rs228996438 SNP Detail

Summary

• ID
  rs228996438
• 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
  Chr15:97875135 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              TCTCCTCTTT CTTTCTTCTA
  AGGCCCAAAG GGACACCGGC GGAGGATGCC AAGAAGGAGC TAAAGAATCG GAGGAGAGAG
  AAGAGCACTC AGGAGGGACC AGCTGAGCCT AGACCACCGG GCACTCACGT GGAAGCCACC
  GTTCATGGTC TCTCCAAACC AGATGTGTTT CTTTTCCTTG CTCTTGCTGC TCCACCAGTT
  Y
  TTCCGAGGGA CAGTCGCTGG GTTGGGGTAG ACGCAAGTCT CGCCGGTCTC CATGTTGCAG
  AAAACTTTCA TGGCGTCCAA GGTGCAGCCC TGGTTGGGAT CAATCCAGTA GTCTCCTGCA
  GGAAAAAGAG GCAGCATCCC ATGATGCTTT GCAAGACAGC CTACTGGGAA ACAAGTCAGG
  GGAGGCTTAC ATGTGGCCTA                                            
  
  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
ss395125780	MGP_WTSI_15_97807685	EVA_MGPV3	EVA_MGPV3	f	SNP	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	C	T	T	T	T
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
rs228996438					SNP	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	C	T	T	T	T

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
ss395125780	MGP_WTSI_15_97807685	SC_MOUSE_GENOMES	SC_MOUSE_GENOMES	f	SNP	C/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr15:97875135 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Col2a1	collagen, type II, alpha 1			Coding-Synonymous
				Intron
				Noncoding-Transcript-Variant
				Noncoding-Transcript-Variant
Rr509000	regulatory region 509000			422 bp distal
Tssr4707	transcription start site region 4707			359 bp upstream
Tssr4708	transcription start site region 4708			1958 bp upstream
Tssr132910	transcription start site region 132910			1624 bp downstream
Tssr136189	transcription start site region 136189			1567 bp upstream
Tssr136190	transcription start site region 136190			1537 bp upstream
Tssr136191	transcription start site region 136191			1333 bp upstream
Tssr136192	transcription start site region 136192			1203 bp upstream
Tssr136193	transcription start site region 136193			1186 bp upstream
Tssr136194	transcription start site region 136194			1135 bp upstream
Tssr136195	transcription start site region 136195			1112 bp upstream
Tssr136196	transcription start site region 136196			1100 bp upstream
Tssr136197	transcription start site region 136197			1082 bp upstream
Tssr136198	transcription start site region 136198			558 bp upstream
Tssr136199	transcription start site region 136199			519 bp upstream
Tssr136200	transcription start site region 136200			494 bp upstream
Tssr136201	transcription start site region 136201			438 bp upstream
Tssr136202	transcription start site region 136202			376 bp upstream
Tssr136203	transcription start site region 136203			23 bp downstream
Tssr136204	transcription start site region 136204			116 bp downstream
Tssr136205	transcription start site region 136205			579 bp downstream
Tssr136206	transcription start site region 136206			618 bp downstream
Tssr136207	transcription start site region 136207			648 bp downstream