rs47496339 SNP Detail

Summary

• ID
  rs47496339
• Variation Type
  SNP
• Alleles
  A/T

• Created in dbSNP Build
  127
• Last Updated in dbSNP Build
  137
• Additional Resources
  JBrowse Genome Browser | Ensembl SNPView | UCSC Browser | Alliance Variant
  

Genome Location and Flanking Sequence

• Location
  Chr13:53530923 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              ATTACAAATT CATTGCCACA
  CGCGGCATTA GAGACTTCTG TAATGAGTAG TCTCTGAGAG AGATGACACA GATATGTCCT
  ATAGGATACA GCAAGATAGC TCAGTTGTCA AATCAGCCTT CTCCCAAGAC CGGCATCTGG
  ATTTCATATT GTCTTGTATA GCTGAATGAA ACCACTCAAG ACCTTCAACC GTTTTTTTTT
  W
  AATCTTTCAA AAAGTTAAAT GCTTATAGCA TAGAAATTGT GGGCAAAGGA TAGGCTACTC
  CATACTCGTC ATTTCCCTAT TACTCTGCTA TTCTAAACTT AAACTTCTCT CTCCGGACCC
  TGGGTAAAGT TTACAATAGA TGAGAAGGCA TTTCTCACAC CTAAGACCTC CCACTCCCAC
  CGACCCCGTC TCGCCATCAG                                            
  
  W = A/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	AKR/J	BALB/cByJ	BTBR T<+> Itpr3/J	CAST/EiJ	DBA/2J	KK/HlJ	LG/J	MOLF/EiJ	NOD/ShiLtJ	NZW/LacJ	PWD/PhJ	SM/J	WSB/EiJ
ss61805842	NES17722867	PERLEGEN	MM_PANEL2	f	SNP	T	A	A	A	A	A		A	T	T	A		A
ss324341580	CHEV_13_53472256	CHEVERUD	SCREENING_POP	f	SNP							A					T
SNP Consensus Information
SNP					Consensus Type	AKR/J	BALB/cByJ	BTBR T<+> Itpr3/J	CAST/EiJ	DBA/2J	KK/HlJ	LG/J	MOLF/EiJ	NOD/ShiLtJ	NZW/LacJ	PWD/PhJ	SM/J	WSB/EiJ
rs47496339					SNP	T	A	A	A	A	A	A	A	T	T	A	T	A

Additional submitted assays for this SNP, where the strain of origin for observed alleles is not specified by the submitter

Assay ID	Submitter SNP ID	Submitter Handle	Population	ss orientation	Variation Type	Alleles
ss61805842	NES17722867	PERLEGEN	MM_PANEL	f	SNP	A/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr13:53530923 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Cpgi5620	CpG island 5620			158 bp proximal
Rr403780	regulatory region 403780			415 bp upstream
Rr480032	regulatory region 480032			500 bp proximal
Sptlc1	serine palmitoyltransferase, long chain base subunit 1			Intron
				Noncoding-Transcript-Variant
Tssr122583	transcription start site region 122583			468 bp downstream