rs2269246

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

PGM1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0217 (6516/29958,GnomAD)
C=0199 (5796/29118,TOPMED)
C=0229 (1147/5008,1000G)
C=0202 (777/3854,ALSPAC)
C=0194 (719/3708,TWINSUK)

Position: chr1:63641820 (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.63641820T>C
GRCh37.p13 chr 1	NC_000001.10:g.64107491T>C
PGM1 RefSeqGene	NG_016966.1:g.53545T>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=0.806	C=0.194
1000Genomes	American	Sub	694	T=0.600	C=0.400
1000Genomes	East Asian	Sub	1008	T=0.791	C=0.209
1000Genomes	Europe	Sub	1006	T=0.767	C=0.233
1000Genomes	Global	Study-wide	5008	T=0.771	C=0.229
1000Genomes	South Asian	Sub	978	T=0.830	C=0.170
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.798	C=0.202
The Genome Aggregation Database	African	Sub	8722	T=0.814	C=0.186
The Genome Aggregation Database	American	Sub	836	T=0.610	C=0.390
The Genome Aggregation Database	East Asian	Sub	1618	T=0.783	C=0.217
The Genome Aggregation Database	Europe	Sub	18480	T=0.775	C=0.224
The Genome Aggregation Database	Global	Study-wide	29958	T=0.782	C=0.217
The Genome Aggregation Database	Other	Sub	302	T=0.790	C=0.210
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.800	C=0.199
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.806	C=0.194

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
rs2269246	7.45E-08	alcohol consumption	21665994

eQTL of rs2269246 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 rs2269246 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	-28978
chr1	64078704	64079142	E067	-28349
chr1	64088634	64089292	E067	-18199
chr1	64078376	64078513	E068	-28978
chr1	64081448	64081915	E068	-25576
chr1	64082007	64082105	E068	-25386
chr1	64088634	64089292	E068	-18199
chr1	64139986	64141001	E068	32495
chr1	64078376	64078513	E069	-28978
chr1	64078704	64079142	E069	-28349
chr1	64081448	64081915	E069	-25576
chr1	64082007	64082105	E069	-25386
chr1	64156823	64156888	E069	49332
chr1	64157137	64157261	E069	49646
chr1	64108723	64108792	E070	1232
chr1	64108901	64108951	E070	1410
chr1	64108983	64109138	E070	1492
chr1	64111546	64111722	E070	4055
chr1	64057933	64058108	E071	-49383
chr1	64081448	64081915	E071	-25576
chr1	64082007	64082105	E071	-25386
chr1	64082217	64082363	E071	-25128
chr1	64139986	64141001	E071	32495
chr1	64088634	64089292	E072	-18199
chr1	64089607	64090320	E072	-17171
chr1	64101428	64101659	E072	-5832
chr1	64102053	64102103	E072	-5388
chr1	64081448	64081915	E073	-25576
chr1	64082007	64082105	E073	-25386
chr1	64082007	64082105	E074	-25386
chr1	64082217	64082363	E074	-25128
chr1	64088634	64089292	E074	-18199
chr1	64091772	64091822	E074	-15669
chr1	64139986	64141001	E074	32495
chr1	64082007	64082105	E081	-25386
chr1	64082217	64082363	E081	-25128
chr1	64086499	64086636	E081	-20855
chr1	64086834	64087062	E081	-20429
chr1	64087157	64087315	E081	-20176
chr1	64087461	64087721	E081	-19770
chr1	64088634	64089292	E081	-18199
chr1	64090756	64090893	E081	-16598
chr1	64090914	64091024	E081	-16467
chr1	64109343	64110000	E081	1852
chr1	64139986	64141001	E081	32495
chr1	64141023	64142025	E081	33532
chr1	64082007	64082105	E082	-25386
chr1	64082217	64082363	E082	-25128
chr1	64086499	64086636	E082	-20855
chr1	64086834	64087062	E082	-20429
chr1	64087157	64087315	E082	-20176
chr1	64087461	64087721	E082	-19770
chr1	64108901	64108951	E082	1410
chr1	64108983	64109138	E082	1492
chr1	64109343	64110000	E082	1852
chr1	64111546	64111722	E082	4055
chr1	64141023	64142025	E082	33532

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	64058305	64060416	E067	-47075
chr1	64058305	64060416	E068	-47075
chr1	64058305	64060416	E069	-47075
chr1	64058305	64060416	E070	-47075
chr1	64058305	64060416	E071	-47075
chr1	64058305	64060416	E072	-47075
chr1	64058305	64060416	E073	-47075
chr1	64058305	64060416	E074	-47075
chr1	64058305	64060416	E082	-47075