rs16824395

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

LSAMP : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0076 (2274/29828,GnomAD)
G=0032 (950/29118,TOPMED)
G=0113 (568/5008,1000G)
G=0049 (189/3854,ALSPAC)
G=0057 (210/3708,TWINSUK)

Position: chr3:116021872 (GRCh38.p7) (3q13.31)

Phenotype: AD

Dataset:

GWASdb2 | GWASCatalog

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 66 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 3	NC_000003.12:g.116021872A>G
GRCh37.p13 chr 3	NC_000003.11:g.115740719A>G

Gene: LSAMP, limbic system-associated membrane protein(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LSAMP transcript variant 2	NM_001318915.1:c.	N/A	Intron Variant
LSAMP transcript variant 1	NM_002338.4:c.	N/A	Intron Variant
LSAMP transcript variant X2	XM_011512840.2:c.	N/A	Intron Variant
LSAMP transcript variant X1	XM_017006383.1:c.	N/A	Intron Variant
LSAMP transcript variant X3	XM_017006384.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.998	G=0.002
1000Genomes	American	Sub	694	A=0.980	G=0.020
1000Genomes	East Asian	Sub	1008	A=0.622	G=0.378
1000Genomes	Europe	Sub	1006	A=0.923	G=0.077
1000Genomes	Global	Study-wide	5008	A=0.887	G=0.113
1000Genomes	South Asian	Sub	978	A=0.900	G=0.100
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.951	G=0.049
The Genome Aggregation Database	African	Sub	8712	A=0.989	G=0.011
The Genome Aggregation Database	American	Sub	836	A=0.970	G=0.030
The Genome Aggregation Database	East Asian	Sub	1604	A=0.664	G=0.336
The Genome Aggregation Database	Europe	Sub	18374	A=0.913	G=0.086
The Genome Aggregation Database	Global	Study-wide	29828	A=0.923	G=0.076
The Genome Aggregation Database	Other	Sub	302	A=0.920	G=0.080
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.967	G=0.032
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.943	G=0.057

PMID	Title	Author	Journal
24962325	Genome-wide survival analysis of age at onset of alcohol dependence in extended high-risk COGA families.	Kapoor M	Drug Alcohol Depend

P-Value

SNP ID	p-value	Traits	Study
rs16824395	6E-06	alcohol dependence (age at onset)	24962325

eQTL of rs16824395 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

meQTL of rs16824395 in Fetal Brain

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

Genomic View

Chromatin Interaction

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

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr3	115717884	115718161	E067	-22558
chr3	115718195	115718245	E067	-22474
chr3	115718579	115718854	E067	-21865
chr3	115721457	115721578	E067	-19141
chr3	115752796	115753408	E067	12077
chr3	115765141	115765191	E067	24422
chr3	115765277	115765508	E067	24558
chr3	115770007	115770218	E067	29288
chr3	115772953	115773039	E067	32234
chr3	115708597	115708657	E068	-32062
chr3	115708793	115709284	E068	-31435
chr3	115718195	115718245	E068	-22474
chr3	115718579	115718854	E068	-21865
chr3	115718876	115719593	E068	-21126
chr3	115739402	115739613	E068	-1106
chr3	115757461	115758041	E068	16742
chr3	115765277	115765508	E068	24558
chr3	115773616	115773860	E068	32897
chr3	115774487	115774840	E068	33768
chr3	115718876	115719593	E069	-21126
chr3	115752796	115753408	E069	12077
chr3	115757461	115758041	E069	16742
chr3	115765141	115765191	E069	24422
chr3	115765277	115765508	E069	24558
chr3	115770007	115770218	E069	29288
chr3	115773616	115773860	E069	32897
chr3	115717884	115718161	E070	-22558
chr3	115718195	115718245	E070	-22474
chr3	115718579	115718854	E070	-21865
chr3	115753546	115753629	E070	12827
chr3	115753808	115753916	E070	13089
chr3	115765277	115765508	E070	24558
chr3	115786252	115786482	E070	45533
chr3	115718579	115718854	E071	-21865
chr3	115718876	115719593	E071	-21126
chr3	115739402	115739613	E071	-1106
chr3	115752796	115753408	E071	12077
chr3	115753546	115753629	E071	12827
chr3	115757461	115758041	E071	16742
chr3	115758262	115758419	E071	17543
chr3	115765277	115765508	E071	24558
chr3	115786252	115786482	E071	45533
chr3	115715813	115715980	E072	-24739
chr3	115718876	115719593	E072	-21126
chr3	115721192	115721411	E072	-19308
chr3	115721457	115721578	E072	-19141
chr3	115765277	115765508	E072	24558
chr3	115718195	115718245	E073	-22474
chr3	115718579	115718854	E073	-21865
chr3	115718876	115719593	E073	-21126
chr3	115753546	115753629	E073	12827
chr3	115758262	115758419	E073	17543
chr3	115758533	115758687	E073	17814
chr3	115735391	115735471	E074	-5248
chr3	115753808	115753916	E074	13089
chr3	115772953	115773039	E074	32234
chr3	115773616	115773860	E074	32897
chr3	115719773	115720091	E081	-20628
chr3	115720095	115720473	E081	-20246
chr3	115721457	115721578	E081	-19141
chr3	115752461	115752584	E081	11742
chr3	115752796	115753408	E082	12077
chr3	115753546	115753629	E082	12827
chr3	115757461	115758041	E082	16742
chr3	115765277	115765508	E082	24558
chr3	115786252	115786482	E082	45533