rs28080625 SNP Detail

Summary

• ID
  rs28080625
• 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
  Chr4:98436287 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              GCAGCGTGAC TTTCTTTTCA
  TTTTCAGTAG AATGACTCAA ATTAGGTTTT CTCCTGCACT TACAGGACAC ATGGAGCAGT
  CTCAATTTAG GCAAGCACAC CTTACTCCTG GCTCTTCTTT CACGATAACT GAGTACAAAC
  TTGCTCTTTT CTGTAACATC ACTTCTGGGC ATTTTAATGA AGGTCCTGCA TAACCTATTA
  Y
  CCAATCTGTA CATTTAGTTT CCAGGAAATA TCTGAACTGT TAAACATGTG TGTCACACAT
  TCCCCAGAGG GATGACGGCC TTCATTGGAT TTGTTTCTCT TATGCAGTTG GAATTGCTTT
  CTGATAGCTG TCATTGTCAA ATGATTGTTT GACAATCTTG TCAAACTTGC ATTGACAAGA
  AACTATGGGG ATGACCAAGA                                            
  
  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
ss38243548	NES09530049	PERLEGEN	MM_PANEL2	f	SNP	T	T	T	T	T	T	T	T	T	T	T	T	T	C	T
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
rs28080625					SNP	T	T	T	T	T	T	T	T	T	T	T	T	T	C	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
ss38243548	NES09530049	PERLEGEN	MM_PANEL	f	SNP	C/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr4:98436287 () rs orientation: forward

Symbol	Name	Function Class
Patj	PATJ, crumbs cell polarity complex component	Intron
Rr595754	regulatory region 595754	1067 bp distal
Rr595755	regulatory region 595755	836 bp distal
Tssr1238	transcription start site region 1238	1426 bp downstream
Tssr37887	transcription start site region 37887	1395 bp downstream
Tssr37888	transcription start site region 37888	1361 bp downstream
Tssr37889	transcription start site region 37889	1341 bp downstream
Tssr37890	transcription start site region 37890	1311 bp downstream
Tssr37891	transcription start site region 37891	1287 bp downstream
Tssr37892	transcription start site region 37892	1245 bp downstream
Tssr37893	transcription start site region 37893	1141 bp downstream
Tssr37894	transcription start site region 37894	1091 bp downstream
Tssr37895	transcription start site region 37895	1628 bp upstream