737	156229849	E073	23616
chr1	156229999	156230049	E073	23878
chr1	156230109	156230188	E073	23988
chr1	156230320	156230422	E073	24199
chr1	156230660	156231038	E073	24539
chr1	156231123	156231174	E073	25002
chr1	156250720	156250764	E073	44599
chr1	156250866	156250920	E073	44745
chr1	156253847	156254168	E073	47726
chr1	156254207	156254342	E073	48086
chr1	156165576	156165682	E074	-40439
chr1	156165780	156165896	E074	-40225
chr1	156165904	156165954	E074	-40167
chr1	156192638	156192819	E074	-13302
chr1	156192839	156193265	E074	-12856
chr1	156212018	156212130	E074	5897
chr1	156212198	156212265	E074	6077
chr1	156212295	156212382	E074	6174
chr1	156212583	156212652	E074	6462
chr1	156212827	156212931	E074	6706
chr1	156213594	156213683	E074	7473
chr1	156214025	156214136	E074	7904
chr1	156214739	156214807	E074	8618
chr1	156214836	156214890	E074	8715
chr1	156217774	156218184	E074	11653
chr1	156218186	156218257	E074	12065
chr1	156218302	156218376	E074	12181
chr1	156218870	156218929	E074	12749
chr1	156218946	156219026	E074	12825
chr1	156220212	156220318	E074	14091
chr1	156220575	156220662	E074	14454
chr1	156221288	156221710	E074	15167
chr1	156227073	156227446	E074	20952
chr1	156227502	156227552	E074	21381
chr1	156227644	156227739	E074	21523
chr1	156229737	156229849	E074	23616
chr1	156229999	156230049	E074	23878
chr1	156230109	156230188	E074	23988
chr1	156230320	156230422	E074	24199
chr1	156230660	156231038	E074	24539
chr1	156231123	156231174	E074	25002
chr1	156232396	156232582	E074	26275
chr1	156232800	156233082	E074	26679
chr1	156253847	156254168	E074	47726
chr1	156164805	156164861	E081	-41260
chr1	156165186	156165316	E081	-40805
chr1	156165576	156165682	E081	-40439
chr1	156165780	156165896	E081	-40225
chr1	156166378	156166489	E081	-39632
chr1	156217598	156217762	E081	11477
chr1	156217774	156218184	E081	11653
chr1	156164805	156164861	E082	-41260
chr1	156165186	156165316	E082	-40805
chr1	156165576	156165682	E082	-40439
chr1	156165780	156165896	E082	-40225
chr1	156165904	156165954	E082	-40167
chr1	156166378	156166489	E082	-39632
chr1	156195169	156195620	E082	-10501
chr1	156250866	156250920	E082	44745
chr1	156253847	156254168	E082	47726

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	156163081	156164402	E067	-41719
chr1	156182302	156183586	E067	-22535
chr1	156251539	156253388	E067	45418
chr1	156163081	156164402	E068	-41719
chr1	156182302	156183586	E068	-22535
chr1	156251539	156253388	E068	45418
chr1	156163081	156164402	E069	-41719
chr1	156182302	156183586	E069	-22535
chr1	156251539	156253388	E069	45418
chr1	156163081	156164402	E070	-41719
chr1	156182302	156183586	E070	-22535
chr1	156251539	156253388	E070	45418
chr1	156163081	156164402	E071	-41719
chr1	156182302	156183586	E071	-22535
chr1	156251539	156253388	E071	45418
chr1	156163081	156164402	E072	-41719
chr1	156182302	156183586	E072	-22535
chr1	156251539	156253388	E072	45418
chr1	156163081	156164402	E073	-41719
chr1	156182302	156183586	E073	-22535
chr1	156251539	156253388	E073	45418
chr1	156163081	156164402	E074	-41719
chr1	156182302	156183586	E074	-22535
chr1	156251539	156253388	E074	45418
chr1	156163081	156164402	E081	-41719
chr1	156182302	156183586	E081	-22535
chr1	156251539	156253388	E081	45418
chr1	156163081	156164402	E082	-41719
chr1	156182302	156183586	E082	-22535
chr1	156251539	156253388	E082	45418