rs11623923

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

SLC35F4 : Intron Variant
LOC105370519 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0122 (3587/29328,GnomAD)
A=0111 (3236/29118,TOPMED)
A=0091 (456/5008,1000G)
A=0166 (641/3854,ALSPAC)
A=0165 (610/3708,TWINSUK)

Position: chr14:57576035 (GRCh38.p7) (14q22.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 9 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 14	NC_000014.9:g.57576035G>A
GRCh37.p13 chr 14	NC_000014.8:g.58042753G>A

Gene: SLC35F4, solute carrier family 35 member F4(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLC35F4 transcript variant 2	NM_001206920.1:c.	N/A	Intron Variant
SLC35F4 transcript variant 1	NM_001306087.1:c.	N/A	Intron Variant
SLC35F4 transcript variant X1	XM_011536720.2:c.	N/A	Intron Variant
SLC35F4 transcript variant X3	XM_011536721.2:c.	N/A	Intron Variant
SLC35F4 transcript variant X4	XM_011536723.2:c.	N/A	Intron Variant
SLC35F4 transcript variant X5	XM_011536724.2:c.	N/A	Intron Variant
SLC35F4 transcript variant X9	XM_011536725.1:c.	N/A	Intron Variant
SLC35F4 transcript variant X2	XM_017021258.1:c.	N/A	Intron Variant
SLC35F4 transcript variant X8	XM_017021260.1:c.	N/A	Intron Variant
SLC35F4 transcript variant X6	XM_017021259.1:c.	N/A	Genic Downstream Transcript Variant
SLC35F4 transcript variant X10	XM_017021261.1:c.	N/A	Genic Downstream Transcript Variant
SLC35F4 transcript variant X9	XR_001750297.1:n.	N/A	Intron Variant
SLC35F4 transcript variant X11	XR_001750298.1:n.	N/A	Intron Variant
SLC35F4 transcript variant X12	XR_001750299.1:n.	N/A	Intron Variant
SLC35F4 transcript variant X7	XR_943418.2:n.	N/A	Intron Variant
SLC35F4 transcript variant X10	XR_943419.2:n.	N/A	Intron Variant

Gene: LOC105370519, uncharacterized LOC105370519(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105370519 transcript	XR_943909.2:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.973	A=0.027
1000Genomes	American	Sub	694	G=0.850	A=0.150
1000Genomes	East Asian	Sub	1008	G=0.963	A=0.037
1000Genomes	Europe	Sub	1006	G=0.816	A=0.184
1000Genomes	Global	Study-wide	5008	G=0.909	A=0.091
1000Genomes	South Asian	Sub	978	G=0.900	A=0.100
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.834	A=0.166
The Genome Aggregation Database	African	Sub	8602	G=0.958	A=0.042
The Genome Aggregation Database	American	Sub	822	G=0.840	A=0.160
The Genome Aggregation Database	East Asian	Sub	1610	G=0.965	A=0.035
The Genome Aggregation Database	Europe	Sub	17992	G=0.833	A=0.166
The Genome Aggregation Database	Global	Study-wide	29328	G=0.877	A=0.122
The Genome Aggregation Database	Other	Sub	302	G=0.850	A=0.150
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.888	A=0.111
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.835	A=0.165

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
rs11623923	0.000307	alcohol consumption (maxi-drinks)	24277619

eQTL of rs11623923 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 rs11623923 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 )
chr14	58025169	58025310	E070	-17443
chr14	58026120	58026185	E070	-16568
chr14	58032082	58032132	E070	-10621
chr14	58032173	58032442	E070	-10311
chr14	58032173	58032442	E081	-10311
chr14	58032771	58032821	E081	-9932
chr14	58032082	58032132	E082	-10621
chr14	58032173	58032442	E082	-10311
chr14	58032771	58032821	E082	-9932