rs28080629 SNP Detail

Summary

• ID
  rs28080629
• Variation Type
  SNP
• Alleles
  A/G

• 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
  Chr4:98436063 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              CTGCAAGCAT CACCAGCCAC
  TTCCTTGTTA AACATATGCT CTGAAAATTA CTGCTCAGTT GACAGTAGGA GACTCTCAGT
  AGTAAGAGCA TCTGTGTGAC TTTTAAAATG TTGATATGTT AGAACCAGAG CTCCTTCTTT
  TCTGGTTAAA ATGTACAATA TTTAGAACCA ATAAGAGTCT TCATGAGTCC CTTTATCTAC
  R
  GGTCAGTTTA CTCAGAGTCT GATGCAGCGT GACTTTCTTT TCATTTTCAG TAGAATGACT
  CAAATTAGGT TTTCTCCTGC ACTTACAGGA CACATGGAGC AGTCTCAATT TAGGCAAGCA
  CACCTTACTC CTGGCTCTTC TTTCACGATA ACTGAGTACA AACTTGCTCT TTTCTGTAAC
  ATCACTTCTG GGCATTTTAA                                            
  
  R = A/G
  

  
  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
ss38243552	NES09530039	PERLEGEN	MM_PANEL2	f	SNP	G	G	G	G	G	G	G	G	G	G	G	G	G	A	G
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
rs28080629					SNP	G	G	G	G	G	G	G	G	G	G	G	G	G	A	G

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
ss38243552	NES09530039	PERLEGEN	MM_PANEL	f	SNP	A/G

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr4:98436063 () rs orientation: forward

Symbol	Name	Function Class
Patj	PATJ, crumbs cell polarity complex component	Intron
Rr595754	regulatory region 595754	843 bp distal
Rr595755	regulatory region 595755	612 bp distal
Tssr1238	transcription start site region 1238	1202 bp downstream
Tssr37887	transcription start site region 37887	1171 bp downstream
Tssr37888	transcription start site region 37888	1137 bp downstream
Tssr37889	transcription start site region 37889	1117 bp downstream
Tssr37890	transcription start site region 37890	1087 bp downstream
Tssr37891	transcription start site region 37891	1063 bp downstream
Tssr37892	transcription start site region 37892	1021 bp downstream
Tssr37893	transcription start site region 37893	917 bp downstream
Tssr37894	transcription start site region 37894	867 bp downstream
Tssr37895	transcription start site region 37895	1852 bp upstream