rs240470589 SNP Detail

Summary

• ID
  rs240470589
• 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
  Chr3:89177349 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              GTGCAGATAT GCCAGGATAT
  AAAGAGTCTG AAGCACGGCC CCCACGCTAT TGACGATGAT AAGGGTCCCA TCTCCCTTCA
  AGACTCCGTA ACTCAGCCAG CTCAGGTTGC TGTGAGGGAA GGAGGATTAA GGTCCAAGGG
  GCTGCTGGGG TTGCAGCAGG TCTCCAGGGA TCTCTTGCAC CTCCCTCAGC CTTTCCCATC
  W
  CAGCCAACAA CACTCTCACT TGACATCCGT GGTGAGAAAA GGCAGGAACT GGATGTTGTC
  CACGCTCCGT GTCCTCTGCA TATGCCTGAG GTCCGAGCTG GAAGGGATCC AAAGGAAATT
  GTTAGGAGTG GGTAAAAGAT TTCTCGGTGT TTACCAATCA TCCTGAACGA CAAGCAGATC
  TCCCCCCTCA GGCCAAGAGG                                            
  
  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
ss358809634	MGP_WTSI_3_89073964	EVA_MGPV3	EVA_MGPV3	f	SNP	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	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
rs240470589					SNP	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	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
ss358809634	MGP_WTSI_3_89073964	SC_MOUSE_GENOMES	SC_MOUSE_GENOMES	f	SNP	A/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr3:89177349 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Cpgi13416	CpG island 13416			49 bp proximal
Efna1	ephrin A1			1688 bp downstream
Rr580014	regulatory region 580014			752 bp distal
Rr580015	regulatory region 580015			443 bp proximal
Rr580016	regulatory region 580016			570 bp proximal
Rr580017	regulatory region 580017			1830 bp proximal
Slc50a1	solute carrier family 50 (sugar transporter), member 1			Intron
				Noncoding-Transcript-Variant
Tssr30087	transcription start site region 30087			1865 bp upstream
Tssr34108	transcription start site region 34108			439 bp downstream
Tssr34109	transcription start site region 34109			447 bp downstream