rs239960341 SNP Detail

Summary

• ID
  rs239960341
• Variation Type
  SNP
• Alleles
  A/G

• 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
  Chr3:90494268 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              AAAGTAGGTT GGTGAGGAGC
  TCCCAGGCCC CGGGGAGGAG AGGTACACTG AGTGGCTTTG CAAAGGTTTA GAAGAGGACA
  CTGGAGGACC CAAGACCTAC TTTAACTGTG CTGTGCAGGC TGGTTGCCAT GTGAGCCCTA
  GGCAAAGGCC TGGGAGTCTG ACTCTGCTAC CTTTCAGATT TCAGCAGCGT CAACACCAGC
  R
  TCTCCCTAGG TGCTGCCAGG TGAGGGGCTG CACTCTGGTG CTTGTGGGTT GGGGTTTCCG
  GCTGCTGCTC TGGCCCCGGG GAGCAGGGTG TGCCGCTGAC TCACCACCTG GGTATCTGGG
  CTTGGAACCA CGGGTGAGTC ACCCTGCCCT GGGGGAGCTG AGAGAAGCTG CTTGGTGTCT
  GGAGGGGGAA GAGAGCTGGG                                            
  
  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	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
ss358835273	MGP_WTSI_3_90390883	EVA_MGPV3	EVA_MGPV3	f	SNP	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	A	G	G	G	G
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
rs239960341					SNP	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	G	A	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
ss358835273	MGP_WTSI_3_90390883	SC_MOUSE_GENOMES	SC_MOUSE_GENOMES	f	SNP	A/G

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr3:90494268 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Cpgi13467	CpG island 13467			within coordinates
Rr854	regulatory region 854			within coordinates
Rr367471	regulatory region 367471			within coordinates
Rr580406	regulatory region 580406			1101 bp distal
Rr580407	regulatory region 580407			746 bp distal
Rr580408	regulatory region 580408			within coordinates
Rr580409	regulatory region 580409			2 bp proximal
Rr580410	regulatory region 580410			238 bp proximal
S100a3	S100 calcium binding protein A3			Intron
				mRNA-UTR
Tssr945	transcription start site region 945			314 bp upstream
Tssr30230	transcription start site region 30230			294 bp upstream
Tssr30231	transcription start site region 30231			1575 bp upstream