rs2749100

Organism: Homo sapiens

Alleles: G>T

Gene : Feature

PGM1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0312 (9343/29918,GnomAD)
T=0334 (9726/29118,TOPMED)
T=0334 (1671/5008,1000G)
T=0222 (855/3854,ALSPAC)
T=0221 (819/3708,TWINSUK)

Position: chr1:63659308 (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.63659308G>T
GRCh37.p13 chr 1	NC_000001.10:g.64124979G>T
PGM1 RefSeqGene	NG_016966.1:g.71033G>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=0.515	T=0.485
1000Genomes	American	Sub	694	G=0.610	T=0.390
1000Genomes	East Asian	Sub	1008	G=0.714	T=0.286
1000Genomes	Europe	Sub	1006	G=0.726	T=0.274
1000Genomes	Global	Study-wide	5008	G=0.666	T=0.334
1000Genomes	South Asian	Sub	978	G=0.800	T=0.200
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.778	T=0.222
The Genome Aggregation Database	African	Sub	8686	G=0.561	T=0.439
The Genome Aggregation Database	American	Sub	832	G=0.630	T=0.370
The Genome Aggregation Database	East Asian	Sub	1620	G=0.746	T=0.254
The Genome Aggregation Database	Europe	Sub	18478	G=0.744	T=0.255
The Genome Aggregation Database	Global	Study-wide	29918	G=0.687	T=0.312
The Genome Aggregation Database	Other	Sub	302	G=0.720	T=0.280
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.666	T=0.334
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.779	T=0.221

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
rs2749100	7.63E-07	alcohol consumption	21665994

eQTL of rs2749100 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 rs2749100 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	-46466
chr1	64078704	64079142	E067	-45837
chr1	64088634	64089292	E067	-35687
chr1	64078376	64078513	E068	-46466
chr1	64081448	64081915	E068	-43064
chr1	64082007	64082105	E068	-42874
chr1	64088634	64089292	E068	-35687
chr1	64139986	64141001	E068	15007
chr1	64078376	64078513	E069	-46466
chr1	64078704	64079142	E069	-45837
chr1	64081448	64081915	E069	-43064
chr1	64082007	64082105	E069	-42874
chr1	64156823	64156888	E069	31844
chr1	64157137	64157261	E069	32158
chr1	64163403	64163697	E069	38424
chr1	64163884	64164427	E069	38905
chr1	64165152	64165382	E069	40173
chr1	64108723	64108792	E070	-16187
chr1	64108901	64108951	E070	-16028
chr1	64108983	64109138	E070	-15841
chr1	64111546	64111722	E070	-13257
chr1	64168878	64169157	E070	43899
chr1	64169258	64169308	E070	44279
chr1	64169400	64169582	E070	44421
chr1	64081448	64081915	E071	-43064
chr1	64082007	64082105	E071	-42874
chr1	64082217	64082363	E071	-42616
chr1	64139986	64141001	E071	15007
chr1	64163203	64163347	E071	38224
chr1	64163403	64163697	E071	38424
chr1	64165152	64165382	E071	40173
chr1	64088634	64089292	E072	-35687
chr1	64089607	64090320	E072	-34659
chr1	64101428	64101659	E072	-23320
chr1	64102053	64102103	E072	-22876
chr1	64160611	64160818	E072	35632
chr1	64160918	64161040	E072	35939
chr1	64161077	64161221	E072	36098
chr1	64163203	64163347	E072	38224
chr1	64163403	64163697	E072	38424
chr1	64163884	64164427	E072	38905
chr1	64081448	64081915	E073	-43064
chr1	64082007	64082105	E073	-42874
chr1	64082007	64082105	E074	-42874
chr1	64082217	64082363	E074	-42616
chr1	64088634	64089292	E074	-35687
chr1	64091772	64091822	E074	-33157
chr1	64139986	64141001	E074	15007
chr1	64082007	64082105	E081	-42874
chr1	64082217	64082363	E081	-42616
chr1	64086499	64086636	E081	-38343
chr1	64086834	64087062	E081	-37917
chr1	64087157	64087315	E081	-37664
chr1	64087461	64087721	E081	-37258
chr1	64088634	64089292	E081	-35687
chr1	64090756	64090893	E081	-34086
chr1	64090914	64091024	E081	-33955
chr1	64109343	64110000	E081	-14979
chr1	64139986	64141001	E081	15007
chr1	64141023	64142025	E081	16044
chr1	64082007	64082105	E082	-42874
chr1	64082217	64082363	E082	-42616
chr1	64086499	64086636	E082	-38343
chr1	64086834	64087062	E082	-37917
chr1	64087157	64087315	E082	-37664
chr1	64087461	64087721	E082	-37258
chr1	64108901	64108951	E082	-16028
chr1	64108983	64109138	E082	-15841
chr1	64109343	64110000	E082	-14979
chr1	64111546	64111722	E082	-13257
chr1	64141023	64142025	E082	16044
chr1	64168878	64169157	E082	43899
chr1	64169258	64169308	E082	44279