SNP Detail Info-rs9593517

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

LINC00377 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0329 (9847/29898,GnomAD)
G=0370 (10790/29118,TOPMED)
G=0421 (2106/5008,1000G)
G=0263 (1015/3854,ALSPAC)
G=0254 (941/3708,TWINSUK)

Position: chr13:81019942 (GRCh38.p7) (13q31.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 10 Enhancers around

Promoter: 27 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 13	NC_000013.11:g.81019942A>G
GRCh37.p13 chr 13	NC_000013.10:g.81594077A>G

Molecule type	Change	Amino acid[Codon]	SO Term
LINC00377 transcript	NR_125770.1:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.399	G=0.601
1000Genomes	American	Sub	694	A=0.730	G=0.270
1000Genomes	East Asian	Sub	1008	A=0.655	G=0.345
1000Genomes	Europe	Sub	1006	A=0.769	G=0.231
1000Genomes	Global	Study-wide	5008	A=0.579	G=0.421
1000Genomes	South Asian	Sub	978	A=0.440	G=0.560
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.737	G=0.263
The Genome Aggregation Database	African	Sub	8702	A=0.473	G=0.527
The Genome Aggregation Database	American	Sub	832	A=0.690	G=0.310
The Genome Aggregation Database	East Asian	Sub	1614	A=0.667	G=0.333
The Genome Aggregation Database	Europe	Sub	18448	A=0.759	G=0.240
The Genome Aggregation Database	Global	Study-wide	29898	A=0.670	G=0.329
The Genome Aggregation Database	Other	Sub	302	A=0.880	G=0.120
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.629	G=0.370
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.746	G=0.254

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

SNP ID	p-value	Traits	Study
rs9593517	0.000989	alcohol dependence	20201924

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr13:81594077	RP11-521J24.1	ENSG00000229246.1	A>G	6.7889e-9	-23728	Cerebellum

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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr13	81590491	81591077	E067	-3000
chr13	81591237	81591287	E067	-2790
chr13	81635721	81636292	E067	41644
chr13	81563856	81564200	E069	-29877
chr13	81590491	81591077	E069	-3000
chr13	81591237	81591287	E069	-2790
chr13	81635721	81636292	E069	41644
chr13	81590491	81591077	E072	-3000
chr13	81591237	81591287	E072	-2790
chr13	81563856	81564200	E074	-29877

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr13	81562847	81562905	E067	-31172
chr13	81562946	81563247	E067	-30830
chr13	81622324	81622614	E067	28247
chr13	81562847	81562905	E068	-31172
chr13	81562946	81563247	E068	-30830
chr13	81563345	81563405	E068	-30672
chr13	81591435	81592190	E068	-1887
chr13	81622324	81622614	E068	28247
chr13	81562847	81562905	E069	-31172
chr13	81562946	81563247	E069	-30830
chr13	81563345	81563405	E069	-30672
chr13	81591435	81592190	E069	-1887
chr13	81622324	81622614	E069	28247
chr13	81562946	81563247	E071	-30830
chr13	81563345	81563405	E071	-30672
chr13	81591435	81592190	E071	-1887
chr13	81622324	81622614	E071	28247
chr13	81562847	81562905	E072	-31172
chr13	81562946	81563247	E072	-30830
chr13	81563345	81563405	E072	-30672
chr13	81591435	81592190	E072	-1887
chr13	81622324	81622614	E072	28247
chr13	81591435	81592190	E073	-1887
chr13	81562847	81562905	E074	-31172
chr13	81562946	81563247	E074	-30830
chr13	81563345	81563405	E074	-30672
chr13	81622324	81622614	E074	28247

rs9593517