rs1478892

Organism: Homo sapiens

Alleles: G>T

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0357 (10701/29948,GnomAD)
T=0329 (9594/29118,TOPMED)
T=0469 (2347/5008,1000G)
T=0360 (1386/3854,ALSPAC)
T=0359 (1332/3708,TWINSUK)

Position: chr8:11591020 (GRCh38.p7) (8p23.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 13 Enhancers around

Promoter: 1 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 8	NC_000008.11:g.11591020G>T
GRCh37.p13 chr 8	NC_000008.10:g.11448529G>T

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.826	T=0.174
1000Genomes	American	Sub	694	G=0.480	T=0.520
1000Genomes	East Asian	Sub	1008	G=0.065	T=0.935
1000Genomes	Europe	Sub	1006	G=0.661	T=0.339
1000Genomes	Global	Study-wide	5008	G=0.531	T=0.469
1000Genomes	South Asian	Sub	978	G=0.520	T=0.480
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.640	T=0.360
The Genome Aggregation Database	African	Sub	8718	G=0.778	T=0.222
The Genome Aggregation Database	American	Sub	838	G=0.430	T=0.570
The Genome Aggregation Database	East Asian	Sub	1620	G=0.062	T=0.938
The Genome Aggregation Database	Europe	Sub	18470	G=0.637	T=0.362
The Genome Aggregation Database	Global	Study-wide	29948	G=0.642	T=0.357
The Genome Aggregation Database	Other	Sub	302	G=0.750	T=0.250
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.670	T=0.329
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.641	T=0.359

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
rs1478892	0.000442	alcohol consumption (maxi-drinks)	24277619

eQTL of rs1478892 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr8:11448529	RP11-481A20.10	ENSG00000254507.2	G>T	8.0518e-24	-413062	Cerebellum
Chr8:11448529	FAM66A	ENSG00000227888.3	G>T	8.2786e-9	-770998	Cerebellum
Chr8:11448529	RP11-351I21.7	ENSG00000254423.1	G>T	2.3439e-5	-784526	Cerebellum
Chr8:11448529	RP11-351I21.6	ENSG00000255556.2	G>T	1.8524e-6	-789245	Cerebellum
Chr8:11448529	RP11-481A20.10	ENSG00000254507.2	G>T	2.1118e-12	-413062	Frontal_Cortex_BA9
Chr8:11448529	FAM66D	ENSG00000255052.3	G>T	1.5649e-4	-524762	Frontal_Cortex_BA9
Chr8:11448529	FAM66A	ENSG00000227888.3	G>T	4.1081e-8	-770998	Frontal_Cortex_BA9
Chr8:11448529	FAM66A	ENSG00000227888.3	G>T	2.9894e-7	-770998	Hypothalamus
Chr8:11448529	FAM66A	ENSG00000227888.3	G>T	3.9980e-10	-770998	Cortex
Chr8:11448529	RP11-481A20.10	ENSG00000254507.2	G>T	1.2140e-19	-413062	Cerebellar_Hemisphere
Chr8:11448529	RP11-481A20.11	ENSG00000255098.1	G>T	3.5424e-19	-424514	Cerebellar_Hemisphere
Chr8:11448529	FAM66A	ENSG00000227888.3	G>T	3.3520e-10	-770998	Cerebellar_Hemisphere
Chr8:11448529	RP11-351I21.7	ENSG00000254423.1	G>T	9.1850e-7	-784526	Cerebellar_Hemisphere
Chr8:11448529	RP11-351I21.6	ENSG00000255556.2	G>T	1.7321e-7	-789245	Cerebellar_Hemisphere
Chr8:11448529	FAM90A25P	ENSG00000251402.3	G>T	5.5560e-7	-827070	Cerebellar_Hemisphere
Chr8:11448529	FAM66A	ENSG00000227888.3	G>T	4.6289e-13	-770998	Caudate_basal_ganglia
Chr8:11448529	RP11-351I21.6	ENSG00000255556.2	G>T	4.1891e-7	-789245	Caudate_basal_ganglia
Chr8:11448529	FAM66A	ENSG00000227888.3	G>T	1.7651e-8	-770998	Anterior_cingulate_cortex
Chr8:11448529	RP11-481A20.10	ENSG00000254507.2	G>T	1.0545e-4	-413062	Nucleus_accumbens_basal_ganglia

meQTL of rs1478892 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg21175976	chr8:11421337	BLK	0.0470306382392056	5.5336e-15

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 )
chr8	11450698	11452440	E070	2169
chr8	11456498	11456956	E070	7969
chr8	11457156	11457244	E070	8627
chr8	11457558	11457606	E070	9029
chr8	11458534	11459083	E070	10005
chr8	11459151	11459242	E070	10622
chr8	11498145	11498215	E070	49616
chr8	11496543	11496669	E071	48014
chr8	11410834	11411975	E081	-36554
chr8	11450698	11452440	E081	2169
chr8	11452893	11452943	E081	4364
chr8	11450698	11452440	E082	2169
chr8	11452766	11452889	E082	4237

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr8	11421406	11423242	E082	-25287