rs11208264

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

PGM1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0300 (8991/29942,GnomAD)
C=0313 (9120/29118,TOPMED)
C=0321 (1607/5008,1000G)
C=0223 (860/3854,ALSPAC)
C=0225 (833/3708,TWINSUK)

Position: chr1:63659401 (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.63659401T>C
GRCh37.p13 chr 1	NC_000001.10:g.64125072T>C
PGM1 RefSeqGene	NG_016966.1:g.71126T>C

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	T=0.564	C=0.436
1000Genomes	American	Sub	694	T=0.610	C=0.390
1000Genomes	East Asian	Sub	1008	T=0.712	C=0.288
1000Genomes	Europe	Sub	1006	T=0.726	C=0.274
1000Genomes	Global	Study-wide	5008	T=0.679	C=0.321
1000Genomes	South Asian	Sub	978	T=0.800	C=0.200
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.777	C=0.223
The Genome Aggregation Database	African	Sub	8708	T=0.604	C=0.396
The Genome Aggregation Database	American	Sub	838	T=0.620	C=0.380
The Genome Aggregation Database	East Asian	Sub	1608	T=0.748	C=0.252
The Genome Aggregation Database	Europe	Sub	18486	T=0.743	C=0.256
The Genome Aggregation Database	Global	Study-wide	29942	T=0.699	C=0.300
The Genome Aggregation Database	Other	Sub	302	T=0.720	C=0.280
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.686	C=0.313
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.775	C=0.225

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
rs11208264	9.37E-07	alcohol consumption	21665994

eQTL of rs11208264 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 rs11208264 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	-46559
chr1	64078704	64079142	E067	-45930
chr1	64088634	64089292	E067	-35780
chr1	64078376	64078513	E068	-46559
chr1	64081448	64081915	E068	-43157
chr1	64082007	64082105	E068	-42967
chr1	64088634	64089292	E068	-35780
chr1	64139986	64141001	E068	14914
chr1	64078376	64078513	E069	-46559
chr1	64078704	64079142	E069	-45930
chr1	64081448	64081915	E069	-43157
chr1	64082007	64082105	E069	-42967
chr1	64156823	64156888	E069	31751
chr1	64157137	64157261	E069	32065
chr1	64163403	64163697	E069	38331
chr1	64163884	64164427	E069	38812
chr1	64165152	64165382	E069	40080
chr1	64108723	64108792	E070	-16280
chr1	64108901	64108951	E070	-16121
chr1	64108983	64109138	E070	-15934
chr1	64111546	64111722	E070	-13350
chr1	64168878	64169157	E070	43806
chr1	64169258	64169308	E070	44186
chr1	64169400	64169582	E070	44328
chr1	64081448	64081915	E071	-43157
chr1	64082007	64082105	E071	-42967
chr1	64082217	64082363	E071	-42709
chr1	64139986	64141001	E071	14914
chr1	64163203	64163347	E071	38131
chr1	64163403	64163697	E071	38331
chr1	64165152	64165382	E071	40080
chr1	64088634	64089292	E072	-35780
chr1	64089607	64090320	E072	-34752
chr1	64101428	64101659	E072	-23413
chr1	64102053	64102103	E072	-22969
chr1	64160611	64160818	E072	35539
chr1	64160918	64161040	E072	35846
chr1	64161077	64161221	E072	36005
chr1	64163203	64163347	E072	38131
chr1	64163403	64163697	E072	38331
chr1	64163884	64164427	E072	38812
chr1	64081448	64081915	E073	-43157
chr1	64082007	64082105	E073	-42967
chr1	64082007	64082105	E074	-42967
chr1	64082217	64082363	E074	-42709
chr1	64088634	64089292	E074	-35780
chr1	64091772	64091822	E074	-33250
chr1	64139986	64141001	E074	14914
chr1	64082007	64082105	E081	-42967
chr1	64082217	64082363	E081	-42709
chr1	64086499	64086636	E081	-38436
chr1	64086834	64087062	E081	-38010
chr1	64087157	64087315	E081	-37757
chr1	64087461	64087721	E081	-37351
chr1	64088634	64089292	E081	-35780
chr1	64090756	64090893	E081	-34179
chr1	64090914	64091024	E081	-34048
chr1	64109343	64110000	E081	-15072
chr1	64139986	64141001	E081	14914
chr1	64141023	64142025	E081	15951
chr1	64082007	64082105	E082	-42967
chr1	64082217	64082363	E082	-42709
chr1	64086499	64086636	E082	-38436
chr1	64086834	64087062	E082	-38010
chr1	64087157	64087315	E082	-37757
chr1	64087461	64087721	E082	-37351
chr1	64108901	64108951	E082	-16121
chr1	64108983	64109138	E082	-15934
chr1	64109343	64110000	E082	-15072
chr1	64111546	64111722	E082	-13350
chr1	64141023	64142025	E082	15951
chr1	64168878	64169157	E082	43806
chr1	64169258	64169308	E082	44186