rs258359942 SNP Detail

Summary

• ID
  rs258359942
• Variation Type
  SNP
• Alleles
  A/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
  Chr3:90521295 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              GCCATTGGCC TTCTCGTGGC
  CATCTTCCAC AAGTACTCTG GCAAGGAAGG TGACAAGCAC ACCCTGAGCA AGAAGGAGCT
  GAAGGAGTTG ATCCAGAAGG AGCTCACCAT TGGCTCCGTG AGTAGCCCCT GTCCCGGTTC
  CCCCTCCTGC CTCTCATCTG AGTGGCATTT AATCACAGTT CCTGATCTTA CTTCCTGTGG
  W
  GGGATGCTCG TATGCCTCCA TGCTGCCCTG TCCCCTGAGG GAGGAGCAGG GGCTGAGGAG
  AGTAAATCAA GGTAAACCCA AGCTGAAGGC CCATCTTTGG TCCCAACGAG CACTTGTTTG
  AGAGAGGACT TCCAGGGAAG GGGTAAGGAA TCTAGGGTGT TGGCCACCAC TGAGTGTGGA
  CTTCTCCTTC TTAATGTATT                                            
  
  W = A/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
ss358835924	MGP_WTSI_3_90417910	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	T	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
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
rs258359942					SNP	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	A	T	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

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
ss358835924	MGP_WTSI_3_90417910	SC_MOUSE_GENOMES	SC_MOUSE_GENOMES	f	SNP	A/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr3:90521295 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Cpgi13468	CpG island 13468			622 bp distal
Gm57853	predicted gene, 57853			Intron
				Noncoding-Transcript-Variant
Rr397814	regulatory region 397814			1433 bp upstream
Rr580416	regulatory region 580416			1605 bp distal
Rr580417	regulatory region 580417			673 bp distal
Rr580418	regulatory region 580418			1179 bp distal
Rr580419	regulatory region 580419			1594 bp proximal
S100a6	S100 calcium binding protein A6 (calcyclin)			Intron
				Noncoding-Transcript-Variant
Tssr30242	transcription start site region 30242			1692 bp downstream
Tssr30243	transcription start site region 30243			1123 bp downstream
Tssr30244	transcription start site region 30244			1107 bp downstream
Tssr30245	transcription start site region 30245			1009 bp downstream
Tssr30246	transcription start site region 30246			831 bp downstream
Tssr30247	transcription start site region 30247			796 bp downstream
Tssr30248	transcription start site region 30248			696 bp downstream
Tssr30249	transcription start site region 30249			452 bp downstream
Tssr30250	transcription start site region 30250			219 bp downstream
Tssr30251	transcription start site region 30251			135 bp downstream
Tssr30252	transcription start site region 30252			358 bp upstream
Tssr30253	transcription start site region 30253			382 bp upstream
Tssr34246	transcription start site region 34246			423 bp downstream