rs49721996 SNP Detail

Summary

• ID
  rs49721996
• Variation Type
  SNP
• Alleles
  C/T

• Created in dbSNP Build
  127
• Last Updated in dbSNP Build
  138
• Additional Resources
  JBrowse Genome Browser | Ensembl SNPView | UCSC Browser
  

Genome Location and Flanking Sequence

• Location
  Chr13:53627411 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                        AAAGA TGAGAAAGGC TGAGAGGTGG
  Y
  CAAGGGATAT TCAACTAATC TCTAC                                      
  
  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	129X1/SvJ	A/J	BALB/cByJ	DBA/2J	KK/HlJ	LG/J	NOD/ShiLtJ	PWD/PhJ	SM/J
ss61805329	NES17735856	PERLEGEN	MM_PANEL2	f	SNP			C	C	C		C	T
ss149017747	ENSMUSSNP1061528	ENSEMBL	ENSEMBL_Sanger	f	SNP	C	C
ss324342436	CHEV_13_53568744	CHEVERUD	SCREENING_POP	f	SNP						C			C
SNP Consensus Information
SNP					Consensus Type	129X1/SvJ	A/J	BALB/cByJ	DBA/2J	KK/HlJ	LG/J	NOD/ShiLtJ	PWD/PhJ	SM/J
rs49721996					SNP	C	C	C	C	C	C	C	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
ss61805329	NES17735856	PERLEGEN	MM_PANEL	f	SNP	C/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr13:53627411 () rs orientation: forward

Symbol	Name	Function Class
Cpgi5623	CpG island 5623	219 bp distal
Gm33763	predicted gene, 33763	within coordinates
Msx2	msh homeobox 2	595 bp upstream
Rr281405	regulatory region 281405	210 bp distal
Rr281406	regulatory region 281406	1789 bp proximal
Tssr122586	transcription start site region 122586	650 bp upstream
Tssr122587	transcription start site region 122587	588 bp upstream
Tssr122588	transcription start site region 122588	565 bp upstream
Tssr122589	transcription start site region 122589	525 bp upstream