rs6401090 SNP Detail

Summary

• ID
  rs6401090
• Variation Type
  SNP
• Alleles
  C/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
  Chr5:35201883 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              CAACCACTGT GCCTGCAGTT
  CCCACAGAGC ACTGCTTCCT GGGAAATGGT ACAGAGTACC GAGGCGTGGC CAGCACCGCT
  GCCTCGGGCC TGAGCTGCCT GGCCTGGAAT TCTGACCTGC TCTACCAGGA GCTGCACGTG
  GACTCAGTGG CTGCTGCTGT CCTGCTTGGC CTGGGCCCTC ACGCTTACTG CCGGTCAGCA
  Y
  CTAATGGCTG CTATACATAC TCTTTCTGCA TAAGCAAAGG ATTGGACAGA GGGTCTTCCC
  AGACTCTGCA GGGGACAACA GTGCCTAGAT GGCTGTTAGC CTCTGCCTCT TGGGATGGTG
  GGTTCATGTG TGCCCACCGT GGTCTGCAGA GAGAGCACAT AGCTCTGGGT GTTAGGATGG
  TCCTCTAGGG AGAGTGATGG                                            
  
  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	C57BL/6J	CAST/EiJ	CZECHII/EiJ	DBA/2J	FVB/NJ	KK/HlJ	MOLF/EiJ	NOD/ShiLtJ	NZW/LacJ	PWD/PhJ	WSB/EiJ
ss8807286	WI_WGS_5_33752070	WI	MOUSE	f	SNP							C		T
ss47678809	NES10266567	PERLEGEN	MM_PANEL2	f	SNP	C	C	C	C	C	C		C		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	C57BL/6J	CAST/EiJ	CZECHII/EiJ	DBA/2J	FVB/NJ	KK/HlJ	MOLF/EiJ	NOD/ShiLtJ	NZW/LacJ	PWD/PhJ	WSB/EiJ
rs6401090					SNP	C	C	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
ss47678809	NES10266567	PERLEGEN	MM_PANEL	f	SNP	C/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr5:35201883 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Hgfac	hepatocyte growth factor activator			Intron
				Noncoding-Transcript-Variant
				Splice-Site
Rr609835	regulatory region 609835			1382 bp distal
Rr609836	regulatory region 609836			1301 bp distal
Tssr45927	transcription start site region 45927			1971 bp downstream
Tssr45928	transcription start site region 45928			724 bp upstream
Tssr45929	transcription start site region 45929			736 bp upstream
Tssr45930	transcription start site region 45930			1944 bp upstream