rs2269247

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

PGM1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0184 (5358/29118,TOPMED)
T=0222 (1110/5008,1000G)
T=0187 (719/3854,ALSPAC)
T=0179 (662/3708,TWINSUK)

Position: chr1:63641613 (GRCh38.p7) (1p31.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 57 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.63641613C>T
GRCh37.p13 chr 1	NC_000001.10:g.64107284C>T
PGM1 RefSeqGene	NG_016966.1:g.53338C>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	C=0.806	T=0.194
1000Genomes	American	Sub	694	C=0.610	T=0.390
1000Genomes	East Asian	Sub	1008	C=0.791	T=0.209
1000Genomes	Europe	Sub	1006	C=0.794	T=0.206
1000Genomes	Global	Study-wide	5008	C=0.778	T=0.222
1000Genomes	South Asian	Sub	978	C=0.830	T=0.170
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.813	T=0.187
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.816	T=0.184
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.821	T=0.179

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
rs2269247	2.98E-07	alcohol consumption	21665994

eQTL of rs2269247 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 rs2269247 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	-28771
chr1	64078704	64079142	E067	-28142
chr1	64088634	64089292	E067	-17992
chr1	64078376	64078513	E068	-28771
chr1	64081448	64081915	E068	-25369
chr1	64082007	64082105	E068	-25179
chr1	64088634	64089292	E068	-17992
chr1	64139986	64141001	E068	32702
chr1	64078376	64078513	E069	-28771
chr1	64078704	64079142	E069	-28142
chr1	64081448	64081915	E069	-25369
chr1	64082007	64082105	E069	-25179
chr1	64156823	64156888	E069	49539
chr1	64157137	64157261	E069	49853
chr1	64108723	64108792	E070	1439
chr1	64108901	64108951	E070	1617
chr1	64108983	64109138	E070	1699
chr1	64111546	64111722	E070	4262
chr1	64057933	64058108	E071	-49176
chr1	64081448	64081915	E071	-25369
chr1	64082007	64082105	E071	-25179
chr1	64082217	64082363	E071	-24921
chr1	64139986	64141001	E071	32702
chr1	64088634	64089292	E072	-17992
chr1	64089607	64090320	E072	-16964
chr1	64101428	64101659	E072	-5625
chr1	64102053	64102103	E072	-5181
chr1	64081448	64081915	E073	-25369
chr1	64082007	64082105	E073	-25179
chr1	64082007	64082105	E074	-25179
chr1	64082217	64082363	E074	-24921
chr1	64088634	64089292	E074	-17992
chr1	64091772	64091822	E074	-15462
chr1	64139986	64141001	E074	32702
chr1	64082007	64082105	E081	-25179
chr1	64082217	64082363	E081	-24921
chr1	64086499	64086636	E081	-20648
chr1	64086834	64087062	E081	-20222
chr1	64087157	64087315	E081	-19969
chr1	64087461	64087721	E081	-19563
chr1	64088634	64089292	E081	-17992
chr1	64090756	64090893	E081	-16391
chr1	64090914	64091024	E081	-16260
chr1	64109343	64110000	E081	2059
chr1	64139986	64141001	E081	32702
chr1	64141023	64142025	E081	33739
chr1	64082007	64082105	E082	-25179
chr1	64082217	64082363	E082	-24921
chr1	64086499	64086636	E082	-20648
chr1	64086834	64087062	E082	-20222
chr1	64087157	64087315	E082	-19969
chr1	64087461	64087721	E082	-19563
chr1	64108901	64108951	E082	1617
chr1	64108983	64109138	E082	1699
chr1	64109343	64110000	E082	2059
chr1	64111546	64111722	E082	4262
chr1	64141023	64142025	E082	33739

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	64058305	64060416	E067	-46868
chr1	64058305	64060416	E068	-46868
chr1	64058305	64060416	E069	-46868
chr1	64058305	64060416	E070	-46868
chr1	64058305	64060416	E071	-46868
chr1	64058305	64060416	E072	-46868
chr1	64058305	64060416	E073	-46868
chr1	64058305	64060416	E074	-46868
chr1	64058305	64060416	E082	-46868