rs49171898 SNP Detail

Summary

• ID
  rs49171898
• Variation Type
  SNP
• Alleles
  G/T

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

Genome Location and Flanking Sequence

• Location
  Chr6:52148965 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              TCCTAAAGAT GGTTCTATCT
  AGAGGTCAGA ATTCCCAACA CTGGAACAAG GAGGGATTCC AACTTCACCA GGCTCAAACC
  GCCTTAGAGA GGCCCAGAGG GACTTCAGTC AGATTTATGT CTGAGGGATC CTCTCACAGT
  AACCGTATCA CCTTCCTAAG TAGCAAAGAT TCTGGAAAGA TTTGTTTTCC CTGGTGTGTG
  K
  GGGGGGGGGG GGCGGGGAGG GCACATTTCT GGAGATGTTT CTCTCCTCCT AGGCTGGCTG
  TAATAGCTAG AAGTGGCTTG GAGCGTGGAG CTGGTACAAG GCCAGAGGCC CCACCTCCTA
  AAGGCATTCA TTTACCTGAG CTGGAGCCGC TGGTTTTCTG CTTAGTGTTC TGCCTTGACT
  CTTTCATCCA GGGAAAGATT                                            
  
  K = G/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	A/J	B10.RIII-H2 H2-T18/(71NS)SnJ	BALB/cByJ	BALB/cJ	BUB/BnJ	C3H/HeJ	C57BL/6J	C57BL/6NJ	C57BL/10SnJ	C58/J	CAST/EiJ	CBA/J	CE/J	CZECHII/EiJ	DBA/1J	DBA/2J	FVB/NJ	JF1/MsJ	MA/MyJ	MOLF/EiJ	NOD/ShiLtJ	NZB/BlNJ	NZO/HlLtJ	NZW/LacJ	PWK/PhJ	QSi3/Ianm	RIIIS/J	SEA/GnJ	SJL/J	SM/J	SPRET/EiJ	ST/bJ	SWR/J	WSB/EiJ	ZALENDE/EiJ
ss368308270	MGP_WTSI_6_52121984	EVA_MGPV3	EVA_MGPV3	f	SNP	T	T	T	T	T	T	T	T	T	T	T	T	G	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T
SNP Consensus Information
SNP					Consensus Type	A/J	B10.RIII-H2 H2-T18/(71NS)SnJ	BALB/cByJ	BALB/cJ	BUB/BnJ	C3H/HeJ	C57BL/6J	C57BL/6NJ	C57BL/10SnJ	C58/J	CAST/EiJ	CBA/J	CE/J	CZECHII/EiJ	DBA/1J	DBA/2J	FVB/NJ	JF1/MsJ	MA/MyJ	MOLF/EiJ	NOD/ShiLtJ	NZB/BlNJ	NZO/HlLtJ	NZW/LacJ	PWK/PhJ	QSi3/Ianm	RIIIS/J	SEA/GnJ	SJL/J	SM/J	SPRET/EiJ	ST/bJ	SWR/J	WSB/EiJ	ZALENDE/EiJ
rs49171898					SNP	T	T	T	T	T	T	T	T	T	T	T	T	G	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	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
ss368308270	MGP_WTSI_6_52121984	SC_MOUSE_GENOMES	SC_MOUSE_GENOMES	f	SNP	G/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr6:52148965 () rs orientation: forward

Symbol	Name	Function Class
Cpgi17416	CpG island 17416	918 bp distal
Cpgi17417	CpG island 17417	375 bp proximal
Gm15050	predicted gene 15050	896 bp upstream
Gm28308	predicted gene 28308	within coordinates
Hoxa3	homeobox A3	within coordinates
Rr630350	regulatory region 630350	406 bp proximal
Rr630351	regulatory region 630351	907 bp proximal
Tssr56504	transcription start site region 56504	825 bp upstream
Tssr56505	transcription start site region 56505	890 bp upstream
Tssr56506	transcription start site region 56506	962 bp upstream