chr1:113812320:T>G Detail (hg38) (RSBN1)

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Information

Genome

Assembly	Position
hg19	chr1:114,354,942-114,354,942 View the variant detail on this assembly version.
hg38	chr1:113,812,320-113,812,320

Summary

Links

Type	Database	ID	Link
Gene	MIM	615858	OMIM
	HGNC	25642	HGNC
	Ensembl	ENSG00000081019	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar	tgv2863650	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
0.145	Graves Disease	We genotyped the five SNPs (rs12760457, rs2797415, rs1310182, rs2476599, and rs3...	BeFree	20615141	Detail
0.001	Autoimmune thyroid disease	We genotyped the five SNPs (rs12760457, rs2797415, rs1310182, rs2476599, and rs3...	BeFree	20615141	Detail
<0.001	thyroiditis	We genotyped the five SNPs (rs12760457, rs2797415, rs1310182, rs2476599, and rs3...	BeFree	20615141	Detail
0.001	thyroiditis	We genotyped the five SNPs (rs12760457, rs2797415, rs1310182, rs2476599, and rs3...	BeFree	20615141	Detail
0.524	rheumatoid arthritis	We compared the allele frequencies of five haplotype-tagging SNPs in the PTPN22 ...	BeFree	20510318	Detail
0.145	Graves Disease	The AA genotype of PTPN22 rs3789604 and AA genotype of FCRL3 rs7528684 were corr...	BeFree	19438904	Detail
0.228	Graves Disease	These preliminary results demonstrate that the immune-regulatory gene CTLA-4 and...	BeFree	19438904	Detail

Annotation

Descrption	Source	Links
We genotyped the five SNPs (rs12760457, rs2797415, rs1310182, rs2476599, and rs3789604) of the PTPN2...	DisGeNET	Detail
We genotyped the five SNPs (rs12760457, rs2797415, rs1310182, rs2476599, and rs3789604) of the PTPN2...	DisGeNET	Detail
We genotyped the five SNPs (rs12760457, rs2797415, rs1310182, rs2476599, and rs3789604) of the PTPN2...	DisGeNET	Detail
We genotyped the five SNPs (rs12760457, rs2797415, rs1310182, rs2476599, and rs3789604) of the PTPN2...	DisGeNET	Detail
We compared the allele frequencies of five haplotype-tagging SNPs in the PTPN22 gene, 2 of which are...	DisGeNET	Detail
The AA genotype of PTPN22 rs3789604 and AA genotype of FCRL3 rs7528684 were correlated with a reduce...	DisGeNET	Detail
These preliminary results demonstrate that the immune-regulatory gene CTLA-4 and the thyroid-specifi...	DisGeNET	Detail

Gene	Transcript ID	Exon Number	Chromosome	Start	Stop	Type	Amino Mutation	Transcript Position	Links

Gene	Transcript ID	Chromosome	Start	Stop	Links

Gene: -
Genome: hg38
Position: chr1:113,812,320-113,812,320
Variant Type: snv
Reference Allele: T
Alternative Allele: G
Filtering Status (HGVD): PASS
# of samples (HGVD): 1199
Mean of sample read depth (HGVD): 285.08
Standard deviation of sample read depth (HGVD): 156.28
Number of reference allele (HGVD): 1921
Number of alternative allele (HGVD): 477
Allele Frequency (HGVD): 0.1989157631359466
Gene Symbol (HGVD): RSBN1
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)): rs3789604
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 0.1984
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 3325
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 16760
East Asian Chromosome Counts (ExAC): 8240
East Asian Allele Counts (ExAC): 1921
East Asian Heterozygous Counts (ExAC): 1517
East Asian Homozygous Counts (ExAC): 202
East Asian Allele Frequency (ExAC): 0.23313106796116506
Chromosome Counts in All Race (ExAC): 113252
Allele Counts in All Race (ExAC): 19331
Heterozygous Counts in All Race (ExAC): 15910
Homozygous Counts in All Race (ExAC): 1710
Allele Frequency in All Race (ExAC): 0.17069014233744217

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