rs28080636 SNP Detail

Summary

• ID
  rs28080636
• Variation Type
  SNP
• Alleles
  C/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
  Chr4:98435325 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              TCGTGGGAAG AGAGGACAGA
  GTTGGAGAGA GTGGAGCTGC TTCCAGCATC TTCCTGTCAG GAATGCAGCA ACCCTGAAGA
  GAGCAGTCCT GCAGCATGGT CCACGGGGGC TTCCCAGGTA AGGCTTCCGC TGCTGACGAG
  AGCTGCAGGT CTTGCTACAT GCAGTCAAAT GCTGCTTTAA TGTTGGTGCA GAGTAGCATG
  Y
  CGTTTAATGA TCTAAACAGG AGTAAGCTAA GGCATCTCTC TGAAGTGAGA GGGTAGGGGC
  TCTTGGGCAT GAGCAAGGTG GACGCATGCT GGAATCCTCA CAGCACCTTT AGCTGGAGGC
  AGCCTTAGAG GGCTTTTAGA AAATACGGCA CTTTATCAGA CTGTCAAGAA TGCGTTAGGA
  GTTTCTGCAC CCAAATCTTT                                            
  
  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	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
ss38243559	NES09530025	PERLEGEN	MM_PANEL2	f	SNP	C	C	C	C	C	C	T	C	C	C	C	C	C	C	C
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
rs28080636					SNP	C	C	C	C	C	C	T	C	C	C	C	C	C	C	C

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
ss38243559	NES09530025	PERLEGEN	MM_PANEL	f	SNP	C/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr4:98435325 () rs orientation: forward

Symbol	Name	Function Class
Patj	PATJ, crumbs cell polarity complex component	Intron
Rr595752	regulatory region 595752	1379 bp distal
Rr595753	regulatory region 595753	1503 bp distal
Rr595754	regulatory region 595754	105 bp distal
Rr595755	regulatory region 595755	within coordinates
Tssr1238	transcription start site region 1238	464 bp downstream
Tssr37887	transcription start site region 37887	433 bp downstream
Tssr37888	transcription start site region 37888	399 bp downstream
Tssr37889	transcription start site region 37889	379 bp downstream
Tssr37890	transcription start site region 37890	349 bp downstream
Tssr37891	transcription start site region 37891	325 bp downstream
Tssr37892	transcription start site region 37892	283 bp downstream
Tssr37893	transcription start site region 37893	179 bp downstream
Tssr37894	transcription start site region 37894	129 bp downstream