rs6239080 SNP Detail

Summary

• ID
  rs6239080
• Variation Type
  SNP
• Alleles
  A/C

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

Genome Location and Flanking Sequence

• Location
  Chr6:96093724 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              AGCTTTTTCA TTGCAAAGTC
  GCTCCAGGGT TTCGATTGTT TTTAAGCTTC CTGGTTGGTT CTCAGAAAGG TTTCTTTCTG
  TTTTCTGCGT AGCTGTGTTT AGCCTTTGTG TCCTGTCCTT TCGCCGCACC CCCTACCTCA
  AAGTCCTTGG TGGTACCCTC TGATGGTGAA GTCCAACGTT CCGGGGGACC AGTTGCACGC
  M
  CAAGTTCCCG CTCTTCGGTT CGTGGGTGCT GCCGCCCCTC CCTCCAGGCC CCTCTCCACA
  TCCTTCCCTG GCCTCCTGCC ATCCACAGGG CTTCTCCGTG TGGCAGGTCC GCGGTCTGCA
  TGCTGTCTTT TGTGGCTCCG CAACCTTGAC TGTGATTCCC CTGCTCTTGT TTTGGCCTTC
  TCCAGCCCCT CTCCCGGTGT                                            
  
  M = A/C
  

  
  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	C57BL/6J	CAST/EiJ	CZECHII/EiJ	DBA/2J	FVB/NJ	KK/HlJ	MOLF/EiJ	NOD/ShiLtJ	NZW/LacJ	PWD/PhJ	WSB/EiJ
ss8644823	WI_WGS_6_96933528	WI	MOUSE	f	SNP							A		C
ss48024665	NES11911969	PERLEGEN	MM_PANEL2	f	SNP	A	A	A	A	A	A		C		A	A	A	C	A	A	C	C
SNP Consensus Information
SNP					Consensus Type	129S1/SvImJ	A/J	AKR/J	BALB/cByJ	BTBR T<+> Itpr3/J	C3H/HeJ	C57BL/6J	CAST/EiJ	CZECHII/EiJ	DBA/2J	FVB/NJ	KK/HlJ	MOLF/EiJ	NOD/ShiLtJ	NZW/LacJ	PWD/PhJ	WSB/EiJ
rs6239080					SNP	A	A	A	A	A	A	A	C	C	A	A	A	C	A	A	C	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
ss48024665	NES11911969	PERLEGEN	MM_PANEL	f	SNP	A/C

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr6:96093724 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
2900060L22Rik	RIKEN cDNA 2900060L22 gene			Noncoding-Transcript-Variant
Cpgi17767	CpG island 17767			within coordinates
Rr635053	regulatory region 635053			within coordinates
Rr635054	regulatory region 635054			352 bp distal
Rr635055	regulatory region 635055			30 bp distal
Rr635056	regulatory region 635056			212 bp proximal
Rr635057	regulatory region 635057			376 bp proximal
Tafa1	TAFA chemokine like family member 1			Intron
				Noncoding-Transcript-Variant
Tssr57828	transcription start site region 57828			1472 bp downstream
Tssr62190	transcription start site region 62190			825 bp upstream
Tssr62191	transcription start site region 62191			228 bp downstream