rs2269238

Organism: Homo sapiens

Alleles: G>A / G>T

Gene : Feature

PGM1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0256 (7659/29910,GnomAD)
T=0259 (7559/29118,TOPMED)
G==0228 (2966/13006,GO-ESP)
T=0276 (1383/5008,1000G)
T=0191 (735/3854,ALSPAC)
T=0184 (681/3708,TWINSUK)

Position: chr1:63651866 (GRCh38.p7) (1p31.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 56 Enhancers around

Promoter: 9 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.63651866G>A
GRCh38.p7 chr 1	NC_000001.11:g.63651866G>T
GRCh37.p13 chr 1	NC_000001.10:g.64117537G>A
GRCh37.p13 chr 1	NC_000001.10:g.64117537G>T
PGM1 RefSeqGene	NG_016966.1:g.63591G>A
PGM1 RefSeqGene	NG_016966.1:g.63591G>T

Gene: PGM1, phosphoglucomutase 1(plus strand)

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

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.619	T=0.381
1000Genomes	American	Sub	694	G=0.590	T=0.410
1000Genomes	East Asian	Sub	1008	G=0.794	T=0.206
1000Genomes	Europe	Sub	1006	G=0.776	T=0.224
1000Genomes	Global	Study-wide	5008	G=0.724	T=0.276
1000Genomes	South Asian	Sub	978	G=0.830	T=0.170
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.809	T=0.191
The Genome Aggregation Database	African	Sub	8706	G=0.667	T=0.333
The Genome Aggregation Database	American	Sub	836	G=0.610	T=0.390
The Genome Aggregation Database	East Asian	Sub	1608	G=0.787	T=0.213
The Genome Aggregation Database	Europe	Sub	18458	G=0.781	T=0.218
The Genome Aggregation Database	Global	Study-wide	29910	G=0.743	T=0.256
The Genome Aggregation Database	Other	Sub	302	G=0.780	T=0.220
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.740	T=0.259
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.816	T=0.184

PMID	Title	Author	Journal
21665994	Genome-wide association study identifies two loci strongly affecting transferrin glycosylation.	Kutalik Z	Hum Mol Genet
19761607	Detecting purely epistatic multi-locus interactions by an omnibus permutation test on ensembles of two-locus analyses.	Wongseree W	BMC Bioinformatics

P-Value

SNP ID	p-value	Traits	Study
rs2269238	7.19E-08	alcohol consumption	21665994

eQTL of rs2269238 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 rs2269238 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	-28515
chr1	64078704	64079142	E067	-27886
chr1	64088634	64089292	E067	-17736
chr1	64078376	64078513	E068	-28515
chr1	64081448	64081915	E068	-25113
chr1	64082007	64082105	E068	-24923
chr1	64088634	64089292	E068	-17736
chr1	64139986	64141001	E068	32958
chr1	64078376	64078513	E069	-28515
chr1	64078704	64079142	E069	-27886
chr1	64081448	64081915	E069	-25113
chr1	64082007	64082105	E069	-24923
chr1	64156823	64156888	E069	49795
chr1	64108723	64108792	E070	1695
chr1	64108901	64108951	E070	1873
chr1	64108983	64109138	E070	1955
chr1	64111546	64111722	E070	4518
chr1	64057933	64058108	E071	-48920
chr1	64081448	64081915	E071	-25113
chr1	64082007	64082105	E071	-24923
chr1	64082217	64082363	E071	-24665
chr1	64139986	64141001	E071	32958
chr1	64088634	64089292	E072	-17736
chr1	64089607	64090320	E072	-16708
chr1	64101428	64101659	E072	-5369
chr1	64102053	64102103	E072	-4925
chr1	64081448	64081915	E073	-25113
chr1	64082007	64082105	E073	-24923
chr1	64082007	64082105	E074	-24923
chr1	64082217	64082363	E074	-24665
chr1	64088634	64089292	E074	-17736
chr1	64091772	64091822	E074	-15206
chr1	64139986	64141001	E074	32958
chr1	64082007	64082105	E081	-24923
chr1	64082217	64082363	E081	-24665
chr1	64086499	64086636	E081	-20392
chr1	64086834	64087062	E081	-19966
chr1	64087157	64087315	E081	-19713
chr1	64087461	64087721	E081	-19307
chr1	64088634	64089292	E081	-17736
chr1	64090756	64090893	E081	-16135
chr1	64090914	64091024	E081	-16004
chr1	64109343	64110000	E081	2315
chr1	64139986	64141001	E081	32958
chr1	64141023	64142025	E081	33995
chr1	64082007	64082105	E082	-24923
chr1	64082217	64082363	E082	-24665
chr1	64086499	64086636	E082	-20392
chr1	64086834	64087062	E082	-19966
chr1	64087157	64087315	E082	-19713
chr1	64087461	64087721	E082	-19307
chr1	64108901	64108951	E082	1873
chr1	64108983	64109138	E082	1955
chr1	64109343	64110000	E082	2315
chr1	64111546	64111722	E082	4518
chr1	64141023	64142025	E082	33995

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	64058305	64060416	E067	-46612
chr1	64058305	64060416	E068	-46612
chr1	64058305	64060416	E069	-46612
chr1	64058305	64060416	E070	-46612
chr1	64058305	64060416	E071	-46612
chr1	64058305	64060416	E072	-46612
chr1	64058305	64060416	E073	-46612
chr1	64058305	64060416	E074	-46612
chr1	64058305	64060416	E082	-46612