rs27045539 SNP Detail

Summary

• ID
  rs27045539
• Variation Type
  SNP
• Alleles
  C/T

• Created in dbSNP Build
  125
• Last Updated in dbSNP Build
  137
• Additional Resources
  JBrowse Genome Browser | Ensembl SNPView | UCSC Browser
  

Genome Location and Flanking Sequence

• Location
  Chr11:96193310 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              TTTTCTCTTT ACTGCCACCC
  ACACCCGAGC AGCAAGCTTC AGGCCCCGTT TTCTTTTCTT CCTTCTCCCT CTCCCCCCTC
  CTTTTTTTAT TTTTAAAGAA AATAGCCGTC TGGCAGAAGG GGCCCAGCTG CGGAGATCTC
  TGGCCGCCCA GCGAGCTCAG CAAGGGGCCG CCGGTCTTCC GAACACCTTC CCAGGGAAGG
  Y
  GGTAAGGCCA TGAGCAAATT CTCCAATTAT TGGCCACCAG CAACACAAGG CTTTGGATTT
  GGTCTCTGAA TGAGATAGCT GGCATCTGGC GAGCTTGTTA AAGGGGATCT GTTTAAACCC
  CAAACTCCCG CAGAAGAGTT ACCACCAAAC CTTAACCGCT CAGACGGTTG TCTCTCTAGT
  CTTTGGCCGA CCGACCATCT                                            
  
  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	A/J	AKR/J	BTBR T<+> Itpr3/J	C3H/HeJ	FVB/NJ	KK/HlJ	PWD/PhJ
ss37295458	NES08567233	PERLEGEN	MM_PANEL2	f	SNP	C	C	C	C	C	C	C	T
SNP Consensus Information
SNP					Consensus Type	129S1/SvImJ	A/J	AKR/J	BTBR T<+> Itpr3/J	C3H/HeJ	FVB/NJ	KK/HlJ	PWD/PhJ
rs27045539					SNP	C	C	C	C	C	C	C	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
ss37295458	NES08567233	PERLEGEN	MM_PANEL	f	SNP	C/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr11:96193310 () rs orientation: forward

Symbol	Name	Function Class
Cpgi3642	CpG island 3642	1350 bp distal
Cpgi3643	CpG island 3643	601 bp proximal
Hoxb5	homeobox B5	1028 bp upstream
Hoxb5os	homeobox B5 and homeobox B6, opposite strand	within coordinates
Hoxb6	homeobox B6	915 bp downstream
Rr238046	regulatory region 238046	491 bp proximal
Rr247589	regulatory region 247589	within coordinates
Tssr104489	transcription start site region 104489	1023 bp upstream
Tssr104490	transcription start site region 104490	1070 bp upstream
Tssr104491	transcription start site region 104491	1089 bp upstream
Tssr104492	transcription start site region 104492	1107 bp upstream
Tssr104493	transcription start site region 104493	1130 bp upstream
Tssr104494	transcription start site region 104494	1166 bp upstream
Tssr104495	transcription start site region 104495	1241 bp upstream
Tssr104496	transcription start site region 104496	1413 bp upstream
Tssr104497	transcription start site region 104497	1540 bp upstream
Tssr104498	transcription start site region 104498	1571 bp upstream
Tssr104499	transcription start site region 104499	1596 bp upstream
Tssr104500	transcription start site region 104500	1638 bp upstream