rs12027168

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

PGM1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0219 (6447/29380,GnomAD)
C=0204 (5959/29118,TOPMED)
C=0239 (1196/5008,1000G)
C=0193 (743/3854,ALSPAC)
C=0187 (694/3708,TWINSUK)

Position: chr1:63654942 (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.63654942T>C
GRCh37.p13 chr 1	NC_000001.10:g.64120613T>C
PGM1 RefSeqGene	NG_016966.1:g.66667T>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=0.825	C=0.175
1000Genomes	American	Sub	694	T=0.600	C=0.400
1000Genomes	East Asian	Sub	1008	T=0.709	C=0.291
1000Genomes	Europe	Sub	1006	T=0.774	C=0.226
1000Genomes	Global	Study-wide	5008	T=0.761	C=0.239
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=0.807	C=0.193
The Genome Aggregation Database	African	Sub	8616	T=0.807	C=0.193
The Genome Aggregation Database	American	Sub	802	T=0.620	C=0.380
The Genome Aggregation Database	East Asian	Sub	1618	T=0.711	C=0.289
The Genome Aggregation Database	Europe	Sub	18046	T=0.781	C=0.218
The Genome Aggregation Database	Global	Study-wide	29380	T=0.780	C=0.219
The Genome Aggregation Database	Other	Sub	298	T=0.790	C=0.210
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.795	C=0.204
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.813	C=0.187

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
rs12027168	6.25E-08	alcohol consumption	21665994

eQTL of rs12027168 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 rs12027168 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	-42100
chr1	64078704	64079142	E067	-41471
chr1	64088634	64089292	E067	-31321
chr1	64078376	64078513	E068	-42100
chr1	64081448	64081915	E068	-38698
chr1	64082007	64082105	E068	-38508
chr1	64088634	64089292	E068	-31321
chr1	64139986	64141001	E068	19373
chr1	64078376	64078513	E069	-42100
chr1	64078704	64079142	E069	-41471
chr1	64081448	64081915	E069	-38698
chr1	64082007	64082105	E069	-38508
chr1	64156823	64156888	E069	36210
chr1	64157137	64157261	E069	36524
chr1	64163403	64163697	E069	42790
chr1	64163884	64164427	E069	43271
chr1	64165152	64165382	E069	44539
chr1	64108723	64108792	E070	-11821
chr1	64108901	64108951	E070	-11662
chr1	64108983	64109138	E070	-11475
chr1	64111546	64111722	E070	-8891
chr1	64168878	64169157	E070	48265
chr1	64169258	64169308	E070	48645
chr1	64169400	64169582	E070	48787
chr1	64081448	64081915	E071	-38698
chr1	64082007	64082105	E071	-38508
chr1	64082217	64082363	E071	-38250
chr1	64139986	64141001	E071	19373
chr1	64163203	64163347	E071	42590
chr1	64163403	64163697	E071	42790
chr1	64165152	64165382	E071	44539
chr1	64088634	64089292	E072	-31321
chr1	64089607	64090320	E072	-30293
chr1	64101428	64101659	E072	-18954
chr1	64102053	64102103	E072	-18510
chr1	64160611	64160818	E072	39998
chr1	64160918	64161040	E072	40305
chr1	64161077	64161221	E072	40464
chr1	64163203	64163347	E072	42590
chr1	64163403	64163697	E072	42790
chr1	64163884	64164427	E072	43271
chr1	64081448	64081915	E073	-38698
chr1	64082007	64082105	E073	-38508
chr1	64082007	64082105	E074	-38508
chr1	64082217	64082363	E074	-38250
chr1	64088634	64089292	E074	-31321
chr1	64091772	64091822	E074	-28791
chr1	64139986	64141001	E074	19373
chr1	64082007	64082105	E081	-38508
chr1	64082217	64082363	E081	-38250
chr1	64086499	64086636	E081	-33977
chr1	64086834	64087062	E081	-33551
chr1	64087157	64087315	E081	-33298
chr1	64087461	64087721	E081	-32892
chr1	64088634	64089292	E081	-31321
chr1	64090756	64090893	E081	-29720
chr1	64090914	64091024	E081	-29589
chr1	64109343	64110000	E081	-10613
chr1	64139986	64141001	E081	19373
chr1	64141023	64142025	E081	20410
chr1	64082007	64082105	E082	-38508
chr1	64082217	64082363	E082	-38250
chr1	64086499	64086636	E082	-33977
chr1	64086834	64087062	E082	-33551
chr1	64087157	64087315	E082	-33298
chr1	64087461	64087721	E082	-32892
chr1	64108901	64108951	E082	-11662
chr1	64108983	64109138	E082	-11475
chr1	64109343	64110000	E082	-10613
chr1	64111546	64111722	E082	-8891
chr1	64141023	64142025	E082	20410
chr1	64168878	64169157	E082	48265
chr1	64169258	64169308	E082	48645