rs239988400 SNP Detail

Summary

• ID
  rs239988400
• 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
  

Genome Location and Flanking Sequence

• Location
  Chr2:74547012 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              TGAAAGTCTG AGGCAATCCC
  ACCTGCACCC CATAGCTTGC GAATCATGCT GGTGTGTGGA CTTCTGTCCC CAACACTCCT
  GCCTCACCAC TGTGCTCGTC GCAGGCCTAC TGTGTGGTTC GCCGGCTGGT CTCCGTTCAA
  AGGTGACAAC TCACCCAGCT TCACTGATCC TCAGTTGACC CCTAGCAATG TCCCCCTCTT
  Y
  GTTAATTTAG GGCAATGATT CTCAGAGGTC TGTGTGAGCC CAAATGTCTG GATAAATGAG
  GTTTCTAGGT TCCACACCAA ACACCCTGAA TTCAAATGTC AAGAAGCAGT GTCCAGGCAT
  CCTGAAAACA CTCTCCCCAA GGCAATGAAG ATATGTACAT AGGTTGGAGA GCCATGGGTT
  AAGGGTGTCT CCTGCTTAGC                                            
  
  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	129P2/OlaHsd	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/HeH	C3H/HeJ	C57BL/6J	C57BL/6NJ	C57BL/10J	C57BL/10SnJ	C57BR/cdJ	C57L/J	C58/J	CAST/EiJ	CBA/J	CE/J	CZECHII/EiJ	DBA/1J	DBA/2J	FVB/NJ	I/LnJ	JF1/MsJ	KK/HlJ	LEWES/EiJ	LG/J	LP/J	MA/MyJ	MOLF/EiJ	NOD/ShiLtJ	NON/ShiLtJ	NZB/BlNJ	NZO/HlLtJ	NZW/LacJ	PL/J	PWK/PhJ	QSi3/Ianm	QSi5/Ianm	RF/J	RIIIS/J	SEA/GnJ	SJL/J	SM/J	SPRET/EiJ	ST/bJ	SWR/J	WSB/EiJ	ZALENDE/EiJ
ss354485181	MGP_WTSI_2_74554725	EVA_MGPV3	EVA_MGPV3	f	SNP	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	C	T	T	C	T	T	T	T	C	T	T	T	T	T	C	T	T	C	T	T	T	C	T	T	T	T	T	T	T	C	T	T	T	T
SNP Consensus Information
SNP					Consensus Type	129P2/OlaHsd	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/HeH	C3H/HeJ	C57BL/6J	C57BL/6NJ	C57BL/10J	C57BL/10SnJ	C57BR/cdJ	C57L/J	C58/J	CAST/EiJ	CBA/J	CE/J	CZECHII/EiJ	DBA/1J	DBA/2J	FVB/NJ	I/LnJ	JF1/MsJ	KK/HlJ	LEWES/EiJ	LG/J	LP/J	MA/MyJ	MOLF/EiJ	NOD/ShiLtJ	NON/ShiLtJ	NZB/BlNJ	NZO/HlLtJ	NZW/LacJ	PL/J	PWK/PhJ	QSi3/Ianm	QSi5/Ianm	RF/J	RIIIS/J	SEA/GnJ	SJL/J	SM/J	SPRET/EiJ	ST/bJ	SWR/J	WSB/EiJ	ZALENDE/EiJ
rs239988400					SNP	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	C	T	T	C	T	T	T	T	C	T	T	T	T	T	C	T	T	C	T	T	T	C	T	T	T	T	T	T	T	C	T	T	T	T

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
ss354485181	MGP_WTSI_2_74554725	SC_MOUSE_GENOMES	SC_MOUSE_GENOMES	f	SNP	C/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr2:74547012 () rs orientation: forward

Symbol	Name	Function Class
Cpgi11802	CpG island 11802	1435 bp distal
Cpgi11803	CpG island 11803	449 bp distal
Hoxd3	homeobox D3	within coordinates
Hoxd3os1	homeobox D3, opposite strand 1	538 bp upstream
Igs15	intergenic site 15	within coordinates
Rr44608	regulatory region 44608	812 bp distal
Rr44609	regulatory region 44609	212 bp distal
Rr57045	regulatory region 57045	within coordinates
Rr57046	regulatory region 57046	988 bp proximal
Tssr533	transcription start site region 533	692 bp upstream
Tssr534	transcription start site region 534	661 bp upstream
Tssr18437	transcription start site region 18437	320 bp upstream
Tssr24625	transcription start site region 24625	668 bp upstream
Tssr24626	transcription start site region 24626	641 bp upstream
Tssr24627	transcription start site region 24627	533 bp upstream
Tssr24628	transcription start site region 24628	511 bp upstream