chr18:12797695:A>G Detail (hg38) (PTPN2)

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Summary
Information
Links
Disease area statistics
MGeND
ClinVar
CIViC
DisGeNET
Annotation
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Information

Genome

Assembly	Position
hg19	chr18:12,797,694-12,797,694 View the variant detail on this assembly version.
hg38	chr18:12,797,695-12,797,695

HGVS

PTPN2

Type	Transcript	Protein
RefSeq	NM_002828.3:c.1041-3210T>C
	NM_080422.2:c.1041-3210T>C
	NM_080423.2:c.1040+4275T>C
	NM_001207013.1:c.1110-3210T>C
	NM_001308287.1:c.954-3210T>C
Ensemble	ENST00000309660.10:c.1041-3210T>C
	ENST00000327283.7:c.1041-3210T>C
	ENST00000353319.8:c.1040+4275T>C
	ENST00000591115.5:c.1110-3210T>C
	ENST00000591497.5:c.954-3210T>C
	ENST00000645191.1:c.744-3210T>C
	ENST00000646492.1:c.744-3210T>C

Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics	Show details

Frequency

JP	HGVD:[No Data.]
	ToMMo:0.355
	NCBN:[No Data.]
	NCBN(Hondo):[No Data.]
	NCBN(Ryukyu):[No Data.]
East asia	ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance
Review star	[No Data.]
Show details

Links

PTPN2

Type	Database	ID	Link
Gene	MIM	176887	OMIM
	HGNC	9650	HGNC
	Ensembl	ENSG00000175354	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar	tgv59300235	TogoVar
	COSMIC
	MONDO

Disease area statistics

[No Data.]

MGeND

[No Data.]

ClinVar

[No Data.]

CIViC

[No Data.]

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
0.248	rheumatoid arthritis	[Our study identified nine loci newly associated with rheumatoid arthritis at a ...	GAD	22446963	Detail
0.248	rheumatoid arthritis	Our study identified nine loci newly associated with rheumatoid arthritis at a t...	GWASCAT	22446963	Detail
0.129	rheumatoid arthritis	Genetic factors regarded as putative risk factors were RA-susceptible polymorphi...	BeFree	23577190	Detail
0.006	rheumatoid arthritis	Genetic factors regarded as putative risk factors were RA-susceptible polymorphi...	BeFree	23577190	Detail
0.248	rheumatoid arthritis	Genetic factors regarded as putative risk factors were RA-susceptible polymorphi...	BeFree	23577190	Detail
0.123	rheumatoid arthritis	Genetic factors regarded as putative risk factors were RA-susceptible polymorphi...	BeFree	23577190	Detail
<0.001	rheumatoid arthritis	Genetic factors regarded as putative risk factors were RA-susceptible polymorphi...	BeFree	23577190	Detail
0.168	rheumatoid arthritis	Genetic factors regarded as putative risk factors were RA-susceptible polymorphi...	BeFree	23577190	Detail
0.243	rheumatoid arthritis	Genetic factors regarded as putative risk factors were RA-susceptible polymorphi...	BeFree	23577190	Detail
0.243	rheumatoid arthritis	Genetic factors regarded as putative risk factors were RA-susceptible polymorphi...	BeFree	23577190	Detail
0.243	rheumatoid arthritis	Genetic factors regarded as putative risk factors were RA-susceptible polymorphi...	BeFree	23577190	Detail
0.123	rheumatoid arthritis	Genetic factors regarded as putative risk factors were RA-susceptible polymorphi...	BeFree	23577190	Detail

Annotation

Annotations

Descrption	Source	Links
[Our study identified nine loci newly associated with rheumatoid arthritis at a threshold of P < 5.0...	DisGeNET	Detail
Our study identified nine loci newly associated with rheumatoid arthritis at a threshold of P < 5...	DisGeNET	Detail
Genetic factors regarded as putative risk factors were RA-susceptible polymorphisms identified by th...	DisGeNET	Detail
Genetic factors regarded as putative risk factors were RA-susceptible polymorphisms identified by th...	DisGeNET	Detail
Genetic factors regarded as putative risk factors were RA-susceptible polymorphisms identified by th...	DisGeNET	Detail
Genetic factors regarded as putative risk factors were RA-susceptible polymorphisms identified by th...	DisGeNET	Detail
Genetic factors regarded as putative risk factors were RA-susceptible polymorphisms identified by th...	DisGeNET	Detail
Genetic factors regarded as putative risk factors were RA-susceptible polymorphisms identified by th...	DisGeNET	Detail
Genetic factors regarded as putative risk factors were RA-susceptible polymorphisms identified by th...	DisGeNET	Detail
Genetic factors regarded as putative risk factors were RA-susceptible polymorphisms identified by th...	DisGeNET	Detail
Genetic factors regarded as putative risk factors were RA-susceptible polymorphisms identified by th...	DisGeNET	Detail
Genetic factors regarded as putative risk factors were RA-susceptible polymorphisms identified by th...	DisGeNET	Detail

Overlapped Transcript

Gene	Transcript ID	Chromosome	Start	Stop	Links

Gene: -
dbSNP: rs2847297 dbSNP
Genome: hg38
Position: chr18:12,797,695-12,797,695
Variant Type: snv
Reference Allele: A
Alternative Allele: G
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): rs2847297
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 0.3552
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 5953
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 16760

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