rs249540978 SNP Detail

Summary

• ID
  rs249540978
• 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
  Chr3:41517683 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              TCACTCAAAC TATTCGCTTT
  AATACCCATG TTCCTAGTCG ACCTGATTTA AAACTAATTT GCAATAAATG CATTTCTGCA
  TGTCGCCCGG AGTTGGAACT GGGGCAGCAG TTTTGGAGGG GGTGATTTCA CAAACCTTCT
  TCCTCCTAGG AGACACCTGG AGGGTTTGCG GGCTCCAGAG GTGGGTGAGG GGGGAGAGCC
  Y
  CTCTGGCTGC AGTCAGGACC CCAAGAGTTA ACGGGAGCAA GCCCCTACCA GCGGCTCCCC
  GCCCCACCGT CCCCACCCTC TCCTTTGGCT GGGGATTAAA GTGCTCCCCC CTGTGGCAGC
  AGTGACCCAG AAATGAGTCT GCGTCCCCGC GCTTCCTCCG CCGCCAGCCG CACGCCCTAC
  CGGGAGGGCC TGGGCGCGCC                                            
  
  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
ss357685332	MGP_WTSI_3_41367170	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	T	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
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
rs249540978					SNP	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	C	T	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

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
ss357685332	MGP_WTSI_3_41367170	SC_MOUSE_GENOMES	SC_MOUSE_GENOMES	f	SNP	C/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr3:41517683 () rs orientation: forward

Symbol	Name	Function Class
Cpgi13118	CpG island 13118	within coordinates
Cpgi13119	CpG island 13119	1266 bp proximal
Gm31266	predicted gene, 31266	within coordinates
Jade1	jade family PHD finger 1	Intron
Rr575965	regulatory region 575965	within coordinates
Rr575966	regulatory region 575966	100 bp proximal
Rr575967	regulatory region 575967	440 bp proximal
Rr575968	regulatory region 575968	694 bp proximal
Rr575969	regulatory region 575969	1116 bp proximal
Rr575970	regulatory region 575970	1683 bp proximal
Rr575971	regulatory region 575971	1952 bp proximal
Tssr29001	transcription start site region 29001	1524 bp downstream
Tssr29002	transcription start site region 29002	108 bp upstream
Tssr29003	transcription start site region 29003	145 bp upstream
Tssr29004	transcription start site region 29004	1624 bp upstream
Tssr29005	transcription start site region 29005	1673 bp upstream
Tssr29006	transcription start site region 29006	1749 bp upstream