rs52539049 SNP Detail

Summary

• ID
  rs52539049
• Variation Type
  SNP
• Alleles
  C/T

• Created in dbSNP Build
  128
• Last Updated in dbSNP Build
  137
• Additional Resources
  JBrowse Genome Browser | Ensembl SNPView | UCSC Browser
  

Genome Location and Flanking Sequence

• Location
  Chr4:135875159 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              CGGGACGCTC CTCCTCAATT
  TTAAGTCTTC CGAGTAGTTA CGGCAGTCCG TGGTTACCAC TCTTTCCCAG GGCCCCCACC
  CTCACCCCCC GGCTGCACCC TTAAAACTTC TCTCTCTGGC TTTCCCGCAA AACTGCAGCT
  CTACCCACTA GCCCGCCTCC AGGCAAGAAG CGGCTCCGCG GCGCCAGGGC CGGGCCGATT
  Y
  TCGGCCCACG TGGCCCAGTG GCTGGGAAGG CGGAGCTCCG GGCCCCGCCT CCCTGCTCGG
  CCCCGCCCCC GGCCCGCTGC CCGCGCTCCC CCGCCCCCCG CGGGCCCTGA GGGCCGCTCG
  CAGGTGTTCG CTGGCGCCCG GATGTCTGAG CTCTGGCTCC ACTCTGGCTC CGGCTCCCTC
  CGCAGCCTGC GGGCGGGGCT                                            
  
  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	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/10SnJ	C57L/J	C58/J	CAST/EiJ	CBA/J	CE/J	CZECHII/EiJ	DBA/2J	FVB/NJ	I/LnJ	JF1/MsJ	KK/HlJ	LG/J	LP/J	MA/MyJ	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
ss363384158	MGP_WTSI_4_135703763	EVA_MGPV3	EVA_MGPV3	f	SNP	T	T	C	C	T	C	C	C	C	C	C	C	C	T	C	C	C	C	C	C	C	C	C	T	T	C	T	C	C	C	C	T	C	C	C	C	C	C	C	T	C	C	C	C	C	C	C
SNP Consensus Information
SNP					Consensus Type	129P2/OlaHsd	129S1/SvImJ	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/10SnJ	C57L/J	C58/J	CAST/EiJ	CBA/J	CE/J	CZECHII/EiJ	DBA/2J	FVB/NJ	I/LnJ	JF1/MsJ	KK/HlJ	LG/J	LP/J	MA/MyJ	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
rs52539049					SNP	T	T	C	C	T	C	C	C	C	C	C	C	C	T	C	C	C	C	C	C	C	C	C	T	T	C	T	C	C	C	C	T	C	C	C	C	C	C	C	T	C	C	C	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
ss363384158	MGP_WTSI_4_135703763	SC_MOUSE_GENOMES	SC_MOUSE_GENOMES	f	SNP	C/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr4:135875159 () rs orientation: forward

Symbol	Name	Function Class
Cpgi15099	CpG island 15099	within coordinates
Gm68296	predicted gene, 68296	314 bp downstream
Rr377254	regulatory region 377254	155 bp downstream
Rr602287	regulatory region 602287	651 bp distal
Rr602288	regulatory region 602288	within coordinates
Rr602289	regulatory region 602289	1965 bp proximal
Tssr39669	transcription start site region 39669	600 bp downstream