rs2188561

Organism: Homo sapiens

Alleles: C>A / C>T

Gene : Feature

SLC26A4 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0186 (5586/29920,GnomAD)
A=0242 (1212/5008,1000G)
A=0209 (807/3854,ALSPAC)
A=0223 (827/3708,TWINSUK)

Position: chr7:107695613 (GRCh38.p7) (7q22.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 7 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 7	NC_000007.14:g.107695613C>A
GRCh38.p7 chr 7	NC_000007.14:g.107695613C>T
GRCh37.p13 chr 7	NC_000007.13:g.107336058C>A
GRCh37.p13 chr 7	NC_000007.13:g.107336058C>T
SLC26A4 RefSeqGene	NG_008489.1:g.39979C>A
SLC26A4 RefSeqGene	NG_008489.1:g.39979C>T

Gene: SLC26A4, solute carrier family 26 member 4(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLC26A4 transcript	NM_000441.1:c.	N/A	Intron Variant
SLC26A4 transcript variant X1	XM_005250425.2:c.	N/A	Intron Variant
SLC26A4 transcript variant X2	XM_017012318.1:c.	N/A	Intron Variant
SLC26A4 transcript variant X3	XM_006716025.3:c.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.985	A=0.015
1000Genomes	American	Sub	694	C=0.750	A=0.250
1000Genomes	East Asian	Sub	1008	C=0.655	A=0.345
1000Genomes	Europe	Sub	1006	C=0.764	A=0.236
1000Genomes	Global	Study-wide	5008	C=0.758	A=0.242
1000Genomes	South Asian	Sub	978	C=0.550	A=0.450
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.791	A=0.209
The Genome Aggregation Database	African	Sub	8718	C=0.954	T=0.000
The Genome Aggregation Database	American	Sub	836	C=0.760	T=0.00,
The Genome Aggregation Database	East Asian	Sub	1614	C=0.636	T=0.000
The Genome Aggregation Database	Europe	Sub	18454	C=0.765	T=0.000
The Genome Aggregation Database	Global	Study-wide	29920	C=0.813	T=0.000
The Genome Aggregation Database	Other	Sub	298	C=0.780	T=0.00,
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.777	A=0.223

PMID	Title	Author	Journal
23743675	A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.	Kapoor M	Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs2188561	9E-06	alcohol consumption	23743675

eQTL of rs2188561 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr7:107336058	AC002467.7	ENSG00000241764.3	C>A	1.1747e-4	-48823	Cerebellum
Chr7:107336058	AC002467.7	ENSG00000241764.3	C>A	2.1985e-5	-48823	Frontal_Cortex_BA9
Chr7:107336058	AC002467.7	ENSG00000241764.3	C>A	1.0521e-4	-48823	Cortex
Chr7:107336058	AC002467.7	ENSG00000241764.3	C>A	4.1131e-5	-48823	Cerebellar_Hemisphere
Chr7:107336058	AC002467.7	ENSG00000241764.3	C>A	4.3055e-3	-48823	Caudate_basal_ganglia
Chr7:107336058	AC002467.7	ENSG00000241764.3	C>A	1.0776e-3	-48823	Nucleus_accumbens_basal_ganglia

meQTL of rs2188561 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 )
chr7	38748130	38748511	E081	-44013
chr7	38748631	38748876	E081	-43648
chr7	38748130	38748511	E082	-44013
chr7	38748631	38748876	E082	-43648
chr7	38815519	38815623	E082	22995
chr7	38815830	38815880	E082	23306
chr7	38815907	38815961	E082	23383