SNP Detail Info-rs2092029

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

HMGXB4 : 2KB Upstream Variant
LOC105373017 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0482 (14414/29902,GnomAD)
T=0460 (13391/29114,TOPMED)
T=0471 (2361/5008,1000G)
C==0314 (1211/3854,ALSPAC)
C==0315 (1168/3708,TWINSUK)

Position: chr22:35256248 (GRCh38.p7) (22q12.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 17 Enhancers around

Promoter: 20 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 22	NC_000022.11:g.35256248C>T
GRCh37.p13 chr 22	NC_000022.10:g.35652241C>T

Molecule type	Change	Amino acid[Codon]	SO Term
HMGXB4 transcript variant 1	NM_001003681.2:c.	N/A	Upstream Transcript Variant
HMGXB4 transcript variant 2	NR_027780.1:n.	N/A	Upstream Transcript Variant
HMGXB4 transcript variant X1	XM_006724100.3:c.	N/A	Upstream Transcript Variant
HMGXB4 transcript variant X2	XM_006724101.3:c.	N/A	Upstream Transcript Variant
HMGXB4 transcript variant X3	XM_006724102.1:c.	N/A	Upstream Transcript Variant

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105373017 transcript variant X1	XR_938209.2:n.	N/A	Intron Variant
LOC105373017 transcript variant X3	XR_938210.2:n.	N/A	Intron Variant
LOC105373017 transcript variant X2	XR_938211.1:n.	N/A	Intron Variant
LOC105373017 transcript variant X4	XR_938212.2:n.	N/A	Intron Variant
LOC105373017 transcript variant X5	XR_938213.2:n.	N/A	Genic Upstream Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.900	T=0.100
1000Genomes	American	Sub	694	C=0.390	T=0.610
1000Genomes	East Asian	Sub	1008	C=0.477	T=0.523
1000Genomes	Europe	Sub	1006	C=0.319	T=0.681
1000Genomes	Global	Study-wide	5008	C=0.529	T=0.471
1000Genomes	South Asian	Sub	978	C=0.390	T=0.610
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.314	T=0.686
The Genome Aggregation Database	African	Sub	8708	C=0.816	T=0.184
The Genome Aggregation Database	American	Sub	838	C=0.380	T=0.620
The Genome Aggregation Database	East Asian	Sub	1614	C=0.449	T=0.551
The Genome Aggregation Database	Europe	Sub	18442	C=0.335	T=0.664
The Genome Aggregation Database	Global	Study-wide	29902	C=0.482	T=0.518
The Genome Aggregation Database	Other	Sub	300	C=0.270	T=0.730
Trans-Omics for Precision Medicine	Global	Study-wide	29114	C=0.540	T=0.460
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.315	T=0.685

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

SNP ID	p-value	Traits	Study
rs2092029	0.000447	alcohol consumption (maxi-drinks)	24277619

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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr22	35654921	35655002	E069	2680
chr22	35655227	35655271	E070	2986
chr22	35655506	35655560	E070	3265
chr22	35656453	35656503	E070	4212
chr22	35654921	35655002	E071	2680
chr22	35655060	35655153	E071	2819
chr22	35654921	35655002	E072	2680
chr22	35655060	35655153	E072	2819
chr22	35698957	35699062	E072	46716
chr22	35699183	35699267	E072	46942
chr22	35699307	35699451	E072	47066
chr22	35654921	35655002	E073	2680
chr22	35655060	35655153	E073	2819
chr22	35654921	35655002	E074	2680
chr22	35655060	35655153	E082	2819
chr22	35655227	35655271	E082	2986
chr22	35655506	35655560	E082	3265

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr22	35653002	35654849	E067	761
chr22	35694717	35696911	E067	42476
chr22	35653002	35654849	E068	761
chr22	35694717	35696911	E068	42476
chr22	35653002	35654849	E069	761
chr22	35694717	35696911	E069	42476
chr22	35653002	35654849	E070	761
chr22	35694717	35696911	E070	42476
chr22	35653002	35654849	E071	761
chr22	35694717	35696911	E071	42476
chr22	35653002	35654849	E072	761
chr22	35694717	35696911	E072	42476
chr22	35653002	35654849	E073	761
chr22	35694717	35696911	E073	42476
chr22	35653002	35654849	E074	761
chr22	35694717	35696911	E074	42476
chr22	35653002	35654849	E081	761
chr22	35694717	35696911	E081	42476
chr22	35653002	35654849	E082	761
chr22	35694717	35696911	E082	42476

rs2092029