rs236842399 SNP Detail

Summary

• ID
  rs236842399
• Variation Type
  SNP
• Alleles
  G/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
  Chr3:90421011 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              GGGTGCTCAA GGGAGGAATT
  TGGGCGGCTC GGTTACCATT CTCATCTATG AGGGGCATCT GGAGGTTGCC TGGAACCCTC
  TAGCAGCTTG GAATTTTATG TAGGGGAGGA TCTGGGCTTG GAGCAGTGGG AAACAAAGAG
  GGAAAAATTA GGGGAGAGAG GAGAGGGGGT CAAGGCTGAG AAAGAAGGGC TAGAGAGGAG
  K
  TCTGTGAGGC AGAGATGGGA CAGTGCACAC CGCCACAGAC CCCCTTCTTT AAGAAAGATA
  CCACATGACG TAAGCTCCAC TGCTAGGAGC CTTCCCTGGC TCTTGAGAAG GCAGAGAGTG
  AGGGTGGAGA AGGGGCAGGG ACAGCTTTTC TTATTCTTAC CCTGAAGGAG CAGGGCTGTA
  TCTCCTCCCT GCCCACACCT                                            
  
  K = G/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	ZALENDE/EiJ
ss358833693	MGP_WTSI_3_90317626	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	T	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
rs236842399					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	T	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
ss358833693	MGP_WTSI_3_90317626	SC_MOUSE_GENOMES	SC_MOUSE_GENOMES	f	SNP	G/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr3:90421011 () rs orientation: forward

Symbol	Name	Function Class
Cpgi13466	CpG island 13466	480 bp proximal
Rr375350	regulatory region 375350	within coordinates
Rr580384	regulatory region 580384	within coordinates
Rr580385	regulatory region 580385	257 bp proximal
Rr580386	regulatory region 580386	374 bp proximal
Rr580387	regulatory region 580387	564 bp proximal
Rr580388	regulatory region 580388	674 bp proximal
Rr580389	regulatory region 580389	678 bp proximal
Rr580390	regulatory region 580390	742 bp proximal
S100a1	S100 calcium binding protein A1	Intron
S100a13	S100 calcium binding protein A13	648 bp upstream
Tssr30209	transcription start site region 30209	1214 bp upstream
Tssr30210	transcription start site region 30210	1280 bp upstream
Tssr34241	transcription start site region 34241	1638 bp upstream
Tssr34242	transcription start site region 34242	546 bp downstream
Tssr34243	transcription start site region 34243	652 bp downstream
Tssr34244	transcription start site region 34244	666 bp downstream
Tssr34245	transcription start site region 34245	701 bp downstream