rs27440509 SNP Detail

Summary

• ID
  rs27440509
• Variation Type
  SNP
• Alleles
  C/T

• Created in dbSNP Build
  125
• Last Updated in dbSNP Build
  138
• Additional Resources
  JBrowse Genome Browser | Ensembl SNPView | UCSC Browser | Alliance Variant
  

Genome Location and Flanking Sequence

• Location
  Chr2:119449292 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                        CGAGA TTGCAGAACG CGATGACCGT
  Y
  CCCTCTGCAG AGGAGCTGGA CTCCT                                      
  
  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	C3H/HeJ	CAST/EiJ	DBA/2J	FVB/NJ	KK/HlJ	LG/J	MOLF/EiJ	NOD/ShiLtJ	NZW/LacJ	PWD/PhJ	SM/J	WSB/EiJ
ss37649940	NES09029749	PERLEGEN	MM_PANEL2	f	SNP	T		T	T	T	T	T	T	T	T	T		C	T	T	C		T
ss147337151	ENSMUSSNP541731	ENSEMBL	ENSEMBL_Sanger	f	SNP		T	T						T
ss320476342	CHEV_2_119444547	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	C3H/HeJ	CAST/EiJ	DBA/2J	FVB/NJ	KK/HlJ	LG/J	MOLF/EiJ	NOD/ShiLtJ	NZW/LacJ	PWD/PhJ	SM/J	WSB/EiJ
rs27440509					SNP	T	T	T	T	T	T	T	T	T	T	T	C	C	T	T	C	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
ss37649940	NES09029749	PERLEGEN	MM_PANEL	f	SNP	C/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr2:119449292 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Cpgi12123	CpG island 12123			within coordinates
Nusap1	nucleolar and spindle associated protein 1			Coding-Synonymous
				mRNA-UTR
				Noncoding-Transcript-Variant
Oip5	Opa interacting protein 5			342 bp upstream
Rr397233	regulatory region 397233			55 bp downstream
Rr563550	regulatory region 563550			503 bp distal
Rr563551	regulatory region 563551			502 bp distal
Rr563552	regulatory region 563552			84 bp distal
Rr563553	regulatory region 563553			1151 bp proximal
Tssr19645	transcription start site region 19645			74 bp downstream
Tssr25824	transcription start site region 25824			301 bp upstream