rs52459406 SNP Detail

Summary

• ID
  rs52459406
• Variation Type
  SNP
• Alleles
  C/T

• Created in dbSNP Build
  128
• Last Updated in dbSNP Build
  137
• Additional Resources
  JBrowse Genome Browser | Ensembl SNPView | UCSC Browser | Alliance Variant
  

Genome Location and Flanking Sequence

• Location
  Chr2:83476507 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              CAGAGAAACT CTTGTCCAAG
  GGAAAATAAA AGAAAGAAAA ATAATTGTCA CCTTTACATC TGAAGAAAAA AATCAGGATT
  TGGGAGACTT AAATCTCTGG GAATAATAAT CTGGTGGCAA TTCAATATTG TGCCAACAAA
  GGACATTCAG AAATAGCATT TTACTTACAA ACTACTGAGA TTGAATAAAT ATAAAATAGA
  Y
  CACAAAACAG TAAAATTTCC ATTCAAAAAT AAATGTTACA AAACATTATA GAATGTATTT
  CAGGCCACTT GGACCTATAA CCACTTTTAA TTAATGAGAC TAAAGGGTTT TTTGTTTCGT
  TAATTTTTGT CACCTGACAG TGGAGATGAC ACTCAGAAGG GCAGAGGCAG GTAGAGCTCT
  GAATTCAAGA GTAGCCTGGT                                            
  
  Y = C/T
  

  
  Note: Sequence in lower case indicates low-complexity or repetitive sequence

  ---

SNP Assays
and
SNP Consensus

Strain alleles of submitted assays, and consensus values for this SNP

Assay ID	Submitter SNP ID	Submitter Handle	Population	ss orientation	Variation Type	129X1/SvJ	A/J	DBA/2J	MSM/Ms
ss146812159	ENSMUSSNP5972502	ENSEMBL	ENSEMBL_Sanger	f	SNP	C	C	C	T
SNP Consensus Information
SNP					Consensus Type	129X1/SvJ	A/J	DBA/2J	MSM/Ms
rs52459406					SNP	C	C	C	T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr2:83476507 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Cpgi11854	CpG island 11854			894 bp distal
Rr397083	regulatory region 397083			1587 bp downstream
Rr560160	regulatory region 560160			1718 bp distal
Rr560161	regulatory region 560161			1919 bp distal
Rr560162	regulatory region 560162			1788 bp distal
Rr560163	regulatory region 560163			1736 bp distal
Rr560164	regulatory region 560164			753 bp distal
Rr560165	regulatory region 560165			1461 bp distal
Tssr18640	transcription start site region 18640			1673 bp downstream
Tssr18641	transcription start site region 18641			1642 bp downstream
Tssr18642	transcription start site region 18642			1616 bp downstream
Tssr18643	transcription start site region 18643			1586 bp downstream
Tssr18644	transcription start site region 18644			1571 bp downstream
Zc3h15	zinc finger CCCH-type containing 15			Intron
				Noncoding-Transcript-Variant