rs2053458

Organism: Homo sapiens

Alleles: C>G

Gene : Feature

PPM1B : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0091 (2735/29972,GnomAD)
C==0072 (2114/29116,TOPMED)
C==0039 (196/5008,1000G)
C==0098 (378/3854,ALSPAC)
C==0112 (415/3708,TWINSUK)

Position: chr2:44215940 (GRCh38.p7) (2p21)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 130 Enhancers around

Promoter: 46 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.44215940C>G
GRCh37.p13 chr 2	NC_000002.11:g.44443079C>G
PPM1B RefSeqGene	NG_011678.1:g.52080C>G

Gene: PPM1B, protein phosphatase, Mg2+/Mn2+ dependent 1B(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PPM1B transcript variant 5	NM_001033557.2:c.	N/A	Intron Variant
PPM1B transcript variant 1	NM_002706.5:c.	N/A	Intron Variant
PPM1B transcript variant 2	NM_177968.3:c.	N/A	Intron Variant
PPM1B transcript variant 3	NM_177969.3:c.	N/A	Intron Variant
PPM1B transcript variant X3	XM_011532936.2:c.	N/A	Intron Variant
PPM1B transcript variant X1	XM_017004395.1:c.	N/A	Intron Variant
PPM1B transcript variant X2	XM_017004396.1:c.	N/A	Intron Variant
PPM1B transcript variant X4	XM_017004397.1:c.	N/A	Intron Variant
PPM1B transcript variant X5	XR_001738794.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.033	G=0.967
1000Genomes	American	Sub	694	C=0.050	G=0.950
1000Genomes	East Asian	Sub	1008	C=0.000	G=1.000
1000Genomes	Europe	Sub	1006	C=0.104	G=0.896
1000Genomes	Global	Study-wide	5008	C=0.039	G=0.961
1000Genomes	South Asian	Sub	978	C=0.010	G=0.990
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.098	G=0.902
The Genome Aggregation Database	African	Sub	8730	C=0.044	G=0.956
The Genome Aggregation Database	American	Sub	838	C=0.060	G=0.940
The Genome Aggregation Database	East Asian	Sub	1614	C=0.001	G=0.999
The Genome Aggregation Database	Europe	Sub	18488	C=0.123	G=0.876
The Genome Aggregation Database	Global	Study-wide	29972	C=0.091	G=0.908
The Genome Aggregation Database	Other	Sub	302	C=0.080	G=0.920
Trans-Omics for Precision Medicine	Global	Study-wide	29116	C=0.072	G=0.927
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.112	G=0.888

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
rs2053458	0.000957	alcohol dependence	21314694

eQTL of rs2053458 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 rs2053458 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 )
chr2	44399978	44400028	E067	-43051
chr2	44400806	44400898	E067	-42181
chr2	44400949	44401003	E067	-42076
chr2	44401883	44401923	E067	-41156
chr2	44402216	44402266	E067	-40813
chr2	44402513	44402769	E067	-40310
chr2	44403659	44403715	E067	-39364
chr2	44406516	44406556	E067	-36523
chr2	44410060	44410141	E067	-32938
chr2	44410618	44410659	E067	-32420
chr2	44410718	44410860	E067	-32219
chr2	44411214	44411577	E067	-31502
chr2	44417672	44418276	E067	-24803
chr2	44428936	44429085	E067	-13994
chr2	44442382	44442442	E067	-637
chr2	44443137	44443214	E067	58
chr2	44447908	44447992	E067	4829
chr2	44472294	44472396	E067	29215
chr2	44398865	44398960	E068	-44119
chr2	44401883	44401923	E068	-41156
chr2	44402216	44402266	E068	-40813
chr2	44402513	44402769	E068	-40310
chr2	44408120	44408170	E068	-34909
chr2	44408952	44409066	E068	-34013
chr2	44410618	44410659	E068	-32420
chr2	44410718	44410860	E068	-32219
chr2	44411214	44411577	E068	-31502
chr2	44414089	44414301	E068	-28778
chr2	44414320	44414779	E068	-28300
chr2	44415673	44415713	E068	-27366
chr2	44415978	44416094	E068	-26985
chr2	44418616	44418767	E068	-24312
chr2	44428936	44429085	E068	-13994
chr2	44434790	44434854	E068	-8225
chr2	44471002	44471260	E068	27923
chr2	44401883	44401923	E069	-41156
chr2	44402513	44402769	E069	-40310
chr2	44418616	44418767	E069	-24312
chr2	44418943	44419003	E069	-24076
chr2	44419042	44419100	E069	-23979
chr2	44419899	44420225	E069	-22854
chr2	44471002	44471260	E069	27923
chr2	44472437	44473057	E069	29358
chr2	44399978	44400028	E070	-43051
chr2	44403659	44403715	E070	-39364
chr2	44398865	44398960	E071	-44119
chr2	44399978	44400028	E071	-43051
chr2	44400806	44400898	E071	-42181
chr2	44400949	44401003	E071	-42076
chr2	44402513	44402769	E071	-40310
chr2	44403659	44403715	E071	-39364
chr2	44404344	44404558	E071	-38521
chr2	44408120	44408170	E071	-34909
chr2	44410060	44410141	E071	-32938
chr2	44410618	44410659	E071	-32420
chr2	44410718	44410860	E071	-32219
chr2	44411214	44411577	E071	-31502
chr2	44417672	44418276	E071	-24803
chr2	44418616	44418767	E071	-24312
chr2	44418943	44419003	E071	-24076
chr2	44419042	44419100	E071	-23979
chr2	44428936	44429085	E071	-13994
chr2	44432476	44432562	E071	-10517
chr2	44432776	44432830	E071	-10249
chr2	44443137	44443214	E071	58
chr2	44470186	44470315	E071	27107
chr2	44471002	44471260	E071	27923
chr2	44472111	44472265	E071	29032
chr2	44472294	44472396	E071	29215
chr2	44398865	44398960	E072	-44119
chr2	44399978	44400028	E072	-43051
chr2	44401883	44401923	E072	-41156
chr2	44402216	44402266	E072	-40813
chr2	44402513	44402769	E072	-40310
chr2	44403659	44403715	E072	-39364
chr2	44404344	44404558	E072	-38521
chr2	44406144	44406379	E072	-36700
chr2	44406516	44406556	E072	-36523
chr2	44408120	44408170	E072	-34909
chr2	44410618	44410659	E072	-32420
chr2	44410718	44410860	E072	-32219
chr2	44411214	44411577	E072	-31502
chr2	44419899	44420225	E072	-22854
chr2	44428936	44429085	E072	-13994
chr2	44447908	44447992	E072	4829
chr2	44457646	44457781	E072	14567
chr2	44472111	44472265	E072	29032
chr2	44472294	44472396	E072	29215
chr2	44472437	44473057	E072	29358
chr2	44399978	44400028	E073	-43051
chr2	44401883	44401923	E073	-41156
chr2	44402216	44402266	E073	-40813
chr2	44402513	44402769	E073	-40310
chr2	44408120	44408170	E073	-34909
chr2	44410618	44410659	E073	-32420
chr2	44411214	44411577	E073	-31502
chr2	44398865	44398960	E074	-44119
chr2	44399978	44400028	E074	-43051
chr2	44400949	44401003	E074	-42076
chr2	44401883	44401923	E074	-41156
chr2	44402216	44402266	E074	-40813
chr2	44402513	44402769	E074	-40310
chr2	44403659	44403715	E074	-39364
chr2	44410060	44410141	E074	-32938
chr2	44410618	44410659	E074	-32420
chr2	44410718	44410860	E074	-32219
chr2	44411214	44411577	E074	-31502
chr2	44419899	44420225	E074	-22854
chr2	44428936	44429085	E074	-13994
chr2	44443137	44443214	E074	58
chr2	44447908	44447992	E074	4829
chr2	44457646	44457781	E074	14567
chr2	44470186	44470315	E074	27107
chr2	44471002	44471260	E074	27923
chr2	44472111	44472265	E074	29032
chr2	44472294	44472396	E074	29215
chr2	44472437	44473057	E074	29358
chr2	44414089	44414301	E081	-28778
chr2	44414320	44414779	E081	-28300
chr2	44415673	44415713	E081	-27366
chr2	44415978	44416094	E081	-26985
chr2	44416254	44416314	E081	-26765
chr2	44416402	44416487	E081	-26592
chr2	44417496	44417567	E081	-25512
chr2	44417672	44418276	E081	-24803
chr2	44425076	44425256	E081	-17823
chr2	44472111	44472265	E081	29032
chr2	44417672	44418276	E082	-24803
chr2	44425076	44425256	E082	-17823
chr2	44472111	44472265	E082	29032

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	44394522	44397099	E067	-45980
chr2	44397214	44397395	E067	-45684
chr2	44397410	44397842	E067	-45237
chr2	44397894	44398007	E067	-45072
chr2	44471277	44471863	E067	28198
chr2	44394522	44397099	E068	-45980
chr2	44397214	44397395	E068	-45684
chr2	44397410	44397842	E068	-45237
chr2	44397894	44398007	E068	-45072
chr2	44471277	44471863	E068	28198
chr2	44394522	44397099	E069	-45980
chr2	44397214	44397395	E069	-45684
chr2	44397410	44397842	E069	-45237
chr2	44397894	44398007	E069	-45072
chr2	44471277	44471863	E069	28198
chr2	44394522	44397099	E070	-45980
chr2	44397214	44397395	E070	-45684
chr2	44397410	44397842	E070	-45237
chr2	44397894	44398007	E070	-45072
chr2	44394522	44397099	E071	-45980
chr2	44397214	44397395	E071	-45684
chr2	44397410	44397842	E071	-45237
chr2	44397894	44398007	E071	-45072
chr2	44471277	44471863	E071	28198
chr2	44394522	44397099	E072	-45980
chr2	44397214	44397395	E072	-45684
chr2	44397410	44397842	E072	-45237
chr2	44397894	44398007	E072	-45072
chr2	44471277	44471863	E072	28198
chr2	44394522	44397099	E073	-45980
chr2	44397214	44397395	E073	-45684
chr2	44397410	44397842	E073	-45237
chr2	44397894	44398007	E073	-45072
chr2	44471277	44471863	E073	28198
chr2	44394522	44397099	E074	-45980
chr2	44397214	44397395	E074	-45684
chr2	44397410	44397842	E074	-45237
chr2	44397894	44398007	E074	-45072
chr2	44394522	44397099	E081	-45980
chr2	44397214	44397395	E081	-45684
chr2	44397410	44397842	E081	-45237
chr2	44397894	44398007	E081	-45072
chr2	44394522	44397099	E082	-45980
chr2	44397214	44397395	E082	-45684
chr2	44397410	44397842	E082	-45237
chr2	44397894	44398007	E082	-45072