rs28080646 SNP Detail

Summary

• ID
  rs28080646
• Variation Type
  SNP
• Alleles
  A/G

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

Genome Location and Flanking Sequence

• Location
  Chr4:98433878 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                        TGTGCATTCA GGTAGATCTC TGCCTCACCA ATAGATGTCA
  GTGTAGCCAA CAGTACTTAC TGACCAAGCA TGGAGCTTGG AGAATGCTCA CTCACTGCCA
  R
  TAGCAGGCAG CATGAGTAGC ACCCAGCTTT TGCTACATAA ACCCTTTTTA TTTTTGATAA
  TGCAAAATAT AAGAGTACTG GTTAAGATTA ATTTTTTTAG                      
  
  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
ss38243569	NES09530008	PERLEGEN	MM_PANEL2	f	SNP	A	A	A	A	A	A	A	A	A	A	G	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
rs28080646					SNP	A	A	A	A	A	A	A	A	A	A	G	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
ss38243569	NES09530008	PERLEGEN	MM_PANEL	f	SNP	A/G

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr4:98433878 () rs orientation: forward

Symbol	Name	Function Class
Patj	PATJ, crumbs cell polarity complex component	Intron
Rr595752	regulatory region 595752	within coordinates
Rr595753	regulatory region 595753	56 bp distal
Rr595754	regulatory region 595754	886 bp proximal
Rr595755	regulatory region 595755	1343 bp proximal
Tssr1238	transcription start site region 1238	973 bp upstream
Tssr37887	transcription start site region 37887	990 bp upstream
Tssr37888	transcription start site region 37888	1021 bp upstream
Tssr37889	transcription start site region 37889	1055 bp upstream
Tssr37890	transcription start site region 37890	1069 bp upstream
Tssr37891	transcription start site region 37891	1105 bp upstream
Tssr37892	transcription start site region 37892	1156 bp upstream
Tssr37893	transcription start site region 37893	1256 bp upstream
Tssr37894	transcription start site region 37894	1278 bp upstream