rs239657089 SNP Detail

Summary

• ID
  rs239657089
• 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
  

Genome Location and Flanking Sequence

• Location
  Chr2:105501166 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              CAGACTTGGA AAAGAAAACC
  AAAGAGAATC CAGCTTCCAG GGAGAGAGGG AGAGAGAAGT AAGGGAGAGA GAGAGGGAAA
  GGGAGAGAGA GAGAGAGAGA GAGAGAGAGA GAGAGAGAGA GAGAGAGAGA GTAAATCTTG
  CATGAGAACT TTCTAGTGCA CTGGCAGAGA TGCTTGGCCA GACCTAGAAG GACGAGTGCC
  W
  GTATTTGTGG TATTATTTTT TCTTTTGCTT CCCTTTTTCA TTCCTTTTCT TTTCGGGAGG
  AATCTGGCTG CAGAGCCTTG ATCCCAGAGT TCGGATATTC TCCCAGGTGG ACCCCGATCT
  CCGAGGAAAC AACCAGGGCT TAATCCCTCA TTGCTCTGTC CCTGACTCCC AATCCCCACA
  AGTTTTTCCC TGATGGGGAG                                            
  
  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
ss355141748	MGP_WTSI_2_105510978	EVA_MGPV3	EVA_MGPV3	f	SNP	T	T	T	T	T	T	T	T	T	T	A	A	T	T	T	T	T	T	T	A	T	A	A	T	T	T	T	A	T	T	T	T	T	A	T	T	T	T	T	T	A	T	T	T	T	T	T	T	A	T	T	T	T
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
rs239657089					SNP	T	T	T	T	T	T	T	T	T	T	A	A	T	T	T	T	T	T	T	A	T	A	A	T	T	T	T	A	T	T	T	T	T	A	T	T	T	T	T	T	A	T	T	T	T	T	T	T	A	T	T	T	T

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
ss355141748	MGP_WTSI_2_105510978	SC_MOUSE_GENOMES	SC_MOUSE_GENOMES	f	SNP	A/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr2:105501166 () rs orientation: forward

Symbol	Name	Function Class
Cpgi12017	CpG island 12017	1678 bp distal
Cpgi12018	CpG island 12018	500 bp distal
Cpgi12019	CpG island 12019	1573 bp proximal
Pax6	paired box 6	within coordinates
Pax6os1	paired box 6 opposite strand 1	491 bp upstream
Rr370602	regulatory region 370602	within coordinates
Tssr19250	transcription start site region 19250	1907 bp downstream
Tssr19251	transcription start site region 19251	1871 bp downstream
Tssr25562	transcription start site region 25562	523 bp upstream
Tssr25563	transcription start site region 25563	499 bp upstream