rs2025607

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

GLMN : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0137 (4123/29944,GnomAD)
T=0119 (3483/29118,TOPMED)
T=0069 (348/5008,1000G)
T=0198 (765/3854,ALSPAC)
T=0194 (720/3708,TWINSUK)

Position: chr1:92424787 (GRCh38.p7) (1p22.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 0 Enhancer 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.92424787C>T
GRCh37.p13 chr 1	NC_000001.10:g.92890344C>T

Gene: GLMN, glomulin, FKBP associated protein(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
GLMN transcript variant 2	NM_001319683.1:c.	N/A	Genic Upstream Transcript Variant
GLMN transcript variant 1	NM_053274.2:c.	N/A	Genic Upstream Transcript Variant
GLMN transcript variant 3	NR_135089.1:n.	N/A	Genic Upstream Transcript Variant
GLMN transcript variant X3	XM_011540546.2:c.	N/A	Intron Variant
GLMN transcript variant X7	XM_005270401.3:c.	N/A	Genic Upstream Transcript Variant
GLMN transcript variant X9	XM_006710309.2:c.	N/A	Genic Upstream Transcript Variant
GLMN transcript variant X1	XM_017000137.1:c.	N/A	Genic Upstream Transcript Variant
GLMN transcript variant X2	XM_017000138.1:c.	N/A	Genic Upstream Transcript Variant
GLMN transcript variant X4	XM_017000139.1:c.	N/A	Genic Upstream Transcript Variant
GLMN transcript variant X5	XM_017000140.1:c.	N/A	Genic Upstream Transcript Variant
GLMN transcript variant X6	XM_017000141.1:c.	N/A	Genic Upstream Transcript Variant
GLMN transcript variant X10	XM_017000142.1:c.	N/A	Genic Upstream Transcript Variant
GLMN transcript variant X11	XM_017000143.1:c.	N/A	Genic Upstream Transcript Variant
GLMN transcript variant X13	XM_017000144.1:c.	N/A	Genic Upstream Transcript Variant
GLMN transcript variant X8	XR_001736941.1:n.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.974	T=0.026
1000Genomes	American	Sub	694	C=0.890	T=0.110
1000Genomes	East Asian	Sub	1008	C=0.998	T=0.002
1000Genomes	Europe	Sub	1006	C=0.806	T=0.194
1000Genomes	Global	Study-wide	5008	C=0.931	T=0.069
1000Genomes	South Asian	Sub	978	C=0.960	T=0.040
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.802	T=0.198
The Genome Aggregation Database	African	Sub	8718	C=0.945	T=0.055
The Genome Aggregation Database	American	Sub	838	C=0.900	T=0.100
The Genome Aggregation Database	East Asian	Sub	1620	C=0.998	T=0.002
The Genome Aggregation Database	Europe	Sub	18466	C=0.808	T=0.191
The Genome Aggregation Database	Global	Study-wide	29944	C=0.862	T=0.137
The Genome Aggregation Database	Other	Sub	302	C=0.910	T=0.090
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.880	T=0.119
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.806	T=0.194

PMID	Title	Author	Journal
23953852	Genome-wide association studies of maximum number of drinks.	Pan Y	J Psychiatr Res

P-Value

SNP ID	p-value	Traits	Study
rs2025607	2.89E-05	alcohol consumption	23953852

eQTL of rs2025607 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:92890344	RP4-621B10.8	ENSG00000273487.1	C>T	2.7662e-4	235550	Frontal_Cortex_BA9

meQTL of rs2025607 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.