rs6399459 SNP Detail

Summary

• ID
  rs6399459
• Variation Type
  SNP
• Alleles
  C/T

• Created in dbSNP Build
  116
• Last Updated in dbSNP Build
  137
• Additional Resources
  JBrowse Genome Browser | Ensembl SNPView | UCSC Browser
  

Genome Location and Flanking Sequence

• Location
  Chr3:123062674 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                        CACATATGAA AGGCTTTTTT TTTAGCTCCT TAAATATAGG
  TGCCTATGTT CTTAGAGGTG TGACGTCATC TAAGTTAGAG AGAAGCCCTA GCATCTTGGA
  Y
  GGAGATGGTT GGAGCTGCCA CTGGCTTGTC CCATTATGAC TCACAAAGAC TATCATCATG
  TCTATCTCAG GTTATATTTG TTGGACTATG GCTTTTCCT                       
  
  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	C57BL/6J	CZECHII/EiJ	DBA/2J	LG/J	SM/J
ss8805650	WI_WGS_3_123666123	WI	MOUSE	f	SNP				C	T
ss45491449	mCV25366955	ABI	CRAMUS_MOUSE	f	SNP	C		T			T
ss135761749	ENSMUSSNP2664405	ENSEMBL	ENSEMBL_Sanger	f	SNP		C	T			T
ss320918515	CHEV_3_122971943	CHEVERUD	SCREENING_POP	f	SNP							C	T
SNP Consensus Information
SNP					Consensus Type	129S1/SvImJ	129X1/SvJ	A/J	C57BL/6J	CZECHII/EiJ	DBA/2J	LG/J	SM/J
rs6399459					SNP	C	C	T	C	T	T	C	T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr3:123062674 () rs orientation: forward

Symbol	Name	Function Class
Cpgi13776	CpG island 13776	813 bp distal
Gm56815	predicted gene, 56815	1671 bp downstream
Gm66521	predicted gene, 66521	1608 bp upstream
Rr77168	regulatory region 77168	73 bp distal
Sec24d	SEC24 homolog D, COPII coat complex component	within coordinates
Tssr31542	transcription start site region 31542	1823 bp downstream
Tssr31543	transcription start site region 31543	1804 bp downstream
Tssr31544	transcription start site region 31544	1525 bp downstream
Tssr31545	transcription start site region 31545	667 bp upstream