rs28080648 SNP Detail

Summary

• ID
  rs28080648
• Variation Type
  SNP
• Alleles
  A/T

• Created in dbSNP Build
  125
• Last Updated in dbSNP Build
  137
• Additional Resources
  JBrowse Genome Browser | Ensembl SNPView | UCSC Browser | Alliance Variant
  

Genome Location and Flanking Sequence

• Location
  Chr4:98433587 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              TCATAACAAG GTATGAATTA
  AATACTATGC ATGTAAGAGA TAGATAACGT TGTAAACAGG TCTCCATTAA AGGAGTGGAA
  ATCAAGTAGC ATGCTGCTCC AGAGAACGGA AAGAAAGTCA CTTGTCTTCT GTAAGGGTGT
  GTGTGTGTGT GTGTGTGTGT GTGTGCCGGG GGTGTGTGGT ATTTCAGTGT TGCAAATCGC
  W
  CCTGAGGCTT GTCAAATTCT GTGGCTGAGA ATCCTGAGAC CAAGAGTCAT TAATTTGCCC
  CATATCACAA AACAGGGTGC TGATGAAGCA AAGGTAGACC CAGGTGTCAC TTTTAAGCTC
  TGCACCCAGT GCTTACCTCC GTGAACAGAG GACAGAGGTC TTTTGTGCAG TCATATCCCC
  CATAGTGCCC TGTGCATTCA                                            
  
  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	129S1/SvImJ	A/J	AKR/J	BALB/cByJ	BTBR T<+> Itpr3/J	C3H/HeJ	CAST/EiJ	DBA/2J	FVB/NJ	KK/HlJ	MOLF/EiJ	NOD/ShiLtJ	NZW/LacJ	PWD/PhJ	WSB/EiJ
ss38243571	NES09530006	PERLEGEN	MM_PANEL2	f	SNP	A	A	A	A	A	A	T	A	A	A	A	A	A	A	A
SNP Consensus Information
SNP					Consensus Type	129S1/SvImJ	A/J	AKR/J	BALB/cByJ	BTBR T<+> Itpr3/J	C3H/HeJ	CAST/EiJ	DBA/2J	FVB/NJ	KK/HlJ	MOLF/EiJ	NOD/ShiLtJ	NZW/LacJ	PWD/PhJ	WSB/EiJ
rs28080648					SNP	A	A	A	A	A	A	T	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
ss38243571	NES09530006	PERLEGEN	MM_PANEL	f	SNP	A/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr4:98433587 () rs orientation: forward

Symbol	Name	Function Class
Patj	PATJ, crumbs cell polarity complex component	Intron
Rr595752	regulatory region 595752	102 bp proximal
Rr595753	regulatory region 595753	214 bp proximal
Rr595754	regulatory region 595754	1177 bp proximal
Rr595755	regulatory region 595755	1634 bp proximal
Tssr1238	transcription start site region 1238	1264 bp upstream
Tssr37887	transcription start site region 37887	1281 bp upstream
Tssr37888	transcription start site region 37888	1312 bp upstream
Tssr37889	transcription start site region 37889	1346 bp upstream
Tssr37890	transcription start site region 37890	1360 bp upstream
Tssr37891	transcription start site region 37891	1396 bp upstream
Tssr37892	transcription start site region 37892	1447 bp upstream
Tssr37893	transcription start site region 37893	1547 bp upstream
Tssr37894	transcription start site region 37894	1569 bp upstream