chr10:6098949:C>T Detail (hg19) (IL2RA)

Information

Genome

Assembly Position
hg19 chr10:6,098,949-6,098,949
hg38 chr10:6,056,986-6,056,986 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000417.2:c.64+5102G>A
NM_001308242.1:c.64+5102G>A
NM_001308243.1:c.64+5102G>A
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.535
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
Type Database ID Link
Gene MIM 147730 OMIM
HGNC 6008 HGNC
Ensembl ENSG00000134460 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv38248547 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
0.293 Diabetes Mellitus, Insulin-Dependent Previous investigations have also demonstrated that two intronic SNPs (rs706778 ... BeFree 20615141 Detail
0.257 rheumatoid arthritis [We also refined associations at two established rheumatoid arthritis risk loci ... GAD 20453842 Detail
0.257 rheumatoid arthritis We also refined associations at two established rheumatoid arthritis risk loci (... GWASCAT 20453842 Detail
0.257 rheumatoid arthritis Genetics of rheumatoid arthritis contributes to biology and drug discovery. GWASCAT 24390342 Detail
Annotation

Annotations

DescrptionSourceLinks
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
Previous investigations have also demonstrated that two intronic SNPs (rs706778 and rs3118470) in th... DisGeNET Detail
[We also refined associations at two established rheumatoid arthritis risk loci (IL2RA and CCL21) an... DisGeNET Detail
We also refined associations at two established rheumatoid arthritis risk loci (IL2RA and CCL21) and... DisGeNET Detail
Genetics of rheumatoid arthritis contributes to biology and drug discovery. DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs706778 dbSNP
Genome
hg19
Position
chr10:6,098,949-6,098,949
Variant Type
snv
Reference Allele
C
Alternative Allele
T
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))
rs706778
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.5351
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
8969
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
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