rs27492090 SNP Detail

Summary

• ID
  rs27492090
• Variation Type
  SNP
• Alleles
  C/T

• Created in dbSNP Build
  125
• Last Updated in dbSNP Build
  142
• Additional Resources
  JBrowse Genome Browser | Ensembl SNPView | UCSC Browser | Alliance Variant
  

Genome Location and Flanking Sequence

• Location
  Chr4:129943784 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                        AGCTC AGTACATGCA TCTGTATGTA
  Y
  TCCTGGATCT CTGGGCAGTG GGGAG                                      
  
  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	C57BL/6J	DBA/2J	FVB/NJ	KK/HlJ	LG/J	MOLF/EiJ	NOD/ShiLtJ	NZW/LacJ	PWD/PhJ	SM/J	WSB/EiJ
ss37717612	NES09175365	PERLEGEN	MM_PANEL2	f	SNP	C		C	C	C	C	C		C	C	T		T	C	C	T		C
ss45724139	mCV22593127	ABI	CRAMUS_MOUSE	f	SNP		C	C					T	C
ss147458274	ENSMUSSNP3594439	ENSEMBL	ENSEMBL_Sanger	f	SNP		C	C						C
ss321316737	CHEV_4_129727235	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	C57BL/6J	DBA/2J	FVB/NJ	KK/HlJ	LG/J	MOLF/EiJ	NOD/ShiLtJ	NZW/LacJ	PWD/PhJ	SM/J	WSB/EiJ
rs27492090					SNP	C	C	C	C	C	C	C	T	C	C	T	C	T	C	C	T	T	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
ss37717612	NES09175365	PERLEGEN	MM_PANEL	f	SNP	C/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr4:129943784 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Col16a1	collagen, type XVI, alpha 1			Intron
				Noncoding-Transcript-Variant
Cpgi14919	CpG island 14919			1889 bp distal
Gm12963	predicted gene 12963			1569 bp upstream
Rr600423	regulatory region 600423			1407 bp distal
Rr600424	regulatory region 600424			102 bp proximal
Tssr39220	transcription start site region 39220			719 bp upstream
Tssr39221	transcription start site region 39221			750 bp upstream