rs3790857

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

PGM1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0192 (5753/29944,GnomAD)
T=0163 (4745/29118,TOPMED)
T=0199 (995/5008,1000G)
T=0191 (736/3854,ALSPAC)
T=0186 (688/3708,TWINSUK)

Position: chr1:63646195 (GRCh38.p7) (1p31.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 59 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.63646195C>T
GRCh37.p13 chr 1	NC_000001.10:g.64111866C>T
PGM1 RefSeqGene	NG_016966.1:g.57920C>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	C=0.904	T=0.096
1000Genomes	American	Sub	694	C=0.610	T=0.390
1000Genomes	East Asian	Sub	1008	C=0.793	T=0.207
1000Genomes	Europe	Sub	1006	C=0.775	T=0.225
1000Genomes	Global	Study-wide	5008	C=0.801	T=0.199
1000Genomes	South Asian	Sub	978	C=0.840	T=0.160
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.809	T=0.191
The Genome Aggregation Database	African	Sub	8722	C=0.887	T=0.113
The Genome Aggregation Database	American	Sub	838	C=0.620	T=0.380
The Genome Aggregation Database	East Asian	Sub	1612	C=0.785	T=0.215
The Genome Aggregation Database	Europe	Sub	18470	C=0.781	T=0.218
The Genome Aggregation Database	Global	Study-wide	29944	C=0.807	T=0.192
The Genome Aggregation Database	Other	Sub	302	C=0.790	T=0.210
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.837	T=0.163
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=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
19761607	Detecting purely epistatic multi-locus interactions by an omnibus permutation test on ensembles of two-locus analyses.	Wongseree W	BMC Bioinformatics

P-Value

SNP ID	p-value	Traits	Study
rs3790857	1.37E-07	alcohol consumption	21665994

eQTL of rs3790857 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 rs3790857 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	-33353
chr1	64078704	64079142	E067	-32724
chr1	64088634	64089292	E067	-22574
chr1	64078376	64078513	E068	-33353
chr1	64081448	64081915	E068	-29951
chr1	64082007	64082105	E068	-29761
chr1	64088634	64089292	E068	-22574
chr1	64139986	64141001	E068	28120
chr1	64078376	64078513	E069	-33353
chr1	64078704	64079142	E069	-32724
chr1	64081448	64081915	E069	-29951
chr1	64082007	64082105	E069	-29761
chr1	64156823	64156888	E069	44957
chr1	64157137	64157261	E069	45271
chr1	64108723	64108792	E070	-3074
chr1	64108901	64108951	E070	-2915
chr1	64108983	64109138	E070	-2728
chr1	64111546	64111722	E070	-144
chr1	64081448	64081915	E071	-29951
chr1	64082007	64082105	E071	-29761
chr1	64082217	64082363	E071	-29503
chr1	64139986	64141001	E071	28120
chr1	64088634	64089292	E072	-22574
chr1	64089607	64090320	E072	-21546
chr1	64101428	64101659	E072	-10207
chr1	64102053	64102103	E072	-9763
chr1	64160611	64160818	E072	48745
chr1	64160918	64161040	E072	49052
chr1	64161077	64161221	E072	49211
chr1	64081448	64081915	E073	-29951
chr1	64082007	64082105	E073	-29761
chr1	64082007	64082105	E074	-29761
chr1	64082217	64082363	E074	-29503
chr1	64088634	64089292	E074	-22574
chr1	64091772	64091822	E074	-20044
chr1	64139986	64141001	E074	28120
chr1	64082007	64082105	E081	-29761
chr1	64082217	64082363	E081	-29503
chr1	64086499	64086636	E081	-25230
chr1	64086834	64087062	E081	-24804
chr1	64087157	64087315	E081	-24551
chr1	64087461	64087721	E081	-24145
chr1	64088634	64089292	E081	-22574
chr1	64090756	64090893	E081	-20973
chr1	64090914	64091024	E081	-20842
chr1	64109343	64110000	E081	-1866
chr1	64139986	64141001	E081	28120
chr1	64141023	64142025	E081	29157
chr1	64082007	64082105	E082	-29761
chr1	64082217	64082363	E082	-29503
chr1	64086499	64086636	E082	-25230
chr1	64086834	64087062	E082	-24804
chr1	64087157	64087315	E082	-24551
chr1	64087461	64087721	E082	-24145
chr1	64108901	64108951	E082	-2915
chr1	64108983	64109138	E082	-2728
chr1	64109343	64110000	E082	-1866
chr1	64111546	64111722	E082	-144
chr1	64141023	64142025	E082	29157