rs39403601 SNP Detail

Summary

• ID
  rs39403601
• Variation Type
  SNP
• Alleles
  C/T

• Created in dbSNP Build
  126
• Last Updated in dbSNP Build
  137
• Additional Resources
  JBrowse Genome Browser | Ensembl SNPView | UCSC Browser | Alliance Variant
  

Genome Location and Flanking Sequence

• Location
  Chr3:97140389 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              CCACCCACCC GGCAGTGGGA
  GTCCCTGCTG CCTGGGTGTA ACTGGACTTT GTCTGGACTG CACTAGAATC ATCTTAAGCT
  GGAAAATGGA CCCGCAGCAG AACTCAGAAA ATGAAACATA AGCTTCTTCG CTTCTTGCCT
  CCTGATCCTT GCTGTCTGTG TCATTTCCCA TAGCAACTGT CCCAAGTGTG ATCCCTACTG
  Y
  TCTACATTGT GAGGTCTGTC TTTCTTGCTT CATCCCACCT TGGGAGAACC AGGCAAAGCT
  GTTTCTGCCT TCTGTTTGGC TTTTATCCCT TTCTTTAGTA AAATCTTAAA GTGATAGCCT
  CTTCCCCTTT CTTTTCATCC AAATCCATCC AAAAACCAAC CCACACGGTA GTTTCTTTGT
  TTGTAAATAC TCCAGCCAGG                                            
  
  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	BALB/cByJ	BTBR T<+> Itpr3/J	C3H/HeJ	CAST/EiJ	DBA/2J	FVB/NJ	KK/HlJ	NOD/ShiLtJ	NZW/LacJ	WSB/EiJ
ss51578534	NES14672291	PERLEGEN	MM_PANEL2	f	SNP	T	T	T	T	T	T	C	T	T	C	T	T	T
SNP Consensus Information
SNP					Consensus Type	129S1/SvImJ	A/J	AKR/J	BALB/cByJ	BTBR T<+> Itpr3/J	C3H/HeJ	CAST/EiJ	DBA/2J	FVB/NJ	KK/HlJ	NOD/ShiLtJ	NZW/LacJ	WSB/EiJ
rs39403601					SNP	T	T	T	T	T	T	C	T	T	C	T	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
ss51578534	NES14672291	PERLEGEN	MM_PANEL	f	SNP	C/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr3:97140389 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Bcl9	B cell CLL/lymphoma 9			Intron
				mRNA-UTR
				Noncoding-Transcript-Variant
Rr581471	regulatory region 581471			1871 bp distal
Rr581472	regulatory region 581472			385 bp distal
Rr581473	regulatory region 581473			1750 bp proximal