rs28147115 SNP Detail

Summary

• ID
  rs28147115
• 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
  Chr4:107225360 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              AACCCTGCCC AGGCAGCGTA
  CCGGGCAGCC CCAGCTGGGT CCTCCCGGGG CCTTCCTGCC TTTGAACAGT GGTGGCGGGC
  GGACACTCTG TCCCCGGCAC GCTTGAGAGC GGGGGCCGCC ATCTCCATGG CCACGGCTGC
  GAGCGGGCCC TGCGCCGGCG GGTCGCCGCG GGACATCCTT TGGCGCGTGA GTTAGCGAGC
  Y
  GTGGCGCTCC CTGCCTCTCT GGCGGTGCCT GCGCGCTTGG CTAAAGGGGC CTGTCTTGGA
  GGCGCTTTAG GAATAGCGTG TAGGGATCTG ACCGCCTCGG GGATTGGGTG CAAGGGTGTG
  TGGGCGTCCC CGAGTGGAAG TTAGGTCTGG GGTGTTGAGC TGGAGTCCGA AGTGGAAGTT
  TGTCAGCGTG GTTGGGATGG                                            
  
  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
ss38285739	NES09488834	PERLEGEN	MM_PANEL2	f	SNP	C	C	C	C	C	C	T	C	C	C	T	C	C	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	MOLF/EiJ	NOD/ShiLtJ	NZW/LacJ	PWD/PhJ	WSB/EiJ
rs28147115					SNP	C	C	C	C	C	C	T	C	C	C	T	C	C	T	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
ss38285739	NES09488834	PERLEGEN	MM_PANEL	f	SNP	C/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr4:107225360 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Cpgi14540	CpG island 14540			within coordinates
Ndc1	NDC1 transmembrane nucleoporin			Intron
				Noncoding-Transcript-Variant
Rr367664	regulatory region 367664			276 bp downstream
Rr596979	regulatory region 596979			369 bp distal
Rr596980	regulatory region 596980			774 bp distal
Rr596981	regulatory region 596981			within coordinates
Rr596982	regulatory region 596982			302 bp distal
Rr596983	regulatory region 596983			121 bp proximal
Tssr38245	transcription start site region 38245			409 bp downstream
Tssr38246	transcription start site region 38246			350 bp downstream
Tssr38247	transcription start site region 38247			125 bp downstream
Tssr38248	transcription start site region 38248			106 bp downstream
Tssr38249	transcription start site region 38249			91 bp downstream
Tssr38250	transcription start site region 38250			79 bp downstream
Tssr38251	transcription start site region 38251			158 bp upstream