rs52490012 SNP Detail

Summary

• ID
  rs52490012
• Variation Type
  SNP
• Alleles
  A/G

• 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
  Chr3:123028939 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                        CATACATACA TACATAAATA CATACTTACA TATTTAAACA
  TTAAAGAAGA ATCCAGAAAT TGGGGAAGGA GGGTACATAG GCAGAGTTGG AGGAAGGAAA
  R
  AGAGTGGAGG GAAATAATGT AATTATATTT TAATAAAATA AATTTTTTAA AAAATAATAA
  AGTATCTATG ACTATCTTGA GCTCTTAGCC ACATGAGTA                       
  
  R = A/G
  

  
  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	LG/J	MSM/Ms	SM/J
ss135760881	ENSMUSSNP4237741	ENSEMBL	ENSEMBL_Sanger	f	SNP	A		G
ss320918235	CHEV_3_122938208	CHEVERUD	SCREENING_POP	f	SNP		A		G
SNP Consensus Information
SNP					Consensus Type	129X1/SvJ	LG/J	MSM/Ms	SM/J
rs52490012					SNP	A	A	G	G

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr3:123028939 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Rr584473	regulatory region 584473			419 bp distal
Rr584474	regulatory region 584474			591 bp distal
Rr584475	regulatory region 584475			796 bp proximal
Rr584476	regulatory region 584476			1630 bp proximal
Synpo2	synaptopodin 2			Intron
				Noncoding-Transcript-Variant
Tssr35497	transcription start site region 35497			821 bp downstream
Tssr35498	transcription start site region 35498			844 bp downstream