rs580890332 SNP Detail

Summary

• ID
  rs580890332
• Variation Type
  SNP
• Alleles
  A/G

• Created in dbSNP Build
  142
• Last Updated in dbSNP Build
  142
• Additional Resources
  JBrowse Genome Browser | Ensembl SNPView | UCSC Browser
  

Genome Location and Flanking Sequence

• Location
  Chr5:120568546 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                        GAAAG AAAGAAAGAA AGAAAGGAAG
  R
  AAGGAAGAAA GAAAGAAAGA AAGAA                                      
  
  R = A/G
  

  
  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	129S1/SvImJ	B10.RIII-H2 H2-T18/(71NS)SnJ	BALB/cJ	BTBR T<+> Itpr3/J	C57BL/6J	C57BL/6NJ	C57BL/10J	C57BL/10SnJ	C57BR/cdJ	C57L/J	C58/J	CAST/EiJ	CBA/J	CE/J	DBA/1J	DBA/2J	I/LnJ	LEWES/EiJ	LG/J	NOD/ShiLtJ	NZB/BlNJ	PL/J	SJL/J	SWR/J
ss917666933	MGP_WTSI_5_120430481	EVA_MGPV3	EVA_MGPV3	f	SNP	G	G	G	G	G	G	G	G	G	G	G	A	G	G	G	G	G	G	G	G	G	G	G	G
SNP Consensus Information
SNP					Consensus Type	129S1/SvImJ	B10.RIII-H2 H2-T18/(71NS)SnJ	BALB/cJ	BTBR T<+> Itpr3/J	C57BL/6J	C57BL/6NJ	C57BL/10J	C57BL/10SnJ	C57BR/cdJ	C57L/J	C58/J	CAST/EiJ	CBA/J	CE/J	DBA/1J	DBA/2J	I/LnJ	LEWES/EiJ	LG/J	NOD/ShiLtJ	NZB/BlNJ	PL/J	SJL/J	SWR/J
rs580890332					SNP	G	G	G	G	G	G	G	G	G	G	G	A	G	G	G	G	G	G	G	G	G	G	G	G

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
ss917666933	MGP_WTSI_5_120430481	SC_MOUSE_GENOMES	SC_MOUSE_GENOMES	f	SNP	A/G

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr5:120568546 () rs orientation: forward

Symbol	Name	Function Class
Cpgi16490	CpG island 16490	378 bp proximal
Lhx5	LIM homeobox protein 5	1218 bp upstream
Lhx5as1	LIM homeobox 5, antisense 1	within coordinates
Rr619309	regulatory region 619309	1116 bp distal
Rr619310	regulatory region 619310	141 bp distal
Rr619311	regulatory region 619311	202 bp proximal
Rr619312	regulatory region 619312	1105 bp proximal
Rr619313	regulatory region 619313	1262 bp proximal
Tssr48502	transcription start site region 48502	1410 bp upstream
Tssr48503	transcription start site region 48503	1428 bp upstream
Tssr48504	transcription start site region 48504	1449 bp upstream
Tssr48505	transcription start site region 48505	1468 bp upstream
Tssr48506	transcription start site region 48506	1488 bp upstream
Tssr52923	transcription start site region 52923	1276 bp downstream