SNP Detail Info-rs7731258

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

LINC01033 : 500B Downstream Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0171 (5125/29956,GnomAD)
A=0175 (5112/29118,TOPMED)
A=0248 (1240/5008,1000G)
A=0127 (491/3854,ALSPAC)
A=0117 (435/3708,TWINSUK)

Position: chr5:54415292 (GRCh38.p7) (5q11.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 31 Enhancers around

Promoter: 7 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 5	NC_000005.10:g.54415292G>A
GRCh37.p13 chr 5	NC_000005.9:g.53711122G>A

Molecule type	Change	Amino acid[Codon]	SO Term
LINC01033 transcript	NR_126379.1:n.	N/A	Downstream Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.745	A=0.255
1000Genomes	American	Sub	694	G=0.760	A=0.240
1000Genomes	East Asian	Sub	1008	G=0.619	A=0.381
1000Genomes	Europe	Sub	1006	G=0.881	A=0.119
1000Genomes	Global	Study-wide	5008	G=0.752	A=0.248
1000Genomes	South Asian	Sub	978	G=0.760	A=0.240
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.873	A=0.127
The Genome Aggregation Database	African	Sub	8728	G=0.777	A=0.223
The Genome Aggregation Database	American	Sub	838	G=0.780	A=0.220
The Genome Aggregation Database	East Asian	Sub	1612	G=0.616	A=0.384
The Genome Aggregation Database	Europe	Sub	18478	G=0.874	A=0.125
The Genome Aggregation Database	Global	Study-wide	29956	G=0.828	A=0.171
The Genome Aggregation Database	Other	Sub	300	G=0.830	A=0.170
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.824	A=0.175
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.883	A=0.117

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
rs7731258	0.00051	alcohol dependence	20201924

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 )
chr5	53750973	53751066	E068	39851
chr5	53751139	53751216	E069	40017
chr5	53750752	53750827	E070	39630
chr5	53750973	53751066	E070	39851
chr5	53751139	53751216	E070	40017
chr5	53752874	53753568	E070	41752
chr5	53736250	53737123	E071	25128
chr5	53752874	53753568	E071	41752
chr5	53751139	53751216	E073	40017
chr5	53751265	53751672	E073	40143
chr5	53680401	53680543	E081	-30579
chr5	53681044	53681117	E081	-30005
chr5	53681876	53682133	E081	-28989
chr5	53682144	53682243	E081	-28879
chr5	53682282	53682505	E081	-28617
chr5	53682945	53683158	E081	-27964
chr5	53683319	53683489	E081	-27633
chr5	53699068	53699260	E081	-11862
chr5	53699345	53699559	E081	-11563
chr5	53699729	53700116	E081	-11006
chr5	53700124	53700273	E081	-10849
chr5	53700440	53700685	E081	-10437
chr5	53749006	53749130	E081	37884
chr5	53750752	53750827	E081	39630
chr5	53750973	53751066	E081	39851
chr5	53751139	53751216	E081	40017
chr5	53751265	53751672	E081	40143
chr5	53681876	53682133	E082	-28989
chr5	53682144	53682243	E082	-28879
chr5	53751139	53751216	E082	40017
chr5	53751265	53751672	E082	40143

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr5	53751749	53751948	E067	40627
chr5	53751749	53751948	E068	40627
chr5	53751749	53751948	E069	40627
chr5	53751749	53751948	E070	40627
chr5	53751749	53751948	E071	40627
chr5	53751749	53751948	E072	40627
chr5	53751749	53751948	E074	40627

rs7731258