rs49596565 SNP Detail

Summary

• ID
  rs49596565
• Variation Type
  SNP
• Alleles
  C/T

• Created in dbSNP Build
  127
• Last Updated in dbSNP Build
  137
• Additional Resources
  JBrowse Genome Browser | Ensembl SNPView | UCSC Browser | Alliance Variant
  

Genome Location and Flanking Sequence

• Location
  Chr9:72893474 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              CCGAAGCCTG TTCTCCGCCC
  GTTCTTCACG CTTCCCCTCC GGGTCCTTAC CAGCGTTTGT TAGGCTGACG GCTTGTCCTA
  AGTAGCAGCT GCGCGTGTGT CGTTTGTGTT TACCTCTCAT TTATCCCAAC TCTGCCAGGG
  GCAGCGCCCG AGTTCTAGAC CGCAACCAGC TGGGGTGTTT TCCTTAAGGG TGAACCATCA
  Y
  GCACTGCCCT CTCCCACTTT TGCTTTATTG GCTGTATGGG GCTGCTTGTC CCTAGAAAGG
  GCAACCAGTT GGTTATTCTC AGTTAGGGGT GCTATGAGAC CTTTCCAGCA AGGTCACATA
  ATGTTTGAAA TGTCAGCACT AACTATCTTA AAGACCCAAT ATTTTTTCTT TCGCCTTTTT
  TTTTTTTTTT TGGAGTGGGT                                            
  
  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	MOLF/EiJ	NOD/ShiLtJ	NZW/LacJ	PWD/PhJ	WSB/EiJ
ss61420824	NES16804899	PERLEGEN	MM_PANEL2	f	SNP	T	T	T	T	T	T	T	T	T	T	T	T	T	C	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	MOLF/EiJ	NOD/ShiLtJ	NZW/LacJ	PWD/PhJ	WSB/EiJ
rs49596565					SNP	T	T	T	T	T	T	T	T	T	T	T	T	T	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
ss61420824	NES16804899	PERLEGEN	MM_PANEL	f	SNP	C/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr9:72893474 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Ccpg1	cell cycle progression 1			Intron
				Noncoding-Transcript-Variant
Cpgi22024	CpG island 22024			15 bp distal
Gm44503	predicted readthrough transcript (NMD candidate), 44503			Intron
Pierce2	piercer of microtubule wall 2			816 bp upstream
Rr401512	regulatory region 401512			570 bp downstream
Rr682884	regulatory region 682884			834 bp distal
Rr682885	regulatory region 682885			577 bp distal
Rr682886	regulatory region 682886			within coordinates
Rr682887	regulatory region 682887			391 bp distal
Tssr2935	transcription start site region 2935			877 bp upstream
Tssr86066	transcription start site region 86066			786 bp downstream
Tssr86067	transcription start site region 86067			768 bp downstream
Tssr86068	transcription start site region 86068			625 bp downstream
Tssr86069	transcription start site region 86069			550 bp downstream
Tssr90501	transcription start site region 90501			895 bp upstream
Tssr90502	transcription start site region 90502			850 bp upstream
Tssr90503	transcription start site region 90503			795 bp upstream