rs6066110

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

EYA2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0486 (14541/29890,GnomAD)
G=0472 (13752/29118,TOPMED)
A==0486 (2432/5008,1000G)
G=0434 (1673/3854,ALSPAC)
G=0447 (1659/3708,TWINSUK)

Position: chr20:46911158 (GRCh38.p7) (20q13.12)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 53 Enhancers around

Promoter: 16 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 20	NC_000020.11:g.46911158A>G
GRCh37.p13 chr 20	NC_000020.10:g.45539797A>G
EYA2 RefSeqGene	NG_011673.2:g.21289A>G

Gene: EYA2, EYA transcriptional coactivator and phosphatase 2(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
EYA2 transcript variant 1	NM_005244.4:c.	N/A	Intron Variant
EYA2 transcript variant 5	NM_172110.3:c.	N/A	Intron Variant
EYA2 transcript variant X2	XM_005260327.2:c.	N/A	Intron Variant
EYA2 transcript variant X1	XM_017027721.1:c.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.495	G=0.505
1000Genomes	American	Sub	694	A=0.600	G=0.400
1000Genomes	East Asian	Sub	1008	A=0.241	G=0.759
1000Genomes	Europe	Sub	1006	A=0.538	G=0.462
1000Genomes	Global	Study-wide	5008	A=0.486	G=0.514
1000Genomes	South Asian	Sub	978	A=0.590	G=0.410
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.566	G=0.434
The Genome Aggregation Database	African	Sub	8690	A=0.481	G=0.519
The Genome Aggregation Database	American	Sub	832	A=0.600	G=0.400
The Genome Aggregation Database	East Asian	Sub	1612	A=0.243	G=0.757
The Genome Aggregation Database	Europe	Sub	18454	A=0.546	G=0.453
The Genome Aggregation Database	Global	Study-wide	29890	A=0.513	G=0.486
The Genome Aggregation Database	Other	Sub	302	A=0.630	G=0.370
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.527	G=0.472
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.553	G=0.447

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

SNP ID	p-value	Traits	Study
rs6066110	0.000673	alcohol dependence	21314694

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

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 )
chr20	45557133	45557220	E067	17336
chr20	45557229	45557749	E067	17432
chr20	45557862	45558040	E067	18065
chr20	45558070	45558120	E067	18273
chr20	45559309	45559599	E068	19512
chr20	45559678	45559835	E068	19881
chr20	45560170	45560809	E068	20373
chr20	45560883	45560933	E068	21086
chr20	45556864	45556928	E069	17067
chr20	45557133	45557220	E069	17336
chr20	45559309	45559599	E069	19512
chr20	45559678	45559835	E069	19881
chr20	45572753	45572803	E069	32956
chr20	45572852	45572913	E069	33055
chr20	45573132	45573182	E069	33335
chr20	45557133	45557220	E071	17336
chr20	45557229	45557749	E071	17432
chr20	45557862	45558040	E071	18065
chr20	45558070	45558120	E071	18273
chr20	45560170	45560809	E071	20373
chr20	45559309	45559599	E072	19512
chr20	45559678	45559835	E072	19881
chr20	45560170	45560809	E072	20373
chr20	45572167	45572355	E072	32370
chr20	45572358	45572412	E072	32561
chr20	45572468	45572518	E072	32671
chr20	45533887	45534417	E073	-5380
chr20	45556864	45556928	E073	17067
chr20	45557133	45557220	E073	17336
chr20	45560170	45560809	E073	20373
chr20	45560883	45560933	E073	21086
chr20	45543506	45544075	E074	3709
chr20	45556673	45556713	E074	16876
chr20	45556864	45556928	E074	17067
chr20	45557133	45557220	E074	17336
chr20	45557229	45557749	E074	17432
chr20	45557133	45557220	E081	17336
chr20	45557229	45557749	E081	17432
chr20	45557862	45558040	E081	18065
chr20	45558070	45558120	E081	18273
chr20	45558288	45558404	E081	18491
chr20	45558591	45558740	E081	18794
chr20	45559073	45559127	E081	19276
chr20	45559309	45559599	E081	19512
chr20	45559678	45559835	E081	19881
chr20	45557133	45557220	E082	17336
chr20	45557229	45557749	E082	17432
chr20	45557862	45558040	E082	18065
chr20	45558070	45558120	E082	18273
chr20	45558288	45558404	E082	18491
chr20	45558591	45558740	E082	18794
chr20	45559073	45559127	E082	19276
chr20	45559309	45559599	E082	19512

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr20	45501047	45501540	E067	-38257
chr20	45523635	45525025	E067	-14772
chr20	45501047	45501540	E068	-38257
chr20	45522900	45523582	E068	-16215
chr20	45523635	45525025	E068	-14772
chr20	45501047	45501540	E069	-38257
chr20	45523635	45525025	E069	-14772
chr20	45501047	45501540	E071	-38257
chr20	45523635	45525025	E071	-14772
chr20	45501047	45501540	E072	-38257
chr20	45523635	45525025	E072	-14772
chr20	45523635	45525025	E073	-14772
chr20	45501047	45501540	E074	-38257
chr20	45523635	45525025	E074	-14772
chr20	45522900	45523582	E082	-16215
chr20	45523635	45525025	E082	-14772

rs6066110

Genomic Coordinates

Gene: EYA2, EYA transcriptional coactivator and phosphatase 2(plus strand)

Population Frequency

P-Value

eQTL of rs6066110 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs6066110 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Promoter Annotation (GRCh37.p13)