rs261962516 SNP Detail

Summary

• ID
  rs261962516
• Variation Type
  SNP
• Alleles
  G/T

• Created in dbSNP Build
  137
• Last Updated in dbSNP Build
  142
• Additional Resources
  JBrowse Genome Browser | Ensembl SNPView | UCSC Browser | Alliance Variant
  

Genome Location and Flanking Sequence

• Location
  Chr6:7845200 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                        GAGGC GCCCGGGGCG GGCCAGCGCC
  K
  AGCGGTCCTG CCCGCCGCCC CGCCC                                      
  
  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	129S1/SvImJ	A/J	AKR/J	B10.RIII-H2 H2-T18/(71NS)SnJ	BALB/cByJ	BALB/cJ	BTBR T<+> Itpr3/J	BUB/BnJ	C3H/HeJ	C57BL/6J	C57BL/6NJ	C57BL/10SnJ	CAST/EiJ	CBA/J	CE/J	CZECHII/EiJ	DBA/2J	FVB/NJ	JF1/MsJ	LP/J	MA/MyJ	NOD/ShiLtJ	NZO/HlLtJ	PL/J	PWK/PhJ	QSi3/Ianm	QSi5/Ianm	RIIIS/J	SJL/J	SPRET/EiJ	SWR/J	WSB/EiJ
ss917824254	MGP_WTSI_6_7845200	EVA_MGPV3	EVA_MGPV3	f	SNP	T	G	G	G	T	T	T	T	T	G	G	G	T	T	G	T	G	G	T	G	G	G	G	T	T	G	G	G	T	T	T	G
SNP Consensus Information
SNP					Consensus Type	129S1/SvImJ	A/J	AKR/J	B10.RIII-H2 H2-T18/(71NS)SnJ	BALB/cByJ	BALB/cJ	BTBR T<+> Itpr3/J	BUB/BnJ	C3H/HeJ	C57BL/6J	C57BL/6NJ	C57BL/10SnJ	CAST/EiJ	CBA/J	CE/J	CZECHII/EiJ	DBA/2J	FVB/NJ	JF1/MsJ	LP/J	MA/MyJ	NOD/ShiLtJ	NZO/HlLtJ	PL/J	PWK/PhJ	QSi3/Ianm	QSi5/Ianm	RIIIS/J	SJL/J	SPRET/EiJ	SWR/J	WSB/EiJ
rs261962516					SNP	T	G	G	G	T	T	T	T	T	G	G	G	T	T	G	T	G	G	T	G	G	G	G	T	T	G	G	G	T	T	T	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
ss917824254	MGP_WTSI_6_7845200	SC_MOUSE_GENOMES	SC_MOUSE_GENOMES	f	SNP	G/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr6:7845200 () rs orientation: forward

Symbol	Name	Function Class
C1galt1	core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1	mRNA-UTR
Cpgi17149	CpG island 17149	within coordinates
Rr399558	regulatory region 399558	475 bp downstream
Rr399559	regulatory region 399559	1586 bp upstream
Rr626324	regulatory region 626324	348 bp distal
Rr626325	regulatory region 626325	623 bp distal
Rr626326	regulatory region 626326	within coordinates
Rr626327	regulatory region 626327	1601 bp proximal
Tssr54889	transcription start site region 54889	523 bp downstream
Tssr54890	transcription start site region 54890	397 bp downstream
Tssr54891	transcription start site region 54891	341 bp downstream
Tssr54892	transcription start site region 54892	51 bp upstream
Tssr54893	transcription start site region 54893	118 bp upstream
Tssr54894	transcription start site region 54894	1777 bp upstream