rs6390042 SNP Detail

Summary

• ID
  rs6390042
• Variation Type
  SNP
• Alleles
  C/T

• Created in dbSNP Build
  116
• Last Updated in dbSNP Build
  125
• Additional Resources
  JBrowse Genome Browser | Ensembl SNPView | UCSC Browser | Alliance Variant
  

Genome Location and Flanking Sequence

• Location
  Chr2:163482782 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                                         AATCTAATAA
  GCTCTCTATT GNCCTCTTCT GTCTTTGGTN NATTATTCCC ATCCTGGGCA TTATTGGCCT
  GCCAAGCCCA NAtctacaag ccaaagaaag taaagattac cagcaaacca anagggcaaa
  ggcacaacgt ctctaatcaa ttgcagaagg ttaacaatcc tgagccacag taatgtcaga
  tctgtagctt ccaCCCATTG CTATAGCTTA TACTGATTTG TGATACTTTG CTTGAAAGTA
  Y
  GAGCAAACTA ATNAtaatgg ttcgtttata cttggcccag ggagaagcac taataagagg
  cgcagcattg ttggagtagg tgtgtcacca cgggcatggg atttaagacc ctctttcgtg
  ctgcctagaa gctagtcttt tcctgtttgc ctttggTTTT TTTTGGGTTT TTTTGTTTTG
  TTTTGTTttt gtttctgttt tttttcgaga cagggtttct ctttatagcc ctggctgtcc
  tggaactcac                                                       
  
  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
ss8796210	WI_WGS_2_164572845	WI	MOUSE	f	SNP							C		T
ss37520862	NES08878597	PERLEGEN	MM_PANEL2	f	SNP	C	C	C	C	C	C		C		C	C	T	C	C	C	C	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
rs6390042					SNP	C	C	C	C	C	C	C	C	T	C	C	T	C	C	C	C	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
ss37520862	NES08878597	PERLEGEN	MM_PANEL	f	SNP	C/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr2:163482782 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Rr397465	regulatory region 397465			1795 bp upstream
Rr569443	regulatory region 569443			60 bp distal
Rr569444	regulatory region 569444			214 bp distal
Rr569445	regulatory region 569445			707 bp proximal
Serinc3	serine incorporator 3			Intron
				Noncoding-Transcript-Variant
Tssr27319	transcription start site region 27319			1520 bp upstream