rs28147116 SNP Detail

Summary

• ID
  rs28147116
• Variation Type
  SNP
• Alleles
  G/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
  Chr4:107225129 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              TCCTCTTCCC CTTGGTTCTC
  AGGGGTCGTC GAGACTACAG TTCCCAGCAT GCAGCACCGT CGCCCTTTGT TTTTGACGCC
  CAGATGGACC CTGCTTCGGA AGGACTTTTT GGACTCCAGA GGACGCTTCC TCGAGTCACA
  GCCCACCTGG AGGCATGTGG CTACGGGGAA GTTCTGGCCG GTTGAGTCTG TTCAGGCGAA
  K
  CTGCGGAGAG ATGGTCTGGC GGCTTTGCAG AACCCTGCCC AGGCAGCGTA CCGGGCAGCC
  CCAGCTGGGT CCTCCCGGGG CCTTCCTGCC TTTGAACAGT GGTGGCGGGC GGACACTCTG
  TCCCCGGCAC GCTTGAGAGC GGGGGCCGCC ATCTCCATGG CCACGGCTGC GAGCGGGCCC
  TGCGCCGGCG GGTCGCCGCG                                            
  
  K = G/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
ss38285740	NES09488833	PERLEGEN	MM_PANEL2	f	SNP	G	G	G	G	G	G	T	G	G	G	T	G	G	T	G
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
rs28147116					SNP	G	G	G	G	G	G	T	G	G	G	T	G	G	T	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
ss38285740	NES09488833	PERLEGEN	MM_PANEL	f	SNP	G/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr4:107225129 () rs orientation: forward

Symbol	Name	Function Class
Cpgi14540	CpG island 14540	within coordinates
Ndc1	NDC1 transmembrane nucleoporin	mRNA-UTR
Rr367664	regulatory region 367664	45 bp downstream
Rr596979	regulatory region 596979	138 bp distal
Rr596980	regulatory region 596980	543 bp distal
Rr596981	regulatory region 596981	within coordinates
Rr596982	regulatory region 596982	71 bp distal
Rr596983	regulatory region 596983	352 bp proximal
Tssr38245	transcription start site region 38245	178 bp downstream
Tssr38246	transcription start site region 38246	119 bp downstream
Tssr38247	transcription start site region 38247	72 bp upstream
Tssr38248	transcription start site region 38248	107 bp upstream
Tssr38249	transcription start site region 38249	129 bp upstream
Tssr38250	transcription start site region 38250	143 bp upstream
Tssr38251	transcription start site region 38251	389 bp upstream