rs239028553 SNP Detail

Summary

• ID
  rs239028553
• Variation Type
  SNP
• Alleles
  A/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
  Chr2:148715777 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              CGCAGGACCA AAAACAGCTC
  TGGATTTGGG AGAATGTCCT GATTTTCCTA CTAGTTAAAG GAGACCTGCA GACCAAAGAA
  CCTACAACTC CTTATACTTT GCTCCATCTG TTGCCACAAT TAAGAGGTGC ACTGGCCCTC
  AAGGTCCAAG GCAGCTGGGA AGTGGAGTTT TCTCAAGGTT GATCCCAGCA GCAGGAGAAA
  W
  AAATGGAGCA GGATTTAACT CGTTTGTATT TTCAAGAGAA GGTAGAAATG AGCTCTACAC
  ACTGGCATAC AACTCTTTGT CGTCTAAAAC CTGGGCTTCC TTTGGGTCAA CTTTGGGGCT
  TTAGCAGCTC CTGCAGCTAG CTCCTCTGTC AGAGTCTAAG TCTAAGGTAG TCTGTCCATC
  TACTCAGTGG GTGGAGGGTG                                            
  
  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	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
ss356083028	MGP_WTSI_2_148699593	EVA_MGPV3	EVA_MGPV3	f	SNP	A	A	A	A	A	A	A	A	A	T	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	T	A	A	A	A
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
rs239028553					SNP	A	A	A	A	A	A	A	A	A	T	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	T	A	A	A	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
ss356083028	MGP_WTSI_2_148699593	SC_MOUSE_GENOMES	SC_MOUSE_GENOMES	f	SNP	A/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr2:148715777 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Cst3	cystatin C			Intron
				Noncoding-Transcript-Variant
Rr374041	regulatory region 374041			275 bp upstream
Rr566976	regulatory region 566976			1675 bp proximal
Rr566977	regulatory region 566977			1709 bp proximal
Tssr20680	transcription start site region 20680			1863 bp downstream
Tssr20681	transcription start site region 20681			966 bp downstream
Tssr20682	transcription start site region 20682			1291 bp upstream
Tssr20683	transcription start site region 20683			1367 bp upstream
Tssr26682	transcription start site region 26682			1897 bp upstream
Tssr26683	transcription start site region 26683			1847 bp upstream
Tssr26684	transcription start site region 26684			1810 bp upstream
Tssr26685	transcription start site region 26685			951 bp upstream
Tssr26686	transcription start site region 26686			918 bp upstream
Tssr26687	transcription start site region 26687			787 bp upstream
Tssr26688	transcription start site region 26688			1564 bp downstream
Tssr26689	transcription start site region 26689			1595 bp downstream
Tssr26690	transcription start site region 26690			1747 bp downstream
Tssr26691	transcription start site region 26691			1766 bp downstream