rs223043856 SNP Detail

Summary

• ID
  rs223043856
• Variation Type
  SNP
• Alleles
  C/G

• 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
  Chr4:109264355 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              CCGACCTTGA GCGCCCGGGT
  CCCACCTGGC CAGCGCCAGG GGCGGGCGCT GCGCTGCGCG GGCGCGGCCA TGGTCCCACT
  GCGCGGGTGG GCAGCCCGAG ACCGGCCCGG CCCCGTCGCC TTCCCCGCCC CCCGGCGCGC
  CCCTCCCCGG CCGCCGCGTC GCTGGGATCC GGCCGCAGCA CCTGGGCTGC GCCTGGCGTC
  S
  GGCGCGCGCA GCGATGACCA CGGCCAGCGG CCCGGGCGAC CTGCCGGCGG GGTGAGTGGC
  GGAGGCCGCC TCGGGGCGCG GGCCGTGCAG GGCGAACGCT GCGGGGGCCT CCTAGGAGGA
  GCCCCGGGAC CGCACTGCGG CTCCAGCCGC TGCGCAGCCT GCAGCCCGCG CCCCGCTGCC
  TCCTGGGGAC CCTGGCTCAG                                            
  
  S = C/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	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	C57BR/cdJ	CAST/EiJ	CBA/J	CE/J	CZECHII/EiJ	DBA/2J	FVB/NJ	I/LnJ	JF1/MsJ	KK/HlJ	LEWES/EiJ	LG/J	LP/J	MA/MyJ	NOD/ShiLtJ	NON/ShiLtJ	NZO/HlLtJ	PL/J	PWK/PhJ	QSi3/Ianm	QSi5/Ianm	RIIIS/J	SEA/GnJ	SJL/J	SPRET/EiJ	ST/bJ	SWR/J	WSB/EiJ	ZALENDE/EiJ
ss362801466	MGP_WTSI_4_109079763	EVA_MGPV3	EVA_MGPV3	f	SNP	C	C	C	C	C	C	C	C	C	C	C	C	G	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
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	C57BR/cdJ	CAST/EiJ	CBA/J	CE/J	CZECHII/EiJ	DBA/2J	FVB/NJ	I/LnJ	JF1/MsJ	KK/HlJ	LEWES/EiJ	LG/J	LP/J	MA/MyJ	NOD/ShiLtJ	NON/ShiLtJ	NZO/HlLtJ	PL/J	PWK/PhJ	QSi3/Ianm	QSi5/Ianm	RIIIS/J	SEA/GnJ	SJL/J	SPRET/EiJ	ST/bJ	SWR/J	WSB/EiJ	ZALENDE/EiJ
rs223043856					SNP	C	C	C	C	C	C	C	C	C	C	C	C	G	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

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
ss362801466	MGP_WTSI_4_109079763	SC_MOUSE_GENOMES	SC_MOUSE_GENOMES	f	SNP	C/G

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr4:109264355 () 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			936 bp distal
Rr597313	regulatory region 597313			38 bp distal
Rr597314	regulatory region 597314			within coordinates
Tssr38345	transcription start site region 38345			395 bp downstream
Tssr38346	transcription start site region 38346			39 bp downstream
Tssr38347	transcription start site region 38347			within coordinates
Tssr42761	transcription start site region 42761			896 bp upstream
Ttc39a	tetratricopeptide repeat domain 39A			Intron
				mRNA-UTR
				Noncoding-Transcript-Variant
				Noncoding-Transcript-Variant
Ttc39aos1	Ttc39a opposite strand RNA 1			925 bp upstream