rs2749097

Organism: Homo sapiens

Alleles: C>G

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0189 (5664/29930,GnomAD)
G=0178 (5209/29118,TOPMED)
G=0203 (1018/5008,1000G)
G=0184 (711/3854,ALSPAC)
G=0179 (662/3708,TWINSUK)

Position: chr1:63661797 (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.63661797C>G
GRCh37.p13 chr 1	NC_000001.10:g.64127468C>G
PGM1 RefSeqGene	NG_016966.1:g.73522C>G

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.871	G=0.129
1000Genomes	American	Sub	694	C=0.660	G=0.340
1000Genomes	East Asian	Sub	1008	C=0.779	G=0.221
1000Genomes	Europe	Sub	1006	C=0.766	G=0.234
1000Genomes	Global	Study-wide	5008	C=0.797	G=0.203
1000Genomes	South Asian	Sub	978	C=0.840	G=0.160
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.816	G=0.184
The Genome Aggregation Database	African	Sub	8708	C=0.860	G=0.140
The Genome Aggregation Database	American	Sub	836	C=0.680	G=0.320
The Genome Aggregation Database	East Asian	Sub	1616	C=0.783	G=0.217
The Genome Aggregation Database	Europe	Sub	18472	C=0.796	G=0.203
The Genome Aggregation Database	Global	Study-wide	29930	C=0.810	G=0.189
The Genome Aggregation Database	Other	Sub	298	C=0.800	G=0.200
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.821	G=0.178
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.821	G=0.179

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
rs2749097	2E-09	alcohol consumption (transferrin glycosylation)	21665994

eQTL of rs2749097 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 rs2749097 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	-48955
chr1	64078704	64079142	E067	-48326
chr1	64088634	64089292	E067	-38176
chr1	64078376	64078513	E068	-48955
chr1	64081448	64081915	E068	-45553
chr1	64082007	64082105	E068	-45363
chr1	64088634	64089292	E068	-38176
chr1	64139986	64141001	E068	12518
chr1	64078376	64078513	E069	-48955
chr1	64078704	64079142	E069	-48326
chr1	64081448	64081915	E069	-45553
chr1	64082007	64082105	E069	-45363
chr1	64156823	64156888	E069	29355
chr1	64157137	64157261	E069	29669
chr1	64163403	64163697	E069	35935
chr1	64163884	64164427	E069	36416
chr1	64165152	64165382	E069	37684
chr1	64108723	64108792	E070	-18676
chr1	64108901	64108951	E070	-18517
chr1	64108983	64109138	E070	-18330
chr1	64111546	64111722	E070	-15746
chr1	64168878	64169157	E070	41410
chr1	64169258	64169308	E070	41790
chr1	64169400	64169582	E070	41932
chr1	64081448	64081915	E071	-45553
chr1	64082007	64082105	E071	-45363
chr1	64082217	64082363	E071	-45105
chr1	64139986	64141001	E071	12518
chr1	64163203	64163347	E071	35735
chr1	64163403	64163697	E071	35935
chr1	64165152	64165382	E071	37684
chr1	64088634	64089292	E072	-38176
chr1	64089607	64090320	E072	-37148
chr1	64101428	64101659	E072	-25809
chr1	64102053	64102103	E072	-25365
chr1	64160611	64160818	E072	33143
chr1	64160918	64161040	E072	33450
chr1	64161077	64161221	E072	33609
chr1	64163203	64163347	E072	35735
chr1	64163403	64163697	E072	35935
chr1	64163884	64164427	E072	36416
chr1	64081448	64081915	E073	-45553
chr1	64082007	64082105	E073	-45363
chr1	64082007	64082105	E074	-45363
chr1	64082217	64082363	E074	-45105
chr1	64088634	64089292	E074	-38176
chr1	64091772	64091822	E074	-35646
chr1	64139986	64141001	E074	12518
chr1	64082007	64082105	E081	-45363
chr1	64082217	64082363	E081	-45105
chr1	64086499	64086636	E081	-40832
chr1	64086834	64087062	E081	-40406
chr1	64087157	64087315	E081	-40153
chr1	64087461	64087721	E081	-39747
chr1	64088634	64089292	E081	-38176
chr1	64090756	64090893	E081	-36575
chr1	64090914	64091024	E081	-36444
chr1	64109343	64110000	E081	-17468
chr1	64139986	64141001	E081	12518
chr1	64141023	64142025	E081	13555
chr1	64082007	64082105	E082	-45363
chr1	64082217	64082363	E082	-45105
chr1	64086499	64086636	E082	-40832
chr1	64086834	64087062	E082	-40406
chr1	64087157	64087315	E082	-40153
chr1	64087461	64087721	E082	-39747
chr1	64108901	64108951	E082	-18517
chr1	64108983	64109138	E082	-18330
chr1	64109343	64110000	E082	-17468
chr1	64111546	64111722	E082	-15746
chr1	64141023	64142025	E082	13555
chr1	64168878	64169157	E082	41410
chr1	64169258	64169308	E082	41790