rs260872942 SNP Detail

Summary

• ID
  rs260872942
• Variation Type
  SNP
• Alleles
  C/G

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

Genome Location and Flanking Sequence

• Location
  Chr6:52204450 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              CAGTCAACAT CAAGAGGTGT
  TTGTCTTGCT GAGGGGTCAC CTCGCCTAGT TTCTGGGCCC TGTATGAACC GCTCTGGTAT
  CCTTCCCTCT TCTGTTTTTT CCTCCTATTC CTCTATCACC CCACTTTTTT TCCCCTTCCT
  TCCCATTCCC CTTTTCCTTC TTTTGTTACT CCCCTCCCTC CCTTCCTCTC TTTCCCCCCC
  S
  CCCCCATCTC CAGCGCCCCT GCCTTGGTTA TCCTTGAAAC AGAACAACAG AGATCCCATA
  GTCAAACTAC AGCTCAAGTC CAGTGCTACA AATTAACCCG GGAGGAACAC TGGACATTGA
  CTTTAATCTC ATCCTTTGGT CAAATGGAGG ATGTTATTTT TCACCCCTTA GAATCTTTGG
  GAATAAGAGA AAAAAAGTGA                                            
  
  S = C/G
  

  
  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	A/J	BALB/cByJ	BALB/cJ	BTBR T<+> Itpr3/J	BUB/BnJ	C3H/HeJ	C57BL/6J	C57BL/6NJ	C57BL/10J	C58/J	CAST/EiJ	CBA/J	CE/J	CZECHII/EiJ	DBA/1J	DBA/2J	FVB/NJ	I/LnJ	JF1/MsJ	KK/HlJ	LG/J	MOLF/EiJ	PWK/PhJ	SEA/GnJ	SM/J	SPRET/EiJ	ST/bJ
ss368308952	MGP_WTSI_6_52177469	EVA_MGPV3	EVA_MGPV3	f	SNP	G	G	G	C	G	G	G	G	G	G	C	G	C	C	G	G	G	C	C	C	G	C	C	G	G	C	G
SNP Consensus Information
SNP					Consensus Type	A/J	BALB/cByJ	BALB/cJ	BTBR T<+> Itpr3/J	BUB/BnJ	C3H/HeJ	C57BL/6J	C57BL/6NJ	C57BL/10J	C58/J	CAST/EiJ	CBA/J	CE/J	CZECHII/EiJ	DBA/1J	DBA/2J	FVB/NJ	I/LnJ	JF1/MsJ	KK/HlJ	LG/J	MOLF/EiJ	PWK/PhJ	SEA/GnJ	SM/J	SPRET/EiJ	ST/bJ
rs260872942					SNP	G	G	G	C	G	G	G	G	G	G	C	G	C	C	G	G	G	C	C	C	G	C	C	G	G	C	G

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
ss368308952	MGP_WTSI_6_52177469	SC_MOUSE_GENOMES	SC_MOUSE_GENOMES	f	SNP	C/G

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr6:52204450 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Cpgi17431	CpG island 17431			1091 bp distal
Cpgi17432	CpG island 17432			1514 bp proximal
Gm57855	predicted gene, 57855			Intron
				Noncoding-Transcript-Variant
Gm68361	predicted gene, 68361			within coordinates
Hoxa9	homeobox A9			Intron
				Noncoding-Transcript-Variant
Rr630377	regulatory region 630377			791 bp distal
Rr630378	regulatory region 630378			269 bp distal
Rr630379	regulatory region 630379			111 bp distal
Rr630380	regulatory region 630380			within coordinates
Rr630381	regulatory region 630381			1949 bp proximal
Tssr61009	transcription start site region 61009			1606 bp upstream
Tssr61010	transcription start site region 61010			1514 bp upstream
Tssr61011	transcription start site region 61011			1308 bp upstream
Tssr61012	transcription start site region 61012			1274 bp upstream