rs238874396 SNP Detail

Summary

• ID
  rs238874396
• 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
  Chr5:120568621 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              CTTGTGAGTG ACTTTACAAA
  CAAGCATTTC CTCACACACC CAGTCGACCC ATGTAAGCAG ACACATAGAG ACACAGACCA
  ACAAGAAAGA AAGAAAGAAA GAAAGAAAGA AAGAAAGAAA GGAAGGAAGG AAGAAAGAAA
  GAAAGAAAGA AAGAAAGAAA GAAAGAAAGA AAGAAAGGTA ATGCACATGT TAACAGGAAA
  W
  TATAAACGAG AAATTTTACA TGCCAAAAAA AGAAAGAAAA AAGAAAAAGA AACAAAAATA
  AAAAAAAATC CCTCCACGTC CCAGGGTTTG ATCGCGAACA CACTATAAAT AGAGAGTTTT
  CAAGCAGTGG ATATTTGCTA ACAAACTCAG TAAATACGCC CAAACAAACA CCCACAGCCA
  AGTCTTGGCA CAATTCCTCT                                            
  
  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	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
ss366475041	MGP_WTSI_5_120880565	EVA_MGPV3	EVA_MGPV3	f	SNP	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	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	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
rs238874396					SNP	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	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
ss366475041	MGP_WTSI_5_120880565	SC_MOUSE_GENOMES	SC_MOUSE_GENOMES	f	SNP	A/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr5:120568621 () rs orientation: forward

Symbol	Name	Function Class
Lhx5	LIM homeobox protein 5	1143 bp upstream
Lhx5as1	LIM homeobox 5, antisense 1	within coordinates
Rr619309	regulatory region 619309	1191 bp distal
Rr619310	regulatory region 619310	216 bp distal
Rr619311	regulatory region 619311	127 bp proximal
Rr619312	regulatory region 619312	1030 bp proximal
Rr619313	regulatory region 619313	1187 bp proximal
Tssr48502	transcription start site region 48502	1335 bp upstream
Tssr48503	transcription start site region 48503	1353 bp upstream
Tssr48504	transcription start site region 48504	1374 bp upstream
Tssr48505	transcription start site region 48505	1393 bp upstream
Tssr48506	transcription start site region 48506	1413 bp upstream
Tssr52923	transcription start site region 52923	1201 bp downstream