rs28052580 SNP Detail

Summary

• ID
  rs28052580
• 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
  Chr4:75940383 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              TTAATAGGAT TTCTGGTACA
  AGCCTTCTGA AAGCTTGCGT TCAATAAACC TGTCATTAAC AAAGAACGGG GTTGCTTCAT
  ATAACCACTT TAATGAATCT GAATACAGAA AAATTATGGT AGTTGTCATC CTGCATAACG
  GTCCATATAT AGGTGTTCTG TACAGTGCTA TGGGAGAGAT CTCTACATGC TCAATGTGTA
  Y
  GTTTCCCGTG AAACAGTTTT CCATCAAGGG AGTGGAGTGT CCATTATTCA AACAAAGAAA
  TGTACAAAGT CCCCACAACT GTTACAGTTA TGCGTGCAAA GATGATACAA AAACAGCACC
  CAAAATTTAA ACACAGATAA AAGAATGTGA TCATTGAGCC GGGTATCTCT GAGATGTTTT
  GCCAAGTTCT TCAAGGGGAT                                            
  
  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	LG/J	MOLF/EiJ	NOD/ShiLtJ	NZW/LacJ	PWD/PhJ	SM/J	WSB/EiJ
ss38197013	NES09601908	PERLEGEN	MM_PANEL2	f	SNP	T	T	T	T	T	T	T	T	T	T		T	C				C
ss47700736	NES10225672	PERLEGEN	MM_PANEL2	r	SNP	A	A	A	A	A	A	A	A	A	A		A	G	A	A		G
ss321169679	CHEV_4_75668050	CHEVERUD	SCREENING_POP	f	SNP											T					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	LG/J	MOLF/EiJ	NOD/ShiLtJ	NZW/LacJ	PWD/PhJ	SM/J	WSB/EiJ
rs28052580					SNP	T	T	T	T	T	T	T	T	T	T	T	T	C	T	T	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
ss38197013	NES09601908	PERLEGEN	MM_PANEL	f	SNP	C/T
ss47700736	NES10225672	PERLEGEN	MM_PANEL	r	SNP	A/G

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr4:75940383 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Ptprd	protein tyrosine phosphatase receptor type D			Intron
				Noncoding-Transcript-Variant
Rr594065	regulatory region 594065			within coordinates
Rr594066	regulatory region 594066			1805 bp proximal