rs239978828 SNP Detail

Summary

• ID
  rs239978828
• Variation Type
  SNP
• Alleles
  C/T

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

Genome Location and Flanking Sequence

• Location
  Chr4:129940916 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              GAGCATTAGC CTAGAATATG
  CAAACTCTAG GCTCAATATC CAGTTAAAAA GAGAACAAAA CCAAGTTTGA GGGCCATGGA
  GATGGCTTAG CAGGTAAATG TGCTGGCCAC CAAGACTGAC CACCTTAGCG GGATTCCCCC
  AGAACCCCTA TTGTGAAAGG AGATAGCTAA CTCCATCAAT TGTTCTCTGG CGTCCACACA
  Y
  ACAACATGGC ATTTACAACT ATGCCTGTGT ACACGTTCCG CACATACACA TACAAAATAA
  ATTAATTTAA AAAAAAGTCT TCTTAAAGCA GGGAGCAGGG AGGGGGCAGG GGGTAGGGAT
  CTGAGTCTTT CCAACCTTCT GGAGTCCAAG AGGACTCCCT GACCCTACTT CTGTAGAAAT
  GGGGACAGAG CAGAAGGAGT                                            
  
  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	129P2/OlaHsd	129S1/SvImJ	129S5/SvEvBrd	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
ss363242565	MGP_WTSI_4_129724367	EVA_MGPV3	EVA_MGPV3	f	SNP	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	C	T	T	T	T	T	T	T	T	T	T	T	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	129P2/OlaHsd	129S1/SvImJ	129S5/SvEvBrd	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
rs239978828					SNP	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	T	C	T	T	T	T	T	T	T	T	T	T	T	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
ss363242565	MGP_WTSI_4_129724367	SC_MOUSE_GENOMES	SC_MOUSE_GENOMES	f	SNP	C/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr4:129940916 () rs orientation: forward

Symbol	Name	Function Class
Col16a1	collagen, type XVI, alpha 1	722 bp upstream
Cpgi14918	CpG island 14918	1126 bp distal
Cpgi14919	CpG island 14919	200 bp proximal
Gm12963	predicted gene 12963	within coordinates
Rr600419	regulatory region 600419	1008 bp distal
Rr600420	regulatory region 600420	1462 bp distal
Rr600421	regulatory region 600421	within coordinates
Rr600422	regulatory region 600422	626 bp proximal
Rr600423	regulatory region 600423	728 bp proximal
Tssr1308	transcription start site region 1308	423 bp upstream
Tssr39217	transcription start site region 39217	237 bp upstream
Tssr39218	transcription start site region 39218	733 bp upstream
Tssr39219	transcription start site region 39219	791 bp upstream