rs4130687

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

RBMS3 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0170 (5099/29898,GnomAD)
G=0147 (4286/29118,TOPMED)
G=0141 (704/5008,1000G)
G=0252 (972/3854,ALSPAC)
G=0251 (929/3708,TWINSUK)

Position: chr3:29402620 (GRCh38.p7) (3p24.1)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 10 Enhancers around

Promoter: 5 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 3	NC_000003.12:g.29402620A>G
GRCh37.p13 chr 3	NC_000003.11:g.29444111A>G

Gene: RBMS3, RNA binding motif single stranded interacting protein 3(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RBMS3 transcript variant 3	NM_001003792.2:c.	N/A	Intron Variant
RBMS3 transcript variant 1	NM_001003793.2:c.	N/A	Intron Variant
RBMS3 transcript variant 5	NM_001177711.1:c.	N/A	Intron Variant
RBMS3 transcript variant 4	NM_001177712.1:c.	N/A	Intron Variant
RBMS3 transcript variant 2	NM_014483.3:c.	N/A	Intron Variant
RBMS3 transcript variant X1	XM_005265060.2:c.	N/A	Intron Variant
RBMS3 transcript variant X5	XM_005265061.2:c.	N/A	Intron Variant
RBMS3 transcript variant X6	XM_005265062.1:c.	N/A	Intron Variant
RBMS3 transcript variant X3	XM_017006178.1:c.	N/A	Intron Variant
RBMS3 transcript variant X4	XM_017006179.1:c.	N/A	Intron Variant
RBMS3 transcript variant X7	XM_017006180.1:c.	N/A	Intron Variant
RBMS3 transcript variant X8	XM_017006181.1:c.	N/A	Intron Variant
RBMS3 transcript variant X9	XM_017006182.1:c.	N/A	Intron Variant
RBMS3 transcript variant X9	XM_005265063.1:c.	N/A	Genic Upstream Transcript Variant
RBMS3 transcript variant X10	XM_005265065.4:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.974	G=0.026
1000Genomes	American	Sub	694	A=0.890	G=0.110
1000Genomes	East Asian	Sub	1008	A=0.854	G=0.146
1000Genomes	Europe	Sub	1006	A=0.782	G=0.218
1000Genomes	Global	Study-wide	5008	A=0.859	G=0.141
1000Genomes	South Asian	Sub	978	A=0.770	G=0.230
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.748	G=0.252
The Genome Aggregation Database	African	Sub	8730	A=0.947	G=0.053
The Genome Aggregation Database	American	Sub	838	A=0.900	G=0.100
The Genome Aggregation Database	East Asian	Sub	1614	A=0.831	G=0.169
The Genome Aggregation Database	Europe	Sub	18414	A=0.772	G=0.227
The Genome Aggregation Database	Global	Study-wide	29898	A=0.829	G=0.170
The Genome Aggregation Database	Other	Sub	302	A=0.720	G=0.280
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.852	G=0.147
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.749	G=0.251

PMID	Title	Author	Journal
19268276	Genome-wide association study of smoking initiation and current smoking.	Vink JM	Am J Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs4130687	0.000882	nicotine smoking	19268276

eQTL of rs4130687 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 rs4130687 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	29451802	29452066	E070	7691
chr3	29470818	29470944	E070	26707
chr3	29489724	29489918	E071	45613
chr3	29489724	29489918	E072	45613
chr3	29489724	29489918	E074	45613
chr3	29467946	29468023	E081	23835
chr3	29468176	29468229	E081	24065
chr3	29468296	29468401	E081	24185
chr3	29469194	29469749	E081	25083
chr3	29470818	29470944	E081	26707

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr3	29481792	29482729	E067	37681
chr3	29481792	29482729	E068	37681
chr3	29481792	29482729	E069	37681
chr3	29481792	29482729	E071	37681
chr3	29481792	29482729	E074	37681