rs16790025 SNP Detail

Summary

• ID
  rs16790025
• Variation Type
  SNP
• Alleles
  A/G

• Created in dbSNP Build
  123
• Last Updated in dbSNP Build
  137
• Additional Resources
  JBrowse Genome Browser | Ensembl SNPView | UCSC Browser
  

Genome Location and Flanking Sequence

• Location
  Chr3:95433990 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              TGTTAAAGGA TAAGACAGGG
  CTTCCTAGGG AATCATGTAG CAACCTGAGA TTTGAGGCGC CTGATCCAAA TGTCTTTATA
  ACTAAATGTT TCCATCTCAG AACCGATGTG AATAAAATGG ACCACCAAAA TGACACAGGG
  TTGGAGGAAA ACTTTGTCCT GTTCTCTGCT GAGGTCATTC TATTGATGGC CTCTACCATG
  R
  AGCCCTCTGG GCAGCTCATT ACACACAAAC TGTCCCAAGG TGAGAAGGAG AGGGCGGAGG
  CAGCTGTTCT CATAAGTCTT TAAATGAAAC CGAAATGAAA GTTCACTTCC TCATTGTGGA
  TGCTTCATGT GACAAGCTCC GATTTCTTTT TAGAGTCATT TCAAGCAGCC TCCTGCTGCC
  AGGGACATCT TTGGAGTGAG                                            
  
  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	C57BL/6J	CAST/EiJ	DBA/2J	FVB	FVB/NJ	KK/HlJ	LP/J	MOLF	MOLF/EiJ	MRL/MpJ	MSM	NOD/ShiLtJ	NZB/BlNJ	NZW/LacJ	PWD/PhJ	WSB/EiJ
ss24742407	Ctss_AN7918_1	ROCHEBIO	RPAMM	f	SNP				G		G	G	G	G	G			G	A		G	A		G
ss46775210	NES10756271	PERLEGEN	MM_PANEL2	f	SNP	G	G	G	G	G	G		G	G		G	G			A			G		G	A	G
SNP Consensus Information
SNP					Consensus Type	129S1/SvImJ	A/J	AKR/J	BALB/cByJ	BTBR T<+> Itpr3/J	C3H/HeJ	C57BL/6J	CAST/EiJ	DBA/2J	FVB	FVB/NJ	KK/HlJ	LP/J	MOLF	MOLF/EiJ	MRL/MpJ	MSM	NOD/ShiLtJ	NZB/BlNJ	NZW/LacJ	PWD/PhJ	WSB/EiJ
rs16790025					SNP	G	G	G	G	G	G	G	G	G	G	G	G	G	A	A	G	A	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
ss46775210	NES10756271	PERLEGEN	MM_PANEL	f	SNP	A/G

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr3:95433990 () rs orientation: forward

Symbol	Name	Function Class
Ctss	cathepsin S	107 bp upstream
Gm56808	predicted gene, 56808	1794 bp upstream
Rr397840	regulatory region 397840	within coordinates
Rr580965	regulatory region 580965	1805 bp distal
Rr580966	regulatory region 580966	1597 bp distal
Rr580967	regulatory region 580967	within coordinates
Rr580968	regulatory region 580968	118 bp proximal
Tssr30563	transcription start site region 30563	98 bp upstream
Tssr30564	transcription start site region 30564	121 bp upstream
Tssr30565	transcription start site region 30565	140 bp upstream
Tssr30566	transcription start site region 30566	199 bp upstream
Tssr34486	transcription start site region 34486	1840 bp upstream
Tssr34487	transcription start site region 34487	1784 bp upstream