rs6408685 SNP Detail

Summary

• ID
  rs6408685
• Variation Type
  SNP
• Alleles
  A/T

• Created in dbSNP Build
  116
• Last Updated in dbSNP Build
  137
• Additional Resources
  JBrowse Genome Browser | Ensembl SNPView | UCSC Browser | Alliance Variant
  

Genome Location and Flanking Sequence

• Location
  Chr3:27246454 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              AGAGGACTCA AAAGGAAGAA
  AAATAACTTG CTCAGTATGG CAGCGCTGAG GAGGTGGGGC AGGTGAAGGC CAGGCTGCCT
  CGATGCCATG CCTAGGAGCT TCACCATGGT GCTAACTAAC GTGGCACAGG GACCAGCTGA
  GAAAATGGAA GTCAGGCTCT CACAAGAGAG AGGCAAAGGG CATTTTAGCA ACAGAATATG
  W
  ATGAGGGGCT CAAGGAGAGA TTGTGATATA GTTGAGGGTC TAAAAATAGC TTAAACCAGC
  TAGAGCCTTG GAAGTTTTAA GGCCAGAGTG GAGGTCAGAG GGAAGTGTGG GCTGGGTAAG
  GAGTGGCTTT TTGTCTGTGG TCTGGAAAGA CGGCAGGAAG TTGCATGGTA AAGTCTGTGT
  GTTAGAACAA TCTTCAGCAT                                            
  
  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	129S1/SvImJ	A/J	AKR/J	BALB/cByJ	BTBR T<+> Itpr3/J	C3H/HeJ	C57BL/6J	CAST/EiJ	CZECHII/EiJ	DBA/2J	FVB/NJ	KK/HlJ	MOLF/EiJ	NOD/ShiLtJ	NZW/LacJ	PWD/PhJ	WSB/EiJ
ss8814900	WI_WGS_3_27017013	WI	MOUSE	f	SNP							A		T
ss60380378	NES15883642	PERLEGEN	MM_PANEL2	f	SNP	A	A	A	A	A	A		A		A	A	A	T	A	A	T	A
SNP Consensus Information
SNP					Consensus Type	129S1/SvImJ	A/J	AKR/J	BALB/cByJ	BTBR T<+> Itpr3/J	C3H/HeJ	C57BL/6J	CAST/EiJ	CZECHII/EiJ	DBA/2J	FVB/NJ	KK/HlJ	MOLF/EiJ	NOD/ShiLtJ	NZW/LacJ	PWD/PhJ	WSB/EiJ
rs6408685					SNP	A	A	A	A	A	A	A	A	T	A	A	A	T	A	A	T	A

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
ss60380378	NES15883642	PERLEGEN	MM_PANEL	f	SNP	A/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr3:27246454 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Nceh1	neutral cholesterol ester hydrolase 1			Intron
				Noncoding-Transcript-Variant
Rr374718	regulatory region 374718			1099 bp downstream
Rr574361	regulatory region 574361			1073 bp distal
Rr574362	regulatory region 574362			112 bp distal
Rr574363	regulatory region 574363			1482 bp proximal
Tssr28610	transcription start site region 28610			159 bp downstream
Tssr28611	transcription start site region 28611			1955 bp upstream
Tssr32839	transcription start site region 32839			361 bp upstream
Tssr32840	transcription start site region 32840			319 bp upstream
Tssr32841	transcription start site region 32841			1764 bp downstream
Tssr32842	transcription start site region 32842			1819 bp downstream
Tssr32843	transcription start site region 32843			1890 bp downstream