rs1153676

Organism: Homo sapiens

Alleles: C>A

Gene : Feature

ATF2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0208 (6235/29890,GnomAD)
A=0255 (7444/29118,TOPMED)
A=0222 (1112/5008,1000G)
A=0156 (600/3854,ALSPAC)
A=0149 (553/3708,TWINSUK)

Position: chr2:175116266 (GRCh38.p7) (2q31.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 2 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.175116266C>A
GRCh37.p13 chr 2	NC_000002.11:g.175980994C>A
ATF2 RefSeqGene	NG_047045.1:g.56941G>T

Gene: ATF2, activating transcription factor 2(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ATF2 transcript variant 2	NM_001256090.1:c.	N/A	Intron Variant
ATF2 transcript variant 3	NM_001256091.1:c.	N/A	Intron Variant
ATF2 transcript variant 4	NM_001256092.1:c.	N/A	Intron Variant
ATF2 transcript variant 5	NM_001256093.1:c.	N/A	Intron Variant
ATF2 transcript variant 6	NM_001256094.1:c.	N/A	Intron Variant
ATF2 transcript variant 1	NM_001880.3:c.	N/A	Intron Variant
ATF2 transcript variant 7	NR_045768.1:n.	N/A	Intron Variant
ATF2 transcript variant 8	NR_045769.1:n.	N/A	Intron Variant
ATF2 transcript variant 9	NR_045770.1:n.	N/A	Intron Variant
ATF2 transcript variant 10	NR_045771.1:n.	N/A	Intron Variant
ATF2 transcript variant 11	NR_045772.1:n.	N/A	Intron Variant
ATF2 transcript variant 12	NR_045773.1:n.	N/A	Intron Variant
ATF2 transcript variant 13	NR_045774.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.595	A=0.405
1000Genomes	American	Sub	694	C=0.850	A=0.150
1000Genomes	East Asian	Sub	1008	C=0.865	A=0.135
1000Genomes	Europe	Sub	1006	C=0.823	A=0.177
1000Genomes	Global	Study-wide	5008	C=0.778	A=0.222
1000Genomes	South Asian	Sub	978	C=0.840	A=0.160
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.844	A=0.156
The Genome Aggregation Database	African	Sub	8698	C=0.617	A=0.383
The Genome Aggregation Database	American	Sub	838	C=0.870	A=0.130
The Genome Aggregation Database	East Asian	Sub	1618	C=0.886	A=0.114
The Genome Aggregation Database	Europe	Sub	18434	C=0.861	A=0.138
The Genome Aggregation Database	Global	Study-wide	29890	C=0.791	A=0.208
The Genome Aggregation Database	Other	Sub	302	C=0.800	A=0.200
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.744	A=0.255
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.851	A=0.149

PMID	Title	Author	Journal
24277619	ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.	Quillen EE	Am J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID	p-value	Traits	Study
rs1153676	0.00062	alcohol consumption (maxi-drinks)	24277619

eQTL of rs1153676 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:175980994	ATP5G3	ENSG00000154518.5	C>A	8.5565e-10	-67948	Cerebellum
Chr2:175980994	ATP5G3	ENSG00000154518.5	C>A	4.1341e-5	-67948	Cortex

meQTL of rs1153676 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 )
chr2	176021236	176021405	E069	40242
chr2	176021441	176021589	E069	40447