rs52425252 SNP Detail

Summary

• ID
  rs52425252
• Variation Type
  SNP
• Alleles
  A/T

• Created in dbSNP Build
  128
• Last Updated in dbSNP Build
  137
• Additional Resources
  JBrowse Genome Browser | Ensembl SNPView | UCSC Browser | Alliance Variant
  

Genome Location and Flanking Sequence

• Location
  Chr1:152777980 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              ACCCCCAGGT GTGCCGACTT
  CCATCCTCCT CTCTCCTGCA TCGCCCCGGC CAGCACACCA CGTTTCCCGG GCCGTGGGCT
  CCAGACCCCT TCACACCCAC CTCGACTCTG GGTCGCTGCC GGCTCTCCTC TCCCCTACCC
  CGGCCCCGCA GCCTGCGACC AGAGGCGCGC GCGCGCGCGC GCACACGCAC ACACACACAC
  W
  CACACACACG TTCTCGTCTC CCGCTTCCCC AACCTCCCTC CGCTCCTCGC CCGGCTTCCC
  CCGGAGCGCG GCTCGCCCGG CTTCCCGGGG GCCAGGCAGC CATGTGTGTG CCCGCCCCCT
  CCCGCAGCCG CCCGCTCGGC CCCGCGCTCG GCCTCCCCGC CCTGGGGACA GAAGGACGCC
  GCGACTCCCC CACCGCTTCC                                            
  
  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	A/J	B10.RIII-H2 H2-T18/(71NS)SnJ	BALB/cByJ	BALB/cJ	BUB/BnJ	C3H/HeH	C3H/HeJ	C57BL/6J	C57BL/6NJ	C57BL/10J	C57BL/10SnJ	C57BR/cdJ	C57L/J	C58/J	CBA/J	CE/J	DBA/1J	DBA/2J	FVB/NJ	I/LnJ	LG/J	LP/J	MA/MyJ	NOD/ShiLtJ	PL/J	PWK/PhJ	QSi3/Ianm	QSi5/Ianm	RF/J	SEA/GnJ	SJL/J	SPRET/EiJ	SWR/J	WSB/EiJ
ss351959039	MGP_WTSI_1_154749359	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	A	T	T
SNP Consensus Information
SNP					Consensus Type	A/J	B10.RIII-H2 H2-T18/(71NS)SnJ	BALB/cByJ	BALB/cJ	BUB/BnJ	C3H/HeH	C3H/HeJ	C57BL/6J	C57BL/6NJ	C57BL/10J	C57BL/10SnJ	C57BR/cdJ	C57L/J	C58/J	CBA/J	CE/J	DBA/1J	DBA/2J	FVB/NJ	I/LnJ	LG/J	LP/J	MA/MyJ	NOD/ShiLtJ	PL/J	PWK/PhJ	QSi3/Ianm	QSi5/Ianm	RF/J	SEA/GnJ	SJL/J	SPRET/EiJ	SWR/J	WSB/EiJ
rs52425252					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	A	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
ss351959039	MGP_WTSI_1_154749359	SC_MOUSE_GENOMES	SC_MOUSE_GENOMES	f	SNP	A/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr1:152777980 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Cpgi860	CpG island 860			within coordinates
D1Mit502	DNA Segment, Chr 1 Massachusetts Institute of Technology 502			468 bp distal
Gm70930	predicted gene, 70930			1828 bp upstream
Rr396386	regulatory region 396386			98 bp upstream
Rr396387	regulatory region 396387			903 bp upstream
Rr420557	regulatory region 420557			within coordinates
Rr420558	regulatory region 420558			383 bp proximal
Rr420559	regulatory region 420559			1338 bp proximal
Rr420560	regulatory region 420560			1839 bp proximal
Smg7	SMG7 nonsense mediated mRNA decay factor			Intron
				mRNA-UTR
Tssr9437	transcription start site region 9437			615 bp upstream
Tssr9438	transcription start site region 9438			668 bp upstream
Tssr9439	transcription start site region 9439			1574 bp upstream
Tssr14242	transcription start site region 14242			399 bp downstream
Tssr14243	transcription start site region 14243			507 bp downstream
Tssr14244	transcription start site region 14244			528 bp downstream
Tssr14245	transcription start site region 14245			834 bp downstream
Tssr14246	transcription start site region 14246			859 bp downstream