rs49068054 SNP Detail

Summary

• ID
  rs49068054
• Variation Type
  SNP
• Alleles
  C/T

• Created in dbSNP Build
  127
• Last Updated in dbSNP Build
  137
• Additional Resources
  JBrowse Genome Browser | Ensembl SNPView | UCSC Browser | Alliance Variant
  

Genome Location and Flanking Sequence

• Location
  Chr13:53529655 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              GCAACAAAGG AAACAAAATA
  CAAACCCAGG CCATTGTTTG TTTTGTTTTG TTTTTGAGAC AGGTCTCACT ATGTAGTCAT
  GGCTGGCCTG AAACTCACTC TGTAGATCAG GAGTGCTAGA CCGAAGGAAT GAGCCACCAT
  ACCCGCAAGC TCAGGCATTT ATAAGTCAGG CATAGTGGGG TATGCCTGAA ATTCCGGGGG
  Y
  ATTTGGCATT CACAGAGAAC CCAGGCTACT CAGCAAGATC TTATCTTGAA ATGCAGATGC
  GTACTTACAA ACTTAAATAG AAAAACAGAT TACCAATGAA TCATGAATGA TGGTATTTCA
  CCATAATTAA AACAAACAAA CAAACAAACA TACAAACAAA AACACACCCA GATTATGGAG
  ACTGGAAAAC TGCTGACAGA                                            
  
  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	LG/J	MOLF/EiJ	NOD/ShiLtJ	NZW/LacJ	PWD/PhJ	SM/J	WSB/EiJ
ss61805856	NES17722852	PERLEGEN	MM_PANEL2	f	SNP	C	C	T	C	C	C	C	C	C	C		C	T	T	C		C
ss324341566	CHEV_13_53470988	CHEVERUD	SCREENING_POP	f	SNP											C					T
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	LG/J	MOLF/EiJ	NOD/ShiLtJ	NZW/LacJ	PWD/PhJ	SM/J	WSB/EiJ
rs49068054					SNP	C	C	T	C	C	C	C	C	C	C	C	C	T	T	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
ss61805856	NES17722852	PERLEGEN	MM_PANEL	f	SNP	C/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr13:53529655 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Cpgi5620	CpG island 5620			1426 bp proximal
Rr403780	regulatory region 403780			1683 bp upstream
Rr480032	regulatory region 480032			1768 bp proximal
Sptlc1	serine palmitoyltransferase, long chain base subunit 1			Intron
				Noncoding-Transcript-Variant
Tssr122581	transcription start site region 122581			1834 bp upstream
Tssr122582	transcription start site region 122582			1300 bp upstream
Tssr122583	transcription start site region 122583			1736 bp downstream