SNP Detail Info-rs10489530

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

NGF : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0083 (2506/29882,GnomAD)
A=0108 (3155/29118,TOPMED)
A=0101 (506/5008,1000G)
A=0022 (85/3854,ALSPAC)
A=0020 (75/3708,TWINSUK)

Position: chr1:115297059 (GRCh38.p7) (1p13.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 19 Enhancers around

Promoter: 8 Promoters around

Molecule type	Change	Amino acid[Codon]	SO Term
NGF transcript	NM_002506.2:c.	N/A	Intron Variant
NGF transcript variant X2	XM_006710663.3:c.	N/A	Intron Variant
NGF transcript variant X1	XM_011541518.2:c.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.752	A=0.248
1000Genomes	American	Sub	694	G=0.930	A=0.070
1000Genomes	East Asian	Sub	1008	G=0.917	A=0.083
1000Genomes	Europe	Sub	1006	G=0.986	A=0.014
1000Genomes	Global	Study-wide	5008	G=0.899	A=0.101
1000Genomes	South Asian	Sub	978	G=0.970	A=0.030
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.978	A=0.022
The Genome Aggregation Database	African	Sub	8710	G=0.784	A=0.216
The Genome Aggregation Database	American	Sub	836	G=0.940	A=0.060
The Genome Aggregation Database	East Asian	Sub	1616	G=0.918	A=0.082
The Genome Aggregation Database	Europe	Sub	18428	G=0.976	A=0.023
The Genome Aggregation Database	Global	Study-wide	29882	G=0.916	A=0.083
The Genome Aggregation Database	Other	Sub	292	G=0.980	A=0.020
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.891	A=0.108
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.980	A=0.020

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
rs10489530	0.000865	alcohol dependence	21314694

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 )
chr1	115825219	115825310	E067	-14370
chr1	115844568	115844658	E067	4888
chr1	115856784	115856961	E067	17104
chr1	115825219	115825310	E068	-14370
chr1	115825427	115825867	E068	-13813
chr1	115856784	115856961	E068	17104
chr1	115844568	115844658	E069	4888
chr1	115856784	115856961	E069	17104
chr1	115844387	115844514	E070	4707
chr1	115844568	115844658	E070	4888
chr1	115856784	115856961	E070	17104
chr1	115844568	115844658	E071	4888
chr1	115856784	115856961	E071	17104
chr1	115857386	115857740	E071	17706
chr1	115844568	115844658	E072	4888
chr1	115844997	115845602	E072	5317
chr1	115844192	115844358	E074	4512
chr1	115844568	115844658	E074	4888
chr1	115856784	115856961	E081	17104

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	115879953	115880648	E067	40273
chr1	115879953	115880648	E068	40273
chr1	115879953	115880648	E069	40273
chr1	115879953	115880648	E071	40273
chr1	115879953	115880648	E072	40273
chr1	115879953	115880648	E073	40273
chr1	115880680	115881404	E073	41000
chr1	115879953	115880648	E074	40273

rs10489530