rs49559400 SNP Detail

Summary

• ID
  rs49559400
• 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
  Chr3:26207650 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              TCTTCCCCCA GTCCTCTTTC
  CATTATTCAA GGAGACAGTT TTACCAACAC TTCCCGTCAA ATTCAAGCCG AAACGGTCAA
  AGTATTTACC AGTTTGCAGA TGCTTTCTTT TCAACCTCTG GAACTGGGTA ATTCTTGTTT
  CAGAATTCAA GATGCTTCCT TTATTTATTT ATTTTTTTTT TCTTTAAGCA GCCGCAACCC
  Y
  AGATCCACCT CCCCCTCCCT CGTTATTCAC CCACGGACAC TTCCTAAACG TGTGGATTGA
  TGCTTTTTTT CTCTCCAGAT GCTGCCAGGA TCCAGAATCC TGGAGAACCA AAGCCGCATC
  CGTGTAATTC CTACCATCAG GCAAGAAATA CAAACGATCA AACAACGTTA CTTCTTTGAG
  CTGCGATCAG ATAATCCTAC                                            
  
  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	A/J	DBA/2J	MSM/Ms
ss134692054	ENSMUSSNP1437438	ENSEMBL	ENSEMBL_Sanger	f	SNP	C	C	T
SNP Consensus Information
SNP					Consensus Type	A/J	DBA/2J	MSM/Ms
rs49559400					SNP	C	C	T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr3:26207650 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Cpgi13014	CpG island 13014			138 bp distal
Nlgn1	neuroligin 1			Intron
				mRNA-UTR
Rr574308	regulatory region 574308			1579 bp distal
Rr574309	regulatory region 574309			205 bp distal
Rr574310	regulatory region 574310			within coordinates
Tssr32822	transcription start site region 32822			35 bp upstream
Tssr32823	transcription start site region 32823			140 bp downstream
Tssr32824	transcription start site region 32824			395 bp downstream
Tssr32825	transcription start site region 32825			456 bp downstream
Tssr32826	transcription start site region 32826			494 bp downstream