rs240480957 SNP Detail

Summary

• ID
  rs240480957
• 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
  Chr4:109264285 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              CAGCCCGAGT GGGTGGAGGT
  GTTGGCAGCT CCGGTCCATG TCTGCGCCGA TGCTCCAAGG CCAGGCTGTG CCGACCTTGA
  GCGCCCGGGT CCCACCTGGC CAGCGCCAGG GGCGGGCGCT GCGCTGCGCG GGCGCGGCCA
  TGGTCCCACT GCGCGGGTGG GCAGCCCGAG ACCGGCCCGG CCCCGTCGCC TTCCCCGCCC
  Y
  CCGGCGCGCC CCTCCCCGGC CGCCGCGTCG CTGGGATCCG GCCGCAGCAC CTGGGCTGCG
  CCTGGCGTCC GGCGCGCGCA GCGATGACCA CGGCCAGCGG CCCGGGCGAC CTGCCGGCGG
  GGTGAGTGGC GGAGGCCGCC TCGGGGCGCG GGCCGTGCAG GGCGAACGCT GCGGGGGCCT
  CCTAGGAGGA GCCCCGGGAC                                            
  
  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	129S5/SvEvBrd	A/J	AKR/J	B10.RIII-H2 H2-T18/(71NS)SnJ	BALB/cByJ	BALB/cJ	BTBR T<+> Itpr3/J	BUB/BnJ	C3H/HeJ	C57BL/6J	C57BL/6NJ	C57BL/10SnJ	CAST/EiJ	CBA/J	CE/J	CZECHII/EiJ	DBA/2J	FVB/NJ	I/LnJ	JF1/MsJ	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
ss362801464	MGP_WTSI_4_109079693	EVA_MGPV3	EVA_MGPV3	f	SNP	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	T	C	C	C
SNP Consensus Information
SNP					Consensus Type	129S1/SvImJ	129S5/SvEvBrd	A/J	AKR/J	B10.RIII-H2 H2-T18/(71NS)SnJ	BALB/cByJ	BALB/cJ	BTBR T<+> Itpr3/J	BUB/BnJ	C3H/HeJ	C57BL/6J	C57BL/6NJ	C57BL/10SnJ	CAST/EiJ	CBA/J	CE/J	CZECHII/EiJ	DBA/2J	FVB/NJ	I/LnJ	JF1/MsJ	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
rs240480957					SNP	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	T	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
ss362801464	MGP_WTSI_4_109079693	SC_MOUSE_GENOMES	SC_MOUSE_GENOMES	f	SNP	C/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr4:109264285 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Cpgi14573	CpG island 14573			within coordinates
Rr597311	regulatory region 597311			866 bp distal
Rr597312	regulatory region 597312			1984 bp distal
Rr597313	regulatory region 597313			within coordinates
Rr597314	regulatory region 597314			33 bp proximal
Tssr38345	transcription start site region 38345			325 bp downstream
Tssr38346	transcription start site region 38346			6 bp upstream
Tssr38347	transcription start site region 38347			33 bp upstream
Tssr42761	transcription start site region 42761			826 bp upstream
Ttc39a	tetratricopeptide repeat domain 39A			Intron
				mRNA-UTR
				Noncoding-Transcript-Variant
				Noncoding-Transcript-Variant
Ttc39aos1	Ttc39a opposite strand RNA 1			855 bp upstream