rs253240587 SNP Detail

Summary

• ID
  rs253240587
• 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
  Chr15:97874405 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              CCTCTCCTCT TCAATTGTCC
  CCTTGATGGT AGAGCCCTCC TCTACTTGTC TTCCTCCTTC CCACAGAGGG CTTCCTGCCT
  GGGATAGCCT CTCCTCTCCT ATGCTAGTTT CTACGAATAC TTCTATAAGA GTTAGTGAGC
  TTGCCAGCAT CTTTATTGCC TCTGAATGAG GAAGTGGACA AGCCAGTATG GTATACGCTC
  Y
  TCCCCCATCC CTGCCTCTCA GCTTGTCTCC CACATGCCCC CACGACTCAA GCCTCTAATG
  AGTCCCTTCA CTACAGGAAA GTGACATTTG TCACAGGCTG ACCTCAGCCC CACTCACCGT
  GCAGCCATCC TTCAGGGCAG TGTATGTGAA CCTGCTGTTG CCCTCGGCCC TCATCTCTAC
  ATCATTGGAG CCCTGGATGA                                            
  
  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
ss395125764	MGP_WTSI_15_97806955	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
rs253240587					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
ss395125764	MGP_WTSI_15_97806955	SC_MOUSE_GENOMES	SC_MOUSE_GENOMES	f	SNP	C/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr15:97874405 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Col2a1	collagen, type II, alpha 1			Intron
				Noncoding-Transcript-Variant
Rr509000	regulatory region 509000			287 bp proximal
Tssr4707	transcription start site region 4707			364 bp downstream
Tssr132910	transcription start site region 132910			894 bp downstream
Tssr136189	transcription start site region 136189			837 bp upstream
Tssr136190	transcription start site region 136190			807 bp upstream
Tssr136191	transcription start site region 136191			603 bp upstream
Tssr136192	transcription start site region 136192			473 bp upstream
Tssr136193	transcription start site region 136193			456 bp upstream
Tssr136194	transcription start site region 136194			405 bp upstream
Tssr136195	transcription start site region 136195			382 bp upstream
Tssr136196	transcription start site region 136196			370 bp upstream
Tssr136197	transcription start site region 136197			352 bp upstream
Tssr136198	transcription start site region 136198			154 bp downstream
Tssr136199	transcription start site region 136199			200 bp downstream
Tssr136200	transcription start site region 136200			218 bp downstream
Tssr136201	transcription start site region 136201			274 bp downstream
Tssr136202	transcription start site region 136202			328 bp downstream
Tssr136203	transcription start site region 136203			753 bp downstream
Tssr136204	transcription start site region 136204			846 bp downstream
Tssr136205	transcription start site region 136205			1309 bp downstream
Tssr136206	transcription start site region 136206			1348 bp downstream
Tssr136207	transcription start site region 136207			1378 bp downstream