rs220006559 SNP Detail

Summary

• ID
  rs220006559
• 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
  Chr13:48818075 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              TGCCGTTCAC TATAAAAGGA
  CTCTGTTGTT GGCAATTCGT TTGAAGCGGG CAAACAGCCG ATTTAGGGCT AAAGAACATG
  GAGAGGTCTT CATGCTTCTT GGGGGGAGGG GGTCTGAACA GAGGAAACAA GAAAGACAAT
  TTTCAGGTTC AAAGGATGCT TTGGTGACCC TTTCCTCGCC AATGTCCAAG CCTCAGCCAG
  Y
  GATGTAGGTA CAGCGCCCAG AAAAACAAAT GCTCACATTC CACAACGTTC TTTTCCCAAT
  GCAAAAGCTC CCCCACCCCC GCCCCCGCTT CCAAATTCAC CCGTTTCTTC TTAGTTTCTC
  TTTTTCACGA AAGGCATACT CTATGTCCTC GGAGCAGCGA ACTTGCTCTA AAGCATCCTG
  AAATCTCGGA GCCTACTGGC                                            
  
  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
ss388549828	MGP_WTSI_13_48759968	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	T	T	T	C	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
rs220006559					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	T	T	T	C	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
ss388549828	MGP_WTSI_13_48759968	SC_MOUSE_GENOMES	SC_MOUSE_GENOMES	f	SNP	C/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr13:48818075 () rs orientation: forward

Symbol	Name	Function Class
Barx1	BarH-like homeobox 1	within coordinates
Cpgi5567	CpG island 5567	608 bp distal
Cpgi5568	CpG island 5568	287 bp proximal
Cpgi5569	CpG island 5569	905 bp proximal
Gm36606	predicted gene, 36606	1807 bp upstream
Rr281361	regulatory region 281361	within coordinates
Tssr119664	transcription start site region 119664	1711 bp downstream
Tssr119665	transcription start site region 119665	1677 bp downstream
Tssr119666	transcription start site region 119666	1633 bp downstream
Tssr119667	transcription start site region 119667	1553 bp downstream
Tssr119668	transcription start site region 119668	1525 bp downstream
Tssr122399	transcription start site region 122399	1851 bp upstream