rs227755972 SNP Detail

Summary

• ID
  rs227755972
• 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
  Chr5:120571383 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              CCAAAATGAG AAATGCTATG
  GGGCAGCCTA GAAACGCGTG GGTTTTTTTT TTTTTTTTTT TTTTTTTTTT TTTTTTTTTT
  TTTTTTTTTT TTTGGTAGCT GCGCTTTCTG CCCGTTTCCA CCCGGCACCC AGACTGGCTT
  TGTGAGTCTG AATTCCAGGC ACTGAGGGGG CGTGATTAGC TCGGCAAAGG AGAAAGGCTG
  Y
  CGCCTGCCCC AGTGGCCGGG CACTTGGGAA TTTGAATAGG AGAAAATGTC AGCCTCGCCT
  TTACACGTGT AAACTCCCTA GCCCCAGAGG CCCTGGTGCC CCTAATGTGG CATGCTTGCA
  AAGCACCTAA TGATTTTTGA TAAGGTGTAT ATAGCCAATT ATGCTGCCGG ATAAGGCCAA
  AAGTGACTTA TGGTTTCTAA                                            
  
  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
ss366475083	MGP_WTSI_5_120883327	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
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
rs227755972					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

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
ss366475083	MGP_WTSI_5_120883327	SC_MOUSE_GENOMES	SC_MOUSE_GENOMES	f	SNP	C/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr5:120571383 () rs orientation: forward

Symbol	Name	Function Class
Cpgi16490	CpG island 16490	534 bp distal
Cpgi16491	CpG island 16491	1037 bp proximal
Cpgi16492	CpG island 16492	1813 bp proximal
Lhx5	LIM homeobox protein 5	Intron
Lhx5as1	LIM homeobox 5, antisense 1	1551 bp upstream
Rr619311	regulatory region 619311	1733 bp distal
Rr619312	regulatory region 619312	1609 bp distal
Rr619313	regulatory region 619313	1070 bp distal
Tssr48502	transcription start site region 48502	1413 bp downstream
Tssr48503	transcription start site region 48503	1406 bp downstream
Tssr48504	transcription start site region 48504	1381 bp downstream
Tssr48505	transcription start site region 48505	1360 bp downstream
Tssr48506	transcription start site region 48506	1338 bp downstream
Tssr48507	transcription start site region 48507	103 bp downstream
Tssr52923	transcription start site region 52923	1547 bp upstream