rs7173321

Organism: Homo sapiens

Alleles: C>G

Gene : Feature

TRPM7 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0123 (3691/29960,GnomAD)
G=0135 (3958/29118,TOPMED)
G=0132 (660/5008,1000G)
G=0109 (421/3854,ALSPAC)
G=0105 (389/3708,TWINSUK)

Position: chr15:50630403 (GRCh38.p7) (15q21.2)

Phenotype: ND

Dataset:

GWASdb2

Publications: 3 publication(s)

Genomic View: See rs on genome

Enhancer: 0 Enhancer around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 15	NC_000015.10:g.50630403C>G
GRCh37.p13 chr 15	NC_000015.9:g.50922600C>G
TRPM7 RefSeqGene	NG_021363.1:g.61413G>C

Gene: TRPM7, transient receptor potential cation channel subfamily M member 7(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TRPM7 transcript variant 2	NM_001301212.1:c.	N/A	Intron Variant
TRPM7 transcript variant 1	NM_017672.5:c.	N/A	Intron Variant
TRPM7 transcript variant X3	XM_005254486.3:c.	N/A	Intron Variant
TRPM7 transcript variant X1	XM_017022350.1:c.	N/A	Intron Variant
TRPM7 transcript variant X2	XM_017022351.1:c.	N/A	Intron Variant
TRPM7 transcript variant X4	XM_017022352.1:c.	N/A	Intron Variant
TRPM7 transcript variant X5	XM_017022353.1:c.	N/A	Intron Variant
TRPM7 transcript variant X6	XM_017022354.1:c.	N/A	Intron Variant
TRPM7 transcript variant X7	XM_017022355.1:c.	N/A	Intron Variant
TRPM7 transcript variant X12	XM_017022356.1:c.	N/A	Intron Variant
TRPM7 transcript variant X8	XR_001751325.1:n.	N/A	Intron Variant
TRPM7 transcript variant X9	XR_001751326.1:n.	N/A	Intron Variant
TRPM7 transcript variant X10	XR_001751327.1:n.	N/A	Intron Variant
TRPM7 transcript variant X11	XR_001751328.1:n.	N/A	Intron Variant
TRPM7 transcript variant X13	XR_001751329.1:n.	N/A	Intron Variant
TRPM7 transcript variant X14	XR_001751330.1:n.	N/A	Intron Variant
TRPM7 transcript variant X15	XR_001751331.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.788	G=0.212
1000Genomes	American	Sub	694	C=0.940	G=0.060
1000Genomes	East Asian	Sub	1008	C=0.888	G=0.112
1000Genomes	Europe	Sub	1006	C=0.905	G=0.095
1000Genomes	Global	Study-wide	5008	C=0.868	G=0.132
1000Genomes	South Asian	Sub	978	C=0.870	G=0.130
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.891	G=0.109
The Genome Aggregation Database	African	Sub	8704	C=0.802	G=0.198
The Genome Aggregation Database	American	Sub	838	C=0.920	G=0.080
The Genome Aggregation Database	East Asian	Sub	1620	C=0.943	G=0.057
The Genome Aggregation Database	Europe	Sub	18496	C=0.903	G=0.096
The Genome Aggregation Database	Global	Study-wide	29960	C=0.876	G=0.123
The Genome Aggregation Database	Other	Sub	302	C=0.920	G=0.080
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.864	G=0.135
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.895	G=0.105

PMID	Title	Author	Journal
19644062	Gene variation of the transient receptor potential cation channel, subfamily M, member 7 (TRPM7), and risk of incident ischemic stroke: prospective, nested, case-control study.	Romero JR	Stroke
19268276	Genome-wide association study of smoking initiation and current smoking.	Vink JM	Am J Hum Genet
24952306	The association between single-nucleotide polymorphisms of TRPM7 gene and breast cancer in Han Population of Northeast China.	Shen B	Med Oncol

P-Value

SNP ID	p-value	Traits	Study
rs7173321	3.24E-05	nicotine smoking	19268276

eQTL of rs7173321 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr15:50922600	SPPL2A	ENSG00000138600.5	C>G	1.2844e-3	-135405	Cortex
Chr15:50922600	SPPL2A	ENSG00000138600.5	C>G	3.2577e-5	-135405	Cerebellar_Hemisphere

meQTL of rs7173321 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.