rs16790020 SNP Detail

Summary

• ID
  rs16790020
• Variation Type
  SNP
• Alleles
  A/T

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

Genome Location and Flanking Sequence

• Location
  Chr3:95432903 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                 C CCCCCCCGAC ACACACACAA TAATTGTAAA
  AATAGATAAA CCCTTGAAAC ATTTTCATAT GAAACATATT ACNCATGAGA TCTAGGAATT
  W
  TTTCGAAATA ATCTGGGAAA TGGGAGCATA AATGAAACAA GTTGGCAGTT CCAGGANATT
  ATTGAAACAG GAGTTCCTCN CCTCNCTGCC TTNttgtttt gnattttgag gacaaggttt
  tatgtaaccc aggctggcct ganactagca ctatACCTGG CCAGATGTTC TATTTCACCA
  TTTTAAATTT TCAGTAAAAA AAAAAAATCA GTATAAGCAA AGTNAaaaca aacaaacaaa
  caaagaaaaa aacCAATGGA AAACTGTGAN AAGGCAGGCG GAGTGTACGG CACCACCANA
  GACTGCTAGC CAGAACAGTA AAAACAGGCC CTGCAGATCA CCAAGAAAAC CGATAAATAC
  ACTAGAAACN TGAGCAAAAT AATT                                       
  
  W = A/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	BALB/cByJ	BUB	C3H/HeJ	DBA/2J	FVB	LG/J	LP/J	MSM	NZB/BlNJ	NZW/Lac
ss24742395	Ctss_AN7916_2	ROCHEBIO	RPAMM	f	SNP	T	A	A	A	A	A	A	A	A	A
SNP Consensus Information
SNP					Consensus Type	BALB/cByJ	BUB	C3H/HeJ	DBA/2J	FVB	LG/J	LP/J	MSM	NZB/BlNJ	NZW/Lac
rs16790020					SNP	T	A	A	A	A	A	A	A	A	A

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr3:95432903 () rs orientation: forward

Symbol	Name	Function Class
Ctss	cathepsin S	1194 bp upstream
Gm40096	predicted gene, 40096	1093 bp upstream
Gm56808	predicted gene, 56808	707 bp upstream
Rr397840	regulatory region 397840	1010 bp upstream
Rr580964	regulatory region 580964	1487 bp distal
Rr580965	regulatory region 580965	718 bp distal
Rr580966	regulatory region 580966	510 bp distal
Rr580967	regulatory region 580967	913 bp proximal
Rr580968	regulatory region 580968	1205 bp proximal
Tssr30563	transcription start site region 30563	1185 bp upstream
Tssr30564	transcription start site region 30564	1208 bp upstream
Tssr30565	transcription start site region 30565	1227 bp upstream
Tssr30566	transcription start site region 30566	1286 bp upstream
Tssr34486	transcription start site region 34486	753 bp upstream
Tssr34487	transcription start site region 34487	697 bp upstream