rs212349

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

ATF2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0201 (6029/29920,GnomAD)
C=0243 (7091/29118,TOPMED)
C=0212 (1064/5008,1000G)
C=0154 (595/3854,ALSPAC)
C=0147 (546/3708,TWINSUK)

Position: chr2:175079670 (GRCh38.p7) (2q31.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 1 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.175079670T>C
GRCh37.p13 chr 2	NC_000002.11:g.175944398T>C
ATF2 RefSeqGene	NG_047045.1:g.93537A>G

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	T=0.626	C=0.374
1000Genomes	American	Sub	694	T=0.850	C=0.150
1000Genomes	East Asian	Sub	1008	T=0.867	C=0.133
1000Genomes	Europe	Sub	1006	T=0.826	C=0.174
1000Genomes	Global	Study-wide	5008	T=0.788	C=0.212
1000Genomes	South Asian	Sub	978	T=0.840	C=0.160
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.846	C=0.154
The Genome Aggregation Database	African	Sub	8718	T=0.640	C=0.360
The Genome Aggregation Database	American	Sub	838	T=0.870	C=0.130
The Genome Aggregation Database	East Asian	Sub	1608	T=0.887	C=0.113
The Genome Aggregation Database	Europe	Sub	18454	T=0.862	C=0.137
The Genome Aggregation Database	Global	Study-wide	29920	T=0.798	C=0.201
The Genome Aggregation Database	Other	Sub	302	T=0.800	C=0.200
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.756	C=0.243
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.853	C=0.147

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
rs212349	0.00062	alcohol consumption (maxi-drinks)	24277619

eQTL of rs212349 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:175944398	ATP5G3	ENSG00000154518.5	T>C	8.5565e-10	-104544	Cerebellum
Chr2:175944398	ATP5G3	ENSG00000154518.5	T>C	4.1341e-5	-104544	Cortex

meQTL of rs212349 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	175901757	175901821	E071	-42577