rs1487539

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

GLMN : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0135 (4069/29958,GnomAD)
C==0117 (3406/29118,TOPMED)
C==0068 (341/5008,1000G)
C==0199 (766/3854,ALSPAC)
C==0194 (721/3708,TWINSUK)

Position: chr1:92274142 (GRCh38.p7) (1p22.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 9 Enhancers around

Promoter: 13 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.92274142C>T
GRCh37.p13 chr 1	NC_000001.10:g.92739699C>T
GLMN RefSeqGene	NG_009796.1:g.29868G>A

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	Intron Variant
GLMN transcript variant 1	NM_053274.2:c.	N/A	Intron Variant
GLMN transcript variant 3	NR_135089.1:n.	N/A	Intron Variant
GLMN transcript variant X7	XM_005270401.3:c.	N/A	Intron Variant
GLMN transcript variant X9	XM_006710309.2:c.	N/A	Intron Variant
GLMN transcript variant X3	XM_011540546.2:c.	N/A	Intron Variant
GLMN transcript variant X1	XM_017000137.1:c.	N/A	Intron Variant
GLMN transcript variant X2	XM_017000138.1:c.	N/A	Intron Variant
GLMN transcript variant X4	XM_017000139.1:c.	N/A	Intron Variant
GLMN transcript variant X5	XM_017000140.1:c.	N/A	Intron Variant
GLMN transcript variant X6	XM_017000141.1:c.	N/A	Intron Variant
GLMN transcript variant X10	XM_017000142.1:c.	N/A	Intron Variant
GLMN transcript variant X11	XM_017000143.1:c.	N/A	Intron Variant
GLMN transcript variant X13	XM_017000144.1:c.	N/A	Intron Variant
GLMN transcript variant X8	XR_001736941.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.023	T=0.977
1000Genomes	American	Sub	694	C=0.110	T=0.890
1000Genomes	East Asian	Sub	1008	C=0.002	T=0.998
1000Genomes	Europe	Sub	1006	C=0.193	T=0.807
1000Genomes	Global	Study-wide	5008	C=0.068	T=0.932
1000Genomes	South Asian	Sub	978	C=0.040	T=0.960
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.199	T=0.801
The Genome Aggregation Database	African	Sub	8712	C=0.049	T=0.951
The Genome Aggregation Database	American	Sub	838	C=0.100	T=0.900
The Genome Aggregation Database	East Asian	Sub	1620	C=0.002	T=0.998
The Genome Aggregation Database	Europe	Sub	18486	C=0.190	T=0.809
The Genome Aggregation Database	Global	Study-wide	29958	C=0.135	T=0.864
The Genome Aggregation Database	Other	Sub	302	C=0.090	T=0.910
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.117	T=0.883
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.194	T=0.806

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
rs1487539	2.75E-05	alcohol consumption	23953852

eQTL of rs1487539 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:92739699	RP4-621B10.8	ENSG00000273487.1	C>T	2.7662e-4	84905	Frontal_Cortex_BA9

meQTL of rs1487539 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	92765994	92766180	E067	26295
chr1	92765994	92766180	E068	26295
chr1	92765994	92766180	E069	26295
chr1	92765994	92766180	E070	26295
chr1	92705722	92705867	E072	-33832
chr1	92765994	92766180	E072	26295
chr1	92765994	92766180	E073	26295
chr1	92765994	92766180	E074	26295
chr1	92765994	92766180	E082	26295

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	92763588	92763688	E067	23889
chr1	92763733	92765237	E067	24034
chr1	92763733	92765237	E068	24034
chr1	92763733	92765237	E069	24034
chr1	92763588	92763688	E070	23889
chr1	92763733	92765237	E070	24034
chr1	92763733	92765237	E071	24034
chr1	92763733	92765237	E072	24034
chr1	92763733	92765237	E073	24034
chr1	92763733	92765237	E074	24034
chr1	92763733	92765237	E081	24034
chr1	92763588	92763688	E082	23889
chr1	92763733	92765237	E082	24034