rs9826473

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

EAF2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0250 (7494/29892,GnomAD)
T=0265 (7725/29118,TOPMED)
T=0185 (927/5008,1000G)
T=0285 (1098/3854,ALSPAC)
T=0284 (1052/3708,TWINSUK)

Position: chr3:121837372 (GRCh38.p7) (3q13.33)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 7 Enhancers around

Promoter: 10 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 3	NC_000003.12:g.121837372C>T
GRCh37.p13 chr 3	NC_000003.11:g.121556219C>T
IQCB1 RefSeqGene	NG_015887.1:g.2708G>A

Gene: EAF2, ELL associated factor 2(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
EAF2 transcript variant 2	NM_001320041.1:c.	N/A	Intron Variant
EAF2 transcript variant 1	NM_018456.5:c.	N/A	Intron Variant
EAF2 transcript variant X1	XM_005247618.3:c.	N/A	Intron Variant
EAF2 transcript variant X2	XM_017006861.1:c.	N/A	Intron Variant
EAF2 transcript variant X3	XM_017006862.1:c.	N/A	Intron Variant
EAF2 transcript variant X4	XM_017006863.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.733	T=0.267
1000Genomes	American	Sub	694	C=0.860	T=0.140
1000Genomes	East Asian	Sub	1008	C=0.894	T=0.106
1000Genomes	Europe	Sub	1006	C=0.725	T=0.275
1000Genomes	Global	Study-wide	5008	C=0.815	T=0.185
1000Genomes	South Asian	Sub	978	C=0.910	T=0.090
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.715	T=0.285
The Genome Aggregation Database	African	Sub	8698	C=0.745	T=0.255
The Genome Aggregation Database	American	Sub	836	C=0.860	T=0.140
The Genome Aggregation Database	East Asian	Sub	1618	C=0.917	T=0.083
The Genome Aggregation Database	Europe	Sub	18438	C=0.731	T=0.268
The Genome Aggregation Database	Global	Study-wide	29892	C=0.749	T=0.250
The Genome Aggregation Database	Other	Sub	302	C=0.790	T=0.210
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.734	T=0.265
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.716	T=0.284

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

P-Value

SNP ID	p-value	Traits	Study
rs9826473	0.000775	alcohol dependence	21314694

eQTL of rs9826473 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr3:121556219	IQCB1	ENSG00000173226.12	C>T	4.8526e-12	2293	Cerebellum
Chr3:121556219	SLC15A2	ENSG00000163406.6	C>T	7.5866e-24	-56717	Cerebellum
Chr3:121556219	IQCB1	ENSG00000173226.12	C>T	1.3081e-7	2293	Frontal_Cortex_BA9
Chr3:121556219	IQCB1	ENSG00000173226.12	C>T	3.5378e-6	2293	Hypothalamus
Chr3:121556219	IQCB1	ENSG00000173226.12	C>T	2.2547e-11	2293	Cortex
Chr3:121556219	IQCB1	ENSG00000173226.12	C>T	2.9963e-10	2293	Cerebellar_Hemisphere
Chr3:121556219	SLC15A2	ENSG00000163406.6	C>T	6.8466e-9	-56717	Cerebellar_Hemisphere
Chr3:121556219	IQCB1	ENSG00000173226.12	C>T	1.7752e-11	2293	Caudate_basal_ganglia
Chr3:121556219	IQCB1	ENSG00000173226.12	C>T	1.8333e-6	2293	Hippocampus
Chr3:121556219	IQCB1	ENSG00000173226.12	C>T	7.9988e-5	2293	Substantia_nigra
Chr3:121556219	IQCB1	ENSG00000173226.12	C>T	2.2446e-9	2293	Putamen_basal_ganglia
Chr3:121556219	IQCB1	ENSG00000173226.12	C>T	9.6301e-11	2293	Anterior_cingulate_cortex
Chr3:121556219	IQCB1	ENSG00000173226.12	C>T	3.1161e-9	2293	Nucleus_accumbens_basal_ganglia

meQTL of rs9826473 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 )
chr3	121552482	121552578	E067	-3641
chr3	121552482	121552578	E069	-3641
chr3	121555543	121555620	E069	-599
chr3	121552482	121552578	E071	-3641
chr3	121552482	121552578	E072	-3641
chr3	121555543	121555620	E073	-599
chr3	121552482	121552578	E074	-3641

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr3	121552911	121554938	E067	-1281
chr3	121552911	121554938	E068	-1281
chr3	121552911	121554938	E069	-1281
chr3	121552911	121554938	E070	-1281
chr3	121552911	121554938	E071	-1281
chr3	121552911	121554938	E072	-1281
chr3	121552911	121554938	E073	-1281
chr3	121552911	121554938	E074	-1281
chr3	121552911	121554938	E081	-1281
chr3	121552911	121554938	E082	-1281