rs2269235

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

PGM1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0259 (7755/29944,GnomAD)
G=0264 (7690/29118,TOPMED)
G=0279 (1399/5008,1000G)
G=0191 (736/3854,ALSPAC)
G=0183 (680/3708,TWINSUK)

Position: chr1:63653244 (GRCh38.p7) (1p31.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 68 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.63653244A>G
GRCh37.p13 chr 1	NC_000001.10:g.64118915A>G
PGM1 RefSeqGene	NG_016966.1:g.64969A>G

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	A=0.607	G=0.393
1000Genomes	American	Sub	694	A=0.590	G=0.410
1000Genomes	East Asian	Sub	1008	A=0.794	G=0.206
1000Genomes	Europe	Sub	1006	A=0.775	G=0.225
1000Genomes	Global	Study-wide	5008	A=0.721	G=0.279
1000Genomes	South Asian	Sub	978	A=0.830	G=0.170
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.809	G=0.191
The Genome Aggregation Database	African	Sub	8714	A=0.659	G=0.341
The Genome Aggregation Database	American	Sub	828	A=0.610	G=0.390
The Genome Aggregation Database	East Asian	Sub	1610	A=0.786	G=0.214
The Genome Aggregation Database	Europe	Sub	18490	A=0.780	G=0.219
The Genome Aggregation Database	Global	Study-wide	29944	A=0.741	G=0.259
The Genome Aggregation Database	Other	Sub	302	A=0.780	G=0.220
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.735	G=0.264
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.817	G=0.183

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
rs2269235	3.45E-08	alcohol consumption	21665994

eQTL of rs2269235 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 rs2269235 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	-40402
chr1	64078704	64079142	E067	-39773
chr1	64088634	64089292	E067	-29623
chr1	64078376	64078513	E068	-40402
chr1	64081448	64081915	E068	-37000
chr1	64082007	64082105	E068	-36810
chr1	64088634	64089292	E068	-29623
chr1	64139986	64141001	E068	21071
chr1	64078376	64078513	E069	-40402
chr1	64078704	64079142	E069	-39773
chr1	64081448	64081915	E069	-37000
chr1	64082007	64082105	E069	-36810
chr1	64156823	64156888	E069	37908
chr1	64157137	64157261	E069	38222
chr1	64163403	64163697	E069	44488
chr1	64163884	64164427	E069	44969
chr1	64165152	64165382	E069	46237
chr1	64108723	64108792	E070	-10123
chr1	64108901	64108951	E070	-9964
chr1	64108983	64109138	E070	-9777
chr1	64111546	64111722	E070	-7193
chr1	64081448	64081915	E071	-37000
chr1	64082007	64082105	E071	-36810
chr1	64082217	64082363	E071	-36552
chr1	64139986	64141001	E071	21071
chr1	64163203	64163347	E071	44288
chr1	64163403	64163697	E071	44488
chr1	64165152	64165382	E071	46237
chr1	64088634	64089292	E072	-29623
chr1	64089607	64090320	E072	-28595
chr1	64101428	64101659	E072	-17256
chr1	64102053	64102103	E072	-16812
chr1	64160611	64160818	E072	41696
chr1	64160918	64161040	E072	42003
chr1	64161077	64161221	E072	42162
chr1	64163203	64163347	E072	44288
chr1	64163403	64163697	E072	44488
chr1	64163884	64164427	E072	44969
chr1	64081448	64081915	E073	-37000
chr1	64082007	64082105	E073	-36810
chr1	64082007	64082105	E074	-36810
chr1	64082217	64082363	E074	-36552
chr1	64088634	64089292	E074	-29623
chr1	64091772	64091822	E074	-27093
chr1	64139986	64141001	E074	21071
chr1	64082007	64082105	E081	-36810
chr1	64082217	64082363	E081	-36552
chr1	64086499	64086636	E081	-32279
chr1	64086834	64087062	E081	-31853
chr1	64087157	64087315	E081	-31600
chr1	64087461	64087721	E081	-31194
chr1	64088634	64089292	E081	-29623
chr1	64090756	64090893	E081	-28022
chr1	64090914	64091024	E081	-27891
chr1	64109343	64110000	E081	-8915
chr1	64139986	64141001	E081	21071
chr1	64141023	64142025	E081	22108
chr1	64082007	64082105	E082	-36810
chr1	64082217	64082363	E082	-36552
chr1	64086499	64086636	E082	-32279
chr1	64086834	64087062	E082	-31853
chr1	64087157	64087315	E082	-31600
chr1	64087461	64087721	E082	-31194
chr1	64108901	64108951	E082	-9964
chr1	64108983	64109138	E082	-9777
chr1	64109343	64110000	E082	-8915
chr1	64111546	64111722	E082	-7193
chr1	64141023	64142025	E082	22108