rs260643518 SNP Detail

Summary

• ID
  rs260643518
• 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
  Chr4:107109855 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              ACCTGCCTTC TCCCCCAAAC
  TGCAGAAACT CATGTCCTAT CCGGGCCCAT ACTTTGTCCA AGAGCAAGCT AATCTCTCCC
  ACATCTTGAT AGTTTTACCC ACTCTTTAGC TTTTCAAACA GAAAAAATTT CAGTCCCCCA
  CCCCCCAAAT TCTAACCTTC CCCATTCACT CCCAGATCTT CTACCCATCT TCCTCACATC
  Y
  CAGACTCTCC CGTGCCCCTC AAAAGACTCA ACCCCGCCTC CACCTGTCTT CTAGCGACCC
  GTCTCCAGCC CCCATCCTTC TCTCCCTCCT CACGAGTCTT CCTCTCACCA TCGAGGTTCC
  TCTTAGCACC CTAGTCTCCC CATCTCTTTC CCGGTTTTGC GTCCTCAACC TTCAGATTCC
  CCTTTCTTCA CGCCTCACTA                                            
  
  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
ss362755062	MGP_WTSI_4_106925263	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
rs260643518					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
ss362755062	MGP_WTSI_4_106925263	SC_MOUSE_GENOMES	SC_MOUSE_GENOMES	f	SNP	C/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr4:107109855 () rs orientation: forward

Symbol	Name	Function Class
Cpgi14538	CpG island 14538	346 bp proximal
Ift25	intraflagellar transport 25	1034 bp upstream
Lrrc42	leucine rich repeat containing 42	Intron
Rr398372	regulatory region 398372	785 bp upstream
Rr596955	regulatory region 596955	1809 bp distal
Rr596956	regulatory region 596956	1972 bp distal
Rr596957	regulatory region 596957	within coordinates
Rr596958	regulatory region 596958	603 bp proximal
Rr596959	regulatory region 596959	864 bp proximal
Rr596960	regulatory region 596960	1120 bp proximal
Rr596961	regulatory region 596961	1278 bp proximal
Tssr1253	transcription start site region 1253	570 bp upstream
Tssr38232	transcription start site region 38232	597 bp upstream
Tssr38233	transcription start site region 38233	1229 bp upstream
Tssr38234	transcription start site region 38234	1254 bp upstream
Tssr38235	transcription start site region 38235	1261 bp upstream
Tssr42677	transcription start site region 42677	669 bp downstream
Tssr42678	transcription start site region 42678	705 bp downstream
Tssr42679	transcription start site region 42679	730 bp downstream
Tssr42680	transcription start site region 42680	783 bp downstream
Tssr42681	transcription start site region 42681	855 bp downstream