rs220400842 SNP Detail

Summary

• ID
  rs220400842
• 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
  Chr6:42563166 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              AAGGTACACA CACATAAATA
  TATATACATG CATATATTTG TCGTGTGTGT GTGTGTGTGT GTGTGTGTGT GTGTGTGTGT
  GTGTGTGTGT GTGTATGCAC ATGGATGTGG AAGGTAGAGT TTGATGTCAG GAACATTCCT
  CATTTCTCTT CCACTTTCAT TCTTTAAGGA AAAGTCCCCC AATCAAAGCC AAAGCTTGCT
  Y
  GATATGGCTA GTTTGCTGTC TAACTTGCTC TGAGGATTCC TTCCCTCTGC CTGCTACAGC
  TGAGTTTATA GATAGGCTAT TATACCCACT CTACACTTCT GTAGACTCTG GGCATCCTAC
  TCTGGTTCTC TTGCTTGTGT AGTAAGTGCT TTAACTGCTG AACCATCTTC TTAGCCCGTA
  GCTAATGATC TATTTTAAAA                                            
  
  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	ZALENDE/EiJ
ss368091163	MGP_WTSI_6_42536231	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	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	ZALENDE/EiJ
rs220400842					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	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
ss368091163	MGP_WTSI_6_42536231	SC_MOUSE_GENOMES	SC_MOUSE_GENOMES	f	SNP	C/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr6:42563166 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Tcaf3	TRPM8 channel-associated factor 3			Intron
				Noncoding-Transcript-Variant
Tssr56046	transcription start site region 56046			1006 bp downstream
Tssr56047	transcription start site region 56047			857 bp downstream
Tssr56048	transcription start site region 56048			261 bp downstream
Tssr56049	transcription start site region 56049			187 bp downstream
Tssr60620	transcription start site region 60620			479 bp upstream
Tssr60621	transcription start site region 60621			459 bp upstream
Tssr60622	transcription start site region 60622			400 bp upstream
Tssr60623	transcription start site region 60623			351 bp upstream
Tssr60624	transcription start site region 60624			324 bp upstream
Tssr60625	transcription start site region 60625			251 bp upstream
Tssr60626	transcription start site region 60626			235 bp upstream
Tssr60627	transcription start site region 60627			226 bp upstream
Tssr60628	transcription start site region 60628			60 bp upstream
Tssr60629	transcription start site region 60629			20 bp upstream
Tssr60630	transcription start site region 60630			37 bp downstream
Tssr60631	transcription start site region 60631			81 bp downstream
Tssr60632	transcription start site region 60632			133 bp downstream
Tssr60633	transcription start site region 60633			159 bp downstream
Tssr60634	transcription start site region 60634			172 bp downstream
Tssr60635	transcription start site region 60635			238 bp downstream
Tssr60636	transcription start site region 60636			343 bp downstream
Tssr60637	transcription start site region 60637			599 bp downstream
Tssr60638	transcription start site region 60638			639 bp downstream
Tssr60639	transcription start site region 60639			690 bp downstream
Tssr60640	transcription start site region 60640			945 bp downstream