rs259445015 SNP Detail

Summary

• ID
  rs259445015
• Variation Type
  SNP
• Alleles
  C/T

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

Genome Location and Flanking Sequence

• Location
  Chr4:109264305 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              GTTGGCAGCT CCGGTCCATG
  TCTGCGCCGA TGCTCCAAGG CCAGGCTGTG CCGACCTTGA GCGCCCGGGT CCCACCTGGC
  CAGCGCCAGG GGCGGGCGCT GCGCTGCGCG GGCGCGGCCA TGGTCCCACT GCGCGGGTGG
  GCAGCCCGAG ACCGGCCCGG CCCCGTCGCC TTCCCCGCCC CCCGGCGCGC CCCTCCCCGG
  Y
  CGCCGCGTCG CTGGGATCCG GCCGCAGCAC CTGGGCTGCG CCTGGCGTCC GGCGCGCGCA
  GCGATGACCA CGGCCAGCGG CCCGGGCGAC CTGCCGGCGG GGTGAGTGGC GGAGGCCGCC
  TCGGGGCGCG GGCCGTGCAG GGCGAACGCT GCGGGGGCCT CCTAGGAGGA GCCCCGGGAC
  CGCACTGCGG CTCCAGCCGC                                            
  
  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	129S1/SvImJ	A/J	AKR/J	B10.RIII-H2 H2-T18/(71NS)SnJ	BALB/cByJ	BALB/cJ	BTBR T<+> Itpr3/J	C3H/HeJ	C57BL/6J	C57BL/6NJ	C57BL/10SnJ	CAST/EiJ	CBA/J	CE/J	CZECHII/EiJ	DBA/2J	FVB/NJ	JF1/MsJ	LEWES/EiJ	LG/J	LP/J	MA/MyJ	NOD/ShiLtJ	NON/ShiLtJ	NZO/HlLtJ	PL/J	PWK/PhJ	QSi3/Ianm	QSi5/Ianm	RIIIS/J	SJL/J	SPRET/EiJ	SWR/J	WSB/EiJ	ZALENDE/EiJ
ss362801465	MGP_WTSI_4_109079713	EVA_MGPV3	EVA_MGPV3	f	SNP	C	C	C	C	C	C	C	C	C	C	C	T	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C
SNP Consensus Information
SNP					Consensus Type	129S1/SvImJ	A/J	AKR/J	B10.RIII-H2 H2-T18/(71NS)SnJ	BALB/cByJ	BALB/cJ	BTBR T<+> Itpr3/J	C3H/HeJ	C57BL/6J	C57BL/6NJ	C57BL/10SnJ	CAST/EiJ	CBA/J	CE/J	CZECHII/EiJ	DBA/2J	FVB/NJ	JF1/MsJ	LEWES/EiJ	LG/J	LP/J	MA/MyJ	NOD/ShiLtJ	NON/ShiLtJ	NZO/HlLtJ	PL/J	PWK/PhJ	QSi3/Ianm	QSi5/Ianm	RIIIS/J	SJL/J	SPRET/EiJ	SWR/J	WSB/EiJ	ZALENDE/EiJ
rs259445015					SNP	C	C	C	C	C	C	C	C	C	C	C	T	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C

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
ss362801465	MGP_WTSI_4_109079713	SC_MOUSE_GENOMES	SC_MOUSE_GENOMES	f	SNP	C/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr4:109264305 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Rr597311	regulatory region 597311			886 bp distal
Rr597313	regulatory region 597313			within coordinates
Rr597314	regulatory region 597314			13 bp proximal
Tssr38345	transcription start site region 38345			345 bp downstream
Tssr38346	transcription start site region 38346			within coordinates
Tssr38347	transcription start site region 38347			13 bp upstream
Tssr42761	transcription start site region 42761			846 bp upstream
Ttc39a	tetratricopeptide repeat domain 39A			Intron
				mRNA-UTR
				Noncoding-Transcript-Variant
				Noncoding-Transcript-Variant
Ttc39aos1	Ttc39a opposite strand RNA 1			875 bp upstream