rs11789272

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

HACD4 : Intron Variant
LOC105375989 : Non Coding Transcript Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0308 (9223/29926,GnomAD)
A=0289 (8432/29118,TOPMED)
A=0357 (1786/5008,1000G)

Position: chr9:21030852 (GRCh38.p7) (9p21.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 45 Enhancers around

Promoter: 12 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 9	NC_000009.12:g.21030852G>A
GRCh37.p13 chr 9	NC_000009.11:g.21030851G>A

Molecule type	Change	Amino acid[Codon]	SO Term
HACD4 transcript variant 1	NM_001010915.4:c.	N/A	Intron Variant
HACD4 transcript variant 2	NM_001321883.1:c.	N/A	Intron Variant
HACD4 transcript variant 3	NM_001321903.1:c.	N/A	Intron Variant
HACD4 transcript variant X1	XM_017014713.1:c.	N/A	Intron Variant
HACD4 transcript variant X2	XM_017014714.1:c.	N/A	Intron Variant
HACD4 transcript variant X4	XM_011517876.2:c.	N/A	Genic Upstream Transcript Variant
HACD4 transcript variant X3	XR_001746293.1:n.	N/A	Intron Variant

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105375989 transcript variant X1	XR_929514.2:n.431G>A	G>A	Non Coding Transcript Variant
LOC105375989 transcript variant X2	XR_001746633.1:n....XR_001746633.1:n.431G>A	G>A	Non Coding Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.684	A=0.316
1000Genomes	American	Sub	694	G=0.570	A=0.430
1000Genomes	East Asian	Sub	1008	G=0.476	A=0.524
1000Genomes	Europe	Sub	1006	G=0.733	A=0.267
1000Genomes	Global	Study-wide	5008	G=0.643	A=0.357
1000Genomes	South Asian	Sub	978	G=0.720	A=0.280
The Genome Aggregation Database	African	Sub	8708	G=0.688	A=0.312
The Genome Aggregation Database	American	Sub	838	G=0.560	A=0.440
The Genome Aggregation Database	East Asian	Sub	1620	G=0.485	A=0.515
The Genome Aggregation Database	Europe	Sub	18458	G=0.715	A=0.284
The Genome Aggregation Database	Global	Study-wide	29926	G=0.691	A=0.308
The Genome Aggregation Database	Other	Sub	302	G=0.820	A=0.180
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.710	A=0.289

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

SNP ID	p-value	Traits	Study
rs11789272	5.42E-05	alcohol dependence	21314694

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr9:21030851	PTPLAD2	ENSG00000188921.12	G>A	1.1510e-5	-784	Caudate_basal_ganglia

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

There is no significant Hi-C chromatin interaction data for this SNP.

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr9	20990090	20990317	E068	-40534
chr9	20990319	20990463	E068	-40388
chr9	20990614	20990664	E068	-40187
chr9	20990686	20990901	E068	-39950
chr9	20997604	20997752	E068	-33099
chr9	20997776	20997973	E068	-32878
chr9	21069876	21069924	E068	39025
chr9	21069973	21070737	E068	39122
chr9	20989954	20990083	E069	-40768
chr9	20990090	20990317	E069	-40534
chr9	20990319	20990463	E069	-40388
chr9	20990614	20990664	E069	-40187
chr9	20990686	20990901	E069	-39950
chr9	20990980	20991157	E069	-39694
chr9	20990090	20990317	E070	-40534
chr9	20990319	20990463	E070	-40388
chr9	20990614	20990664	E070	-40187
chr9	20990686	20990901	E070	-39950
chr9	21014928	21014988	E070	-15863
chr9	21015253	21015383	E070	-15468
chr9	21015406	21015498	E070	-15353
chr9	21015588	21015696	E070	-15155
chr9	21015968	21016020	E070	-14831
chr9	21016133	21016189	E070	-14662
chr9	21016375	21016463	E070	-14388
chr9	21016480	21016546	E070	-14305
chr9	21016561	21016611	E070	-14240
chr9	20990090	20990317	E071	-40534
chr9	20990319	20990463	E071	-40388
chr9	20990614	20990664	E071	-40187
chr9	20990686	20990901	E071	-39950
chr9	20990980	20991157	E071	-39694
chr9	21015588	21015696	E071	-15155
chr9	21015968	21016020	E071	-14831
chr9	21016133	21016189	E071	-14662
chr9	21069876	21069924	E071	39025
chr9	21069973	21070737	E071	39122
chr9	20990319	20990463	E072	-40388
chr9	20990614	20990664	E072	-40187
chr9	21069876	21069924	E073	39025
chr9	21069973	21070737	E073	39122
chr9	20990090	20990317	E074	-40534
chr9	20990319	20990463	E074	-40388
chr9	20990614	20990664	E074	-40187
chr9	20990686	20990901	E074	-39950

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr9	21030492	21031930	E067	0
chr9	21031987	21032059	E067	1136
chr9	21030492	21031930	E068	0
chr9	21031987	21032059	E068	1136
chr9	21030492	21031930	E069	0
chr9	21030492	21031930	E071	0
chr9	21031987	21032059	E071	1136
chr9	21030492	21031930	E072	0
chr9	21031987	21032059	E072	1136
chr9	21030492	21031930	E073	0
chr9	21031987	21032059	E073	1136
chr9	21030492	21031930	E074	0