rs4907956

Organism: Homo sapiens

Alleles: G>T

Gene : Feature

OLFM3 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0246 (7379/29920,GnomAD)
T=0218 (6367/29118,TOPMED)
T=0157 (785/5008,1000G)
T=0386 (1487/3854,ALSPAC)
T=0389 (1444/3708,TWINSUK)

Position: chr1:101847147 (GRCh38.p7) (1p21.1)

Phenotype: AD | ND

Dataset:

GWASdb2

Publications: 4 publication(s)

Genomic View: See rs on genome

Enhancer: 2 Enhancers around

Promoter: 6 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.101847147G>T
GRCh37.p13 chr 1	NC_000001.10:g.102312703G>T

Gene: OLFM3, olfactomedin 3(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
OLFM3 transcript variant 3	NM_001288823.1:c.	N/A	Intron Variant
OLFM3 transcript variant 2	NM_058170.3:c.	N/A	Intron Variant
OLFM3 transcript variant 1	NM_001288821.1:c.	N/A	Genic Upstream Transcript Variant
OLFM3 transcript variant 4	NR_110210.1:n.	N/A	Intron Variant
OLFM3 transcript variant 5	NR_110211.1:n.	N/A	Intron Variant
OLFM3 transcript variant 6	NR_110212.1:n.	N/A	Genic Upstream Transcript Variant
OLFM3 transcript variant X1	XM_017000240.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.975	T=0.025
1000Genomes	American	Sub	694	G=0.780	T=0.220
1000Genomes	East Asian	Sub	1008	G=0.981	T=0.019
1000Genomes	Europe	Sub	1006	G=0.609	T=0.391
1000Genomes	Global	Study-wide	5008	G=0.843	T=0.157
1000Genomes	South Asian	Sub	978	G=0.810	T=0.190
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.614	T=0.386
The Genome Aggregation Database	African	Sub	8718	G=0.928	T=0.072
The Genome Aggregation Database	American	Sub	834	G=0.780	T=0.220
The Genome Aggregation Database	East Asian	Sub	1622	G=0.989	T=0.011
The Genome Aggregation Database	Europe	Sub	18446	G=0.651	T=0.349
The Genome Aggregation Database	Global	Study-wide	29920	G=0.753	T=0.246
The Genome Aggregation Database	Other	Sub	300	G=0.640	T=0.360
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.781	T=0.218
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.611	T=0.389

PMID	Title	Author	Journal
21703634	A meta-analysis of two genome-wide association studies identifies 3 new loci for alcohol dependence.	Wang KS	J Psychiatr Res
22377092	ANAPC1 and SLCO3A1 are associated with nicotine dependence: meta-analysis of genome-wide association studies.	Wang KS	Drug Alcohol Depend
18682748	Analysis of 17,576 potentially functional SNPs in three case-control studies of myocardial infarction.	Shiffman D	PLoS One
20202923	A genome-wide association study of alcohol dependence.	Bierut LJ	Proc Natl Acad Sci U S A

P-Value

SNP ID	p-value	Traits	Study
rs4907956	0.00000583	alcohol dependence	20202923
rs4907956	0.000024	alcohol dependence	21703634
rs4907956	0.0000507	nicotine dependence (smoking)	22377092

eQTL of rs4907956 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 rs4907956 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 )
chr1	102314583	102314682	E070	1880
chr1	102314900	102315460	E070	2197

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	102312291	102312873	E067	0
chr1	102312291	102312873	E068	0
chr1	102312291	102312873	E070	0
chr1	102312291	102312873	E072	0
chr1	102312291	102312873	E073	0
chr1	102312291	102312873	E082	0