rs258616042 SNP Detail

Summary

• ID
  rs258616042
• Variation Type
  SNP
• Alleles
  G/T

• 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
  Chr3:122039535 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              GTTTCAGCGG CGGCGGCGGT
  GGCGGCCGCA GAAGCCGCAG CGACCGTCCG CGCCGGCGCC TCCCTCCCTT CCTTCCCTCC
  CTCCGGGACC GCCTCTCCGT CGCCGCCCGG CCTCCTCGGG CCCGAGCGCA CACCGGGCTG
  TGGCCGCGCG GAGTCGGCAG CCTCGCGCTC TCCTCTGGGG CCTGGGGCAC CGCCGCGCCC
  K
  GCGAGGCAGC CGTCTGCCCA CTCGCCCGCC CGCCTGCCCG CCCGCTCGCC ATCTCTCCGC
  GGCTCCGGCG CTACCCGGTC CCCTCCGGCG GCAGCTGCCA TGGGCACCGA CAGCCGCGCG
  GCCGGGGCGC TCCTGGCGCG GGCCAGCACC CTGCACCTGC AGACCGGGAA CCTGCTCAAC
  TGGGGCCGCC TGCGAAAAAA                                            
  
  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	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/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	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
ss359496031	MGP_WTSI_3_121948804	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	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	G	T	T	T	T
SNP Consensus Information
SNP					Consensus Type	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/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	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
rs258616042					SNP	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	T	T	T	T	T	T	T	T	T	T	T	T	G	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
ss359496031	MGP_WTSI_3_121948804	SC_MOUSE_GENOMES	SC_MOUSE_GENOMES	f	SNP	G/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr3:122039535 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Cpgi13765	CpG island 13765			within coordinates
Gclm	glutamate-cysteine ligase, modifier subunit			mRNA-UTR
				Noncoding-Transcript-Variant
Gm46822	predicted gene, 46822			380 bp upstream
Rr375675	regulatory region 375675			1409 bp downstream
Rr397979	regulatory region 397979			386 bp downstream
Rr584264	regulatory region 584264			1617 bp distal
Rr584265	regulatory region 584265			547 bp distal
Rr584266	regulatory region 584266			319 bp distal
Rr584267	regulatory region 584267			392 bp distal
Rr584268	regulatory region 584268			336 bp proximal
Rr584269	regulatory region 584269			1837 bp proximal
Tssr1039	transcription start site region 1039			142 bp downstream
Tssr31478	transcription start site region 31478			336 bp downstream
Tssr31479	transcription start site region 31479			308 bp downstream
Tssr31480	transcription start site region 31480			278 bp downstream
Tssr31481	transcription start site region 31481			264 bp downstream
Tssr31482	transcription start site region 31482			164 bp downstream
Tssr31483	transcription start site region 31483			57 bp downstream
Tssr31484	transcription start site region 31484			24 bp upstream
Tssr35443	transcription start site region 35443			657 bp upstream
Tssr35444	transcription start site region 35444			554 bp upstream