rs2834649

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

RUNX1 : Intron Variant
LOC102724584 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0170 (5090/29938,GnomAD)
A=0232 (6768/29118,TOPMED)
A=0171 (858/5008,1000G)
A=0085 (328/3854,ALSPAC)
A=0075 (279/3708,TWINSUK)

Position: chr21:34837353 (GRCh38.p7) (21q22.12)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 7 Enhancers around

Promoter: 3 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 21	NC_000021.9:g.34837353G>A
GRCh37.p13 chr 21	NC_000021.8:g.36209650G>A
RUNX1 RefSeqGene	LRG_482

Gene: RUNX1, runt related transcription factor 1(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RUNX1 transcript variant 2	NM_001001890.2:c.	N/A	Intron Variant
RUNX1 transcript variant 3	NM_001122607.1:c.	N/A	Intron Variant
RUNX1 transcript variant 1	NM_001754.4:c.	N/A	Intron Variant
RUNX1 transcript variant X2	XM_005261068.3:c.	N/A	Intron Variant
RUNX1 transcript variant X5	XM_005261069.4:c.	N/A	Intron Variant
RUNX1 transcript variant X1	XM_011529766.2:c.	N/A	Intron Variant
RUNX1 transcript variant X3	XM_011529767.2:c.	N/A	Intron Variant
RUNX1 transcript variant X6	XM_011529768.2:c.	N/A	Intron Variant
RUNX1 transcript variant X8	XM_011529770.2:c.	N/A	Intron Variant
RUNX1 transcript variant X4	XM_017028487.1:c.	N/A	Intron Variant
RUNX1 transcript variant X7	XR_937576.2:n.	N/A	Intron Variant

Gene: LOC102724584, uncharacterized LOC102724584(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC102724584 transcript variant X1	XR_001755017.1:n.	N/A	Intron Variant
LOC102724584 transcript variant X2	XR_001755018.1:n.	N/A	Intron Variant
LOC102724584 transcript variant X5	XR_937688.2:n.	N/A	Intron Variant
LOC102724584 transcript variant X3	XR_001755019.1:n.	N/A	Genic Upstream Transcript Variant
LOC102724584 transcript variant X4	XR_001755020.1:n.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.527	A=0.473
1000Genomes	American	Sub	694	G=0.870	A=0.130
1000Genomes	East Asian	Sub	1008	G=0.992	A=0.008
1000Genomes	Europe	Sub	1006	G=0.928	A=0.072
1000Genomes	Global	Study-wide	5008	G=0.829	A=0.171
1000Genomes	South Asian	Sub	978	G=0.940	A=0.060
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.915	A=0.085
The Genome Aggregation Database	African	Sub	8702	G=0.591	A=0.409
The Genome Aggregation Database	American	Sub	836	G=0.860	A=0.140
The Genome Aggregation Database	East Asian	Sub	1620	G=0.999	A=0.001
The Genome Aggregation Database	Europe	Sub	18478	G=0.925	A=0.074
The Genome Aggregation Database	Global	Study-wide	29938	G=0.830	A=0.170
The Genome Aggregation Database	Other	Sub	302	G=0.880	A=0.120
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.767	A=0.232
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.925	A=0.075

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
rs2834649	0.000631	nicotine smoking	19268276

eQTL of rs2834649 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 rs2834649 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 )
chr21	36216287	36217518	E070	6637
chr21	36220048	36220282	E070	10398
chr21	36220308	36220413	E070	10658
chr21	36208241	36209246	E072	-404
chr21	36188676	36188995	E082	-20655
chr21	36229158	36229253	E082	19508
chr21	36229282	36229336	E082	19632

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr21	36256709	36257179	E068	47059
chr21	36257244	36257300	E068	47594
chr21	36256592	36256697	E071	46942