rs239085443 SNP Detail

Summary

• ID
  rs239085443
• Variation Type
  SNP
• Alleles
  A/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
  Chr6:52200237 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              ACCTAGAAAA AGAAGGTGCA
  AAGAGCAGAG CCGCACAACG TAAAAGAATC AATATATTTT ATTTGGCAAA AGTTAAATAT
  CTCGACACAA CAATTTGGTC AGTAGGCCTT GAGGTAACTA TTGCAAAATA TACAGTGTAT
  GTTCAATCCG ATGGGAACCC CAAATTCACC AAGGATACAA ATCTACAGTA GCCCAAGAGC
  R
  GTTTCATGGT GTATAATTTA TTATCAATAA AATTAACTCC ATTACAATAA GCACTCACTT
  TCTCCCAATT AAAATTAAGC GTAAACCCAT AGGTAGCAAC CCTCTGCACA CACGTATAGC
  TCCGAATTTC CTCACTTCTC CTCTGGTGCA AAAACAATAT TCAAGCTTTC TGATTATGAA
  TATTTCTTTA ATATGGAGAT                                            
  
  R = A/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	129P2/OlaHsd	129S1/SvImJ	A/J	AKR/J	B10.RIII-H2 H2-T18/(71NS)SnJ	BALB/cByJ	BALB/cJ	BTBR T<+> Itpr3/J	BUB/BnJ	C3H/HeH	C3H/HeJ	C57BL/6J	C57BL/6NJ	C57BL/10J	C57BL/10SnJ	C57BR/cdJ	C57L/J	C58/J	CAST/EiJ	CBA/J	CE/J	CZECHII/EiJ	DBA/1J	DBA/2J	FVB/NJ	I/LnJ	JF1/MsJ	KK/HlJ	LEWES/EiJ	LG/J	LP/J	MA/MyJ	MOLF/EiJ	NOD/ShiLtJ	NON/ShiLtJ	NZB/BlNJ	NZO/HlLtJ	NZW/LacJ	PL/J	PWK/PhJ	QSi3/Ianm	QSi5/Ianm	RF/J	RIIIS/J	SEA/GnJ	SJL/J	SM/J	SPRET/EiJ	ST/bJ	SWR/J	WSB/EiJ	ZALENDE/EiJ
ss368308908	MGP_WTSI_6_52173256	EVA_MGPV3	EVA_MGPV3	f	SNP	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	G	A	A	A	A
SNP Consensus Information
SNP					Consensus Type	129P2/OlaHsd	129S1/SvImJ	A/J	AKR/J	B10.RIII-H2 H2-T18/(71NS)SnJ	BALB/cByJ	BALB/cJ	BTBR T<+> Itpr3/J	BUB/BnJ	C3H/HeH	C3H/HeJ	C57BL/6J	C57BL/6NJ	C57BL/10J	C57BL/10SnJ	C57BR/cdJ	C57L/J	C58/J	CAST/EiJ	CBA/J	CE/J	CZECHII/EiJ	DBA/1J	DBA/2J	FVB/NJ	I/LnJ	JF1/MsJ	KK/HlJ	LEWES/EiJ	LG/J	LP/J	MA/MyJ	MOLF/EiJ	NOD/ShiLtJ	NON/ShiLtJ	NZB/BlNJ	NZO/HlLtJ	NZW/LacJ	PL/J	PWK/PhJ	QSi3/Ianm	QSi5/Ianm	RF/J	RIIIS/J	SEA/GnJ	SJL/J	SM/J	SPRET/EiJ	ST/bJ	SWR/J	WSB/EiJ	ZALENDE/EiJ
rs239085443					SNP	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	G	A	A	A	A

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
ss368308908	MGP_WTSI_6_52173256	SC_MOUSE_GENOMES	SC_MOUSE_GENOMES	f	SNP	A/G

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr6:52200237 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Cpgi17429	CpG island 17429			1140 bp distal
Cpgi17430	CpG island 17430			1068 bp proximal
Cpgi17431	CpG island 17431			1873 bp proximal
Gm57855	predicted gene, 57855			mRNA-UTR
				Noncoding-Transcript-Variant
Hoxa7	homeobox A7			1480 bp upstream
Hoxa9	homeobox A9			mRNA-UTR
				Noncoding-Transcript-Variant
Rr630375	regulatory region 630375			1432 bp distal
Rr630376	regulatory region 630376			1068 bp distal
Tssr61005	transcription start site region 61005			1666 bp upstream
Tssr61006	transcription start site region 61006			1336 bp downstream
Tssr61007	transcription start site region 61007			1959 bp downstream
Tssr61008	transcription start site region 61008			1980 bp downstream