rs261313540 SNP Detail

Summary

• ID
  rs261313540
• 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
  

Genome Location and Flanking Sequence

• Location
  Chr2:74547421 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              CTCCTGGTCC TGAGTTTCTT
  CTTTGTCTAC ACTGGGCATA CCCAAAGCCC CTGGAGTTAC AATCATGACT ATCTGGGTTT
  TGTTTTTGTT TTTGTGTTTT TTTTTTTTTT TTTTAGTTAC CACACTATAG GTGAGTAATT
  TCTTCCATTT TATGCATGAA ATTACGGGGT CTATGCATTC CTCACGCTGG GTTTTGCAAG
  Y
  GCCAAGAGCA GGTTCTAAAC TAAGTTCAGG CTTAATTGGG TTCAAATTCA AACCCTACAC
  TTGCTTGATG CTTGGCCTTC AGTGAGCAGG ACAATGTCTT TGAGCTCATT TCCTTCTTTG
  AAAGTAGGAA TAGAAAGAGT ATCATCAAGA GTTCTTATGA GGATCTTACT TTTTTAGAGA
  CAGGATGTCA TTATGTTACC                                            
  
  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
ss354485194	MGP_WTSI_2_74555134	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
rs261313540					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
ss354485194	MGP_WTSI_2_74555134	SC_MOUSE_GENOMES	SC_MOUSE_GENOMES	f	SNP	C/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr2:74547421 () rs orientation: forward

Symbol	Name	Function Class
Cpgi11802	CpG island 11802	1844 bp distal
Cpgi11803	CpG island 11803	858 bp distal
Hoxd3	homeobox D3	within coordinates
Hoxd3os1	homeobox D3, opposite strand 1	947 bp upstream
Igs15	intergenic site 15	within coordinates
Rr44608	regulatory region 44608	1221 bp distal
Rr44609	regulatory region 44609	621 bp distal
Rr57045	regulatory region 57045	within coordinates
Rr57046	regulatory region 57046	579 bp proximal
Tssr533	transcription start site region 533	1101 bp upstream
Tssr534	transcription start site region 534	1070 bp upstream
Tssr18437	transcription start site region 18437	82 bp downstream
Tssr24625	transcription start site region 24625	1077 bp upstream
Tssr24626	transcription start site region 24626	1050 bp upstream
Tssr24627	transcription start site region 24627	942 bp upstream
Tssr24628	transcription start site region 24628	920 bp upstream