rs4643

Organism: Homo sapiens

Alleles: A>C

Gene : Feature

PGM1 : 3 Prime UTR Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0173 (5199/29966,GnomAD)
C=0153 (4467/29118,TOPMED)
C=0185 (925/5008,1000G)
C=0184 (711/3854,ALSPAC)
C=0178 (661/3708,TWINSUK)

Position: chr1:63659768 (GRCh38.p7) (1p31.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 73 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.63659768A>C
GRCh37.p13 chr 1	NC_000001.10:g.64125439A>C
PGM1 RefSeqGene	NG_016966.1:g.71493A>C

Gene: PGM1, phosphoglucomutase 1(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PGM1 transcript variant 1	NM_002633.2:c.	N/A	3 Prime UTR Variant
PGM1 transcript variant 2	NM_001172818.1:c.	N/A	3 Prime UTR Variant
PGM1 transcript variant 3	NM_001172819.1:c.	N/A	3 Prime UTR Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.936	C=0.064
1000Genomes	American	Sub	694	A=0.670	C=0.330
1000Genomes	East Asian	Sub	1008	A=0.779	C=0.221
1000Genomes	Europe	Sub	1006	A=0.766	C=0.234
1000Genomes	Global	Study-wide	5008	A=0.815	C=0.185
1000Genomes	South Asian	Sub	978	A=0.840	C=0.160
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.816	C=0.184
The Genome Aggregation Database	African	Sub	8716	A=0.915	C=0.085
The Genome Aggregation Database	American	Sub	836	A=0.680	C=0.320
The Genome Aggregation Database	East Asian	Sub	1616	A=0.781	C=0.219
The Genome Aggregation Database	Europe	Sub	18496	A=0.796	C=0.203
The Genome Aggregation Database	Global	Study-wide	29966	A=0.826	C=0.173
The Genome Aggregation Database	Other	Sub	302	A=0.790	C=0.210
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.846	C=0.153
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.822	C=0.178

PMID	Title	Author	Journal
21665994	Genome-wide association study identifies two loci strongly affecting transferrin glycosylation.	Kutalik Z	Hum Mol Genet

P-Value

SNP ID	p-value	Traits	Study
rs4643	2.31E-09	alcohol consumption	21665994

eQTL of rs4643 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 rs4643 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	64078376	64078513	E067	-46926
chr1	64078704	64079142	E067	-46297
chr1	64088634	64089292	E067	-36147
chr1	64078376	64078513	E068	-46926
chr1	64081448	64081915	E068	-43524
chr1	64082007	64082105	E068	-43334
chr1	64088634	64089292	E068	-36147
chr1	64139986	64141001	E068	14547
chr1	64078376	64078513	E069	-46926
chr1	64078704	64079142	E069	-46297
chr1	64081448	64081915	E069	-43524
chr1	64082007	64082105	E069	-43334
chr1	64156823	64156888	E069	31384
chr1	64157137	64157261	E069	31698
chr1	64163403	64163697	E069	37964
chr1	64163884	64164427	E069	38445
chr1	64165152	64165382	E069	39713
chr1	64108723	64108792	E070	-16647
chr1	64108901	64108951	E070	-16488
chr1	64108983	64109138	E070	-16301
chr1	64111546	64111722	E070	-13717
chr1	64168878	64169157	E070	43439
chr1	64169258	64169308	E070	43819
chr1	64169400	64169582	E070	43961
chr1	64081448	64081915	E071	-43524
chr1	64082007	64082105	E071	-43334
chr1	64082217	64082363	E071	-43076
chr1	64139986	64141001	E071	14547
chr1	64163203	64163347	E071	37764
chr1	64163403	64163697	E071	37964
chr1	64165152	64165382	E071	39713
chr1	64088634	64089292	E072	-36147
chr1	64089607	64090320	E072	-35119
chr1	64101428	64101659	E072	-23780
chr1	64102053	64102103	E072	-23336
chr1	64160611	64160818	E072	35172
chr1	64160918	64161040	E072	35479
chr1	64161077	64161221	E072	35638
chr1	64163203	64163347	E072	37764
chr1	64163403	64163697	E072	37964
chr1	64163884	64164427	E072	38445
chr1	64081448	64081915	E073	-43524
chr1	64082007	64082105	E073	-43334
chr1	64082007	64082105	E074	-43334
chr1	64082217	64082363	E074	-43076
chr1	64088634	64089292	E074	-36147
chr1	64091772	64091822	E074	-33617
chr1	64139986	64141001	E074	14547
chr1	64082007	64082105	E081	-43334
chr1	64082217	64082363	E081	-43076
chr1	64086499	64086636	E081	-38803
chr1	64086834	64087062	E081	-38377
chr1	64087157	64087315	E081	-38124
chr1	64087461	64087721	E081	-37718
chr1	64088634	64089292	E081	-36147
chr1	64090756	64090893	E081	-34546
chr1	64090914	64091024	E081	-34415
chr1	64109343	64110000	E081	-15439
chr1	64139986	64141001	E081	14547
chr1	64141023	64142025	E081	15584
chr1	64082007	64082105	E082	-43334
chr1	64082217	64082363	E082	-43076
chr1	64086499	64086636	E082	-38803
chr1	64086834	64087062	E082	-38377
chr1	64087157	64087315	E082	-38124
chr1	64087461	64087721	E082	-37718
chr1	64108901	64108951	E082	-16488
chr1	64108983	64109138	E082	-16301
chr1	64109343	64110000	E082	-15439
chr1	64111546	64111722	E082	-13717
chr1	64141023	64142025	E082	15584
chr1	64168878	64169157	E082	43439
chr1	64169258	64169308	E082	43819