rs13478490 SNP Detail

Summary

• ID
  rs13478490
• Variation Type
  SNP
• Alleles
  C/T

• Created in dbSNP Build
  121
• Last Updated in dbSNP Build
  142
• Additional Resources
  JBrowse Genome Browser | Ensembl SNPView | UCSC Browser
  

Genome Location and Flanking Sequence

• Location
  Chr5:120568793 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                        TCAGT AAATACGCCC AAACAAACAC
  Y
  CACAGCCAAG TCTTGGCACA ATTCC                                      
  
  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	129S1/SvImJ	129X1/SvJ	A/J	AKR/J	BALB/cByJ	BTBR T<+> Itpr3/J	BUB/BnJ	C3H/HeJ	C57BL/6J	C57BL/10J	C57BLKS/J	C57BR/cdJ	C58/J	CAST/EiJ	CBA/J	CE/J	CZECHII/EiJ	DBA/1J	DBA/2J	DDK/Pas	FVB/NJ	I/LnJ	JF1/Ms	KK/HlJ	LG/J	LP/J	MA/MyJ	MAI/Pas	MOLF/EiJ	MSM/Ms	NOD/ShiLtJ	NON/ShiLtJ	NZB/BlNJ	NZW/LacJ	PERA/EiJ	PL/J	PWD/Ph	RIIIS/J	SEA/GnJ	SEG/Pas	SJL/J	SM/J	SPRET/EiJ	ST/bJ	SWR/J	WSB/EiJ	ZALENDE/EiJ
ss16376341	05.117.753	TWGNF	TWGNF-Mouse-2	f	SNP	T	T	T	T	T	C	T	T	C	C	T	C	C	T	T	C	T	C	C	T	T	T	T	T	C	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	C	T	T	T	T	T	T
ss45841875	mCV25013752	ABI	CRAMUS_MOUSE	f	SNP		T	T						C										C
ss149179476	ENSMUSSNP6384682	ENSEMBL	ENSEMBL_Sanger	f	SNP		T																	C
ss321667503	CHEV_5_120880737	CHEVERUD	SCREENING_POP	f	SNP																									C																	T
SNP Consensus Information
SNP					Consensus Type	129S1/SvImJ	129X1/SvJ	A/J	AKR/J	BALB/cByJ	BTBR T<+> Itpr3/J	BUB/BnJ	C3H/HeJ	C57BL/6J	C57BL/10J	C57BLKS/J	C57BR/cdJ	C58/J	CAST/EiJ	CBA/J	CE/J	CZECHII/EiJ	DBA/1J	DBA/2J	DDK/Pas	FVB/NJ	I/LnJ	JF1/Ms	KK/HlJ	LG/J	LP/J	MA/MyJ	MAI/Pas	MOLF/EiJ	MSM/Ms	NOD/ShiLtJ	NON/ShiLtJ	NZB/BlNJ	NZW/LacJ	PERA/EiJ	PL/J	PWD/Ph	RIIIS/J	SEA/GnJ	SEG/Pas	SJL/J	SM/J	SPRET/EiJ	ST/bJ	SWR/J	WSB/EiJ	ZALENDE/EiJ
rs13478490					SNP	T	T	T	T	T	C	T	T	C	C	T	C	C	T	T	C	T	C	C	T	T	T	T	T	C	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	C	T	T	T	T	T	T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr5:120568793 () rs orientation: forward

Symbol	Name	Function Class
Cpgi16490	CpG island 16490	131 bp proximal
Lhx5	LIM homeobox protein 5	971 bp upstream
Lhx5as1	LIM homeobox 5, antisense 1	within coordinates
Rr619309	regulatory region 619309	1363 bp distal
Rr619310	regulatory region 619310	388 bp distal
Rr619311	regulatory region 619311	within coordinates
Rr619312	regulatory region 619312	858 bp proximal
Rr619313	regulatory region 619313	1015 bp proximal
Tssr48502	transcription start site region 48502	1163 bp upstream
Tssr48503	transcription start site region 48503	1181 bp upstream
Tssr48504	transcription start site region 48504	1202 bp upstream
Tssr48505	transcription start site region 48505	1221 bp upstream
Tssr48506	transcription start site region 48506	1241 bp upstream
Tssr52923	transcription start site region 52923	1029 bp downstream