rs258999089 SNP Detail

Summary

• ID
  rs258999089
• 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
  Chr13:49342165 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              GCACCAGGCT GGGATTTTCC
  ACAAGTCTTT GCGGTGCAAA ATAAACCAGA ACAGAGACTT TCTGCCCAGG TCCATATAGT
  GGAAACAGGG AACACCAACG TCTCCTGGGA CTACTTCAGG TGTGCCAGCT GAGACTTGGG
  CTCTGCCAAA ATGTGTGAAC ACTCCGGAAG CAGTGGGCCA GGGACACCCC GGGCTGAGTT
  Y
  CTTTAGGGAG CCCATCAACT GTCTGGGCCT TTTGTATGTG GGTCTACAAT AAAGAACCAG
  TGATCTCTAG GCCTTTAAGG ACAAGGGATG CAAATCAGGA ACAGGTGGGC CCGTGGTTCA
  GCTGCGGATT TGAAGGGAAA CTGGCTGTCT CTGAGCAGCA GCCTCCCCCT TCAGCTCTGC
  AGACAGCTGG ATCAGCTGTG                                            
  
  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
ss388559531	MGP_WTSI_13_49284058	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	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	T	C	C	C	C
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
rs258999089					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	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	T	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
ss388559531	MGP_WTSI_13_49284058	SC_MOUSE_GENOMES	SC_MOUSE_GENOMES	f	SNP	C/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr13:49342165 () rs orientation: forward

Symbol	Name	Function Class
Cpgi5580	CpG island 5580	338 bp distal
Ninj1	ninjurin 1	within coordinates
Rr479364	regulatory region 479364	1154 bp distal
Rr479365	regulatory region 479365	within coordinates
Tssr119678	transcription start site region 119678	1150 bp downstream
Tssr119679	transcription start site region 119679	522 bp downstream
Tssr119680	transcription start site region 119680	473 bp downstream
Tssr119681	transcription start site region 119681	428 bp downstream
Tssr119682	transcription start site region 119682	131 bp downstream
Tssr119683	transcription start site region 119683	1640 bp upstream
Tssr119684	transcription start site region 119684	1663 bp upstream
Tssr122445	transcription start site region 122445	765 bp upstream
Tssr122446	transcription start site region 122446	737 bp upstream
Tssr122447	transcription start site region 122447	728 bp upstream
Tssr122448	transcription start site region 122448	678 bp upstream
Tssr122449	transcription start site region 122449	660 bp upstream
Tssr122450	transcription start site region 122450	1462 bp downstream
Tssr122451	transcription start site region 122451	1509 bp downstream