rs254525309 SNP Detail

Summary

• ID
  rs254525309
• 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
  Chr1:57009463 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              TGCTCTGTCT CAGGTCCCAA
  GAGTTAGCCC TCAGTTGTGT GGACAGAGTC GGACCTCGAA GCCTTTAAGC AGTACCCCAT
  TCATTGCGGG CAGCGCTGGC ATTATCCTCT CTTTGATAAA GAGCCACCAC CACCATAAGC
  CCCACTTGGG GTGTCAGGGT TTTGAAAGGA GCGTACTTAT GGGCGAGAGG TCCCACCAGG
  Y
  CAGGGAGGGA GCAAGGACTT ACACGGGTCC TTAAGCAAAT TAATTGCTTG ATAAATGCGC
  TGTGGATGGC CAAGCTGGAT CAATGGATCC ATGGAATCCC CACCTTTTAC CTTTATGGAC
  CAAGTACACT TGTGTACACA AACACACACC TTTGCACACA AAAAAATTAA CTATAATTTC
  ACGTGAGCGA GCATCCCAAA                                            
  
  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
ss349733829	MGP_WTSI_1_57027148	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
rs254525309					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
ss349733829	MGP_WTSI_1_57027148	SC_MOUSE_GENOMES	SC_MOUSE_GENOMES	f	SNP	C/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr1:57009463 () rs orientation: forward

Symbol	Name	Function Class
9130024F11Rik	RIKEN cDNA 9130024F11 gene	1165 bp upstream
Cpgi267	CpG island 267	303 bp distal
Cpgi268	CpG island 268	525 bp proximal
Cpgi269	CpG island 269	1158 bp proximal
Rr411276	regulatory region 411276	within coordinates
Rr411277	regulatory region 411277	388 bp proximal
Rr411278	regulatory region 411278	658 bp proximal
Rr411279	regulatory region 411279	1187 bp proximal
Rr411280	regulatory region 411280	1544 bp proximal
Satb2	special AT-rich sequence binding protein 2	Intron
Tssr6736	transcription start site region 6736	1147 bp upstream
Tssr6737	transcription start site region 6737	1729 bp upstream
Tssr6738	transcription start site region 6738	1876 bp upstream
Tssr11745	transcription start site region 11745	454 bp upstream
Tssr11746	transcription start site region 11746	429 bp upstream
Tssr11747	transcription start site region 11747	963 bp downstream
Tssr11748	transcription start site region 11748	977 bp downstream
Tssr11749	transcription start site region 11749	1009 bp downstream
Tssr11750	transcription start site region 11750	1034 bp downstream
Tssr11751	transcription start site region 11751	1390 bp downstream
Tssr11752	transcription start site region 11752	1408 bp downstream
Tssr11753	transcription start site region 11753	1446 bp downstream
Tssr11754	transcription start site region 11754	1458 bp downstream
Tssr11755	transcription start site region 11755	1879 bp downstream
Tssr11756	transcription start site region 11756	1928 bp downstream