rs2072538

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

ATF2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0053 (1604/29976,GnomAD)
T=0041 (1202/29118,TOPMED)
T=0064 (322/5008,1000G)
T=0066 (256/3854,ALSPAC)
T=0067 (248/3708,TWINSUK)

Position: chr2:175097936 (GRCh38.p7) (2q31.1)

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 2	NC_000002.12:g.175097936C>T
GRCh37.p13 chr 2	NC_000002.11:g.175962664C>T
ATF2 RefSeqGene	NG_047045.1:g.75271G>A

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 1	NM_001880.3:c.	N/A	Intron Variant
ATF2 transcript variant 6	NM_001256094.1:c.	N/A	Genic Downstream Transcript 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=0.991	T=0.009
1000Genomes	American	Sub	694	C=0.950	T=0.050
1000Genomes	East Asian	Sub	1008	C=0.872	T=0.128
1000Genomes	Europe	Sub	1006	C=0.927	T=0.073
1000Genomes	Global	Study-wide	5008	C=0.936	T=0.064
1000Genomes	South Asian	Sub	978	C=0.930	T=0.070
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.934	T=0.066
The Genome Aggregation Database	African	Sub	8732	C=0.977	T=0.023
The Genome Aggregation Database	American	Sub	836	C=0.940	T=0.060
The Genome Aggregation Database	East Asian	Sub	1616	C=0.892	T=0.108
The Genome Aggregation Database	Europe	Sub	18490	C=0.937	T=0.062
The Genome Aggregation Database	Global	Study-wide	29976	C=0.946	T=0.053
The Genome Aggregation Database	Other	Sub	302	C=0.910	T=0.090
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.958	T=0.041
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.933	T=0.067

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
rs2072538	0.000236	alcohol consumption (maxi-drinks)	24277619

eQTL of rs2072538 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 rs2072538 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg05624214	chr4:17783261	FAM184B	0.0103143617013461	6.1189e-9

Genomic View

Chromatin Interaction

There is no significant Hi-C chromatin interaction data for this SNP.