SNP Detail Info-rs11576729

Organism: Homo sapiens

Alleles: G>A / G>T

Gene : Feature

PGM1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0213 (6382/29952,GnomAD)
T=0226 (1130/5008,1000G)
T=0192 (739/3854,ALSPAC)
T=0186 (690/3708,TWINSUK)

Position: chr1:63648758 (GRCh38.p7) (1p31.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 56 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.63648758G>A
GRCh38.p7 chr 1	NC_000001.11:g.63648758G>T
GRCh37.p13 chr 1	NC_000001.10:g.64114429G>A
GRCh37.p13 chr 1	NC_000001.10:g.64114429G>T
PGM1 RefSeqGene	NG_016966.1:g.60483G>A
PGM1 RefSeqGene	NG_016966.1:g.60483G>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=0.804	T=0.196
1000Genomes	American	Sub	694	G=0.600	T=0.400
1000Genomes	East Asian	Sub	1008	G=0.792	T=0.208
1000Genomes	Europe	Sub	1006	G=0.776	T=0.224
1000Genomes	Global	Study-wide	5008	G=0.774	T=0.226
1000Genomes	South Asian	Sub	978	G=0.840	T=0.160
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.808	T=0.192
The Genome Aggregation Database	African	Sub	8718	G=0.816	T=0.184
The Genome Aggregation Database	American	Sub	838	G=0.620	T=0.380
The Genome Aggregation Database	East Asian	Sub	1612	G=0.787	T=0.213
The Genome Aggregation Database	Europe	Sub	18482	G=0.780	T=0.219
The Genome Aggregation Database	Global	Study-wide	29952	G=0.786	T=0.213
The Genome Aggregation Database	Other	Sub	302	G=0.790	T=0.210
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.814	T=0.186

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
rs11576729	9.15E-08	alcohol consumption	21665994

eQTL of rs11576729 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 rs11576729 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr1	64078376	64078513	E067	-30751
chr1	64078704	64079142	E067	-30122
chr1	64088634	64089292	E067	-19972
chr1	64078376	64078513	E068	-30751
chr1	64081448	64081915	E068	-27349
chr1	64082007	64082105	E068	-27159
chr1	64088634	64089292	E068	-19972
chr1	64139986	64141001	E068	30722
chr1	64078376	64078513	E069	-30751
chr1	64078704	64079142	E069	-30122
chr1	64081448	64081915	E069	-27349
chr1	64082007	64082105	E069	-27159
chr1	64156823	64156888	E069	47559
chr1	64157137	64157261	E069	47873
chr1	64108723	64108792	E070	-472
chr1	64108901	64108951	E070	-313
chr1	64108983	64109138	E070	-126
chr1	64111546	64111722	E070	2282
chr1	64081448	64081915	E071	-27349
chr1	64082007	64082105	E071	-27159
chr1	64082217	64082363	E071	-26901
chr1	64139986	64141001	E071	30722
chr1	64088634	64089292	E072	-19972
chr1	64089607	64090320	E072	-18944
chr1	64101428	64101659	E072	-7605
chr1	64102053	64102103	E072	-7161
chr1	64081448	64081915	E073	-27349
chr1	64082007	64082105	E073	-27159
chr1	64082007	64082105	E074	-27159
chr1	64082217	64082363	E074	-26901
chr1	64088634	64089292	E074	-19972
chr1	64091772	64091822	E074	-17442
chr1	64139986	64141001	E074	30722
chr1	64082007	64082105	E081	-27159
chr1	64082217	64082363	E081	-26901
chr1	64086499	64086636	E081	-22628
chr1	64086834	64087062	E081	-22202
chr1	64087157	64087315	E081	-21949
chr1	64087461	64087721	E081	-21543
chr1	64088634	64089292	E081	-19972
chr1	64090756	64090893	E081	-18371
chr1	64090914	64091024	E081	-18240
chr1	64109343	64110000	E081	79
chr1	64139986	64141001	E081	30722
chr1	64141023	64142025	E081	31759
chr1	64082007	64082105	E082	-27159
chr1	64082217	64082363	E082	-26901
chr1	64086499	64086636	E082	-22628
chr1	64086834	64087062	E082	-22202
chr1	64087157	64087315	E082	-21949
chr1	64087461	64087721	E082	-21543
chr1	64108901	64108951	E082	-313
chr1	64108983	64109138	E082	-126
chr1	64109343	64110000	E082	79
chr1	64111546	64111722	E082	2282
chr1	64141023	64142025	E082	31759

rs11576729