rs33099388 SNP Detail

Summary

• ID
  rs33099388
• Variation Type
  SNP
• Alleles
  C/T

• Created in dbSNP Build
  125
• Last Updated in dbSNP Build
  137
• Additional Resources
  JBrowse Genome Browser | Ensembl SNPView | UCSC Browser | Alliance Variant
  

Genome Location and Flanking Sequence

• Location
  Chr3:95040394 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              TGATGATTCG AGTCTGGGTT
  AGCAAAGGAG CCTGGTGATG AAGAGACAGA GTTAGAGCTG TTAGGAGCAA ACGTTCCCTC
  AAGCCTGTTG TGTGAAGTAT AGCCCTGTCT AAACCACACC TGATGCCCTC TCACCTCAGT
  TTTGCTTTCT GTCTTCAATT CGTTCTGCTG TCTTGGATTT TGCTCTGTTC CCTTGCCTGT
  Y
  TGCTTTTTGC CATAGAAAAG CTTCAGACCT GAGAACAAAA GCAAGGAGGA ATGAAAAGCA
  CAATGCCTGG TGGCTTGCTC TCCATCTCCC GCCCTCCCCA CTTCTCTGAT ACTTACTGGA
  CAAATGCTTC TTGCCTGCAC GGTGGGCTGT CAACATGGCC AGCGTGTCTA GTACTGGTCG
  ATGGGGGCAG ATGGCACAAG                                            
  
  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	BALB/cByJ	BTBR T<+> Itpr3/J	C3H/HeJ	CAST/EiJ	FVB/NJ	MOLF/EiJ	NOD/ShiLtJ	NZW/LacJ	PWD/PhJ	WSB/EiJ
ss46771826	NES10666768	PERLEGEN	MM_PANEL2	f	SNP	T	T	T	T	T	C	T	T	T	T	T	T
SNP Consensus Information
SNP					Consensus Type	129S1/SvImJ	A/J	BALB/cByJ	BTBR T<+> Itpr3/J	C3H/HeJ	CAST/EiJ	FVB/NJ	MOLF/EiJ	NOD/ShiLtJ	NZW/LacJ	PWD/PhJ	WSB/EiJ
rs33099388					SNP	T	T	T	T	T	C	T	T	T	T	T	T

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
ss46771826	NES10666768	PERLEGEN	MM_PANEL	f	SNP	C/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr3:95040394 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Lysmd1	LysM, putative peptidoglycan-binding, domain containing 1			1005 bp upstream
Rr367480	regulatory region 367480			823 bp upstream
Rr580822	regulatory region 580822			494 bp distal
Rr580823	regulatory region 580823			918 bp proximal
Rr580824	regulatory region 580824			1016 bp proximal
Scnm1	sodium channel modifier 1			Coding-Synonymous
				Noncoding-Transcript-Variant
Tssr30498	transcription start site region 30498			1643 bp downstream
Tssr34419	transcription start site region 34419			815 bp downstream
Tssr34420	transcription start site region 34420			853 bp downstream
Tssr34421	transcription start site region 34421			906 bp downstream