rs39641947 SNP Detail

Summary

• ID
  rs39641947
• Variation Type
  SNP
• Alleles
  A/G

• Created in dbSNP Build
  126
• Last Updated in dbSNP Build
  137
• Additional Resources
  JBrowse Genome Browser | Ensembl SNPView | UCSC Browser | Alliance Variant
  

Genome Location and Flanking Sequence

• Location
  Chr5:87843754 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              CAAAAGCCAT TGACTCTGCT
  GAAAGTCAAT TAACTCCATG CATGAGAAAT TCTTATTAAT GTTTTTGGCC TAGGAATAAA
  GTAAATATAC TACAAAGAGG CTAATCAGCA AGATTCTTCA TCTGGTAGGT GGTCAGTTCA
  GTGCCACATG GTTAGCATGT CCTTTCACTG ACATGTTCAC TTAGAAAATA AAAGGAACAT
  R
  ATTTCTACTG GAGAGAAGCT TATGTTCATT ATTAAACACA GATAACTCCA CTAGTAACTG
  CAGTCATGAT GGAAAAAATG TATTGGTGCC CACATGAGCT TTCTAGACAT AACTTATTGA
  TGAGTAGTTT ACCTCTGCCT GCAGCTGTCC CATGAGATTC ACCTTCTGAA GTTTCTGCTA
  GAAATAAACA ATACATTAAA                                            
  
  R = A/G
  

  
  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	CAST/EiJ	DBA/2J	FVB/NJ	KK/HlJ	MOLF/EiJ	NOD/ShiLtJ	NZW/LacJ	WSB/EiJ
ss51174926	NES13825888	PERLEGEN	MM_PANEL2	f	SNP	A	A	A	A	A	G	A	A	A	A	A	A	A
SNP Consensus Information
SNP					Consensus Type	129S1/SvImJ	A/J	AKR/J	BALB/cByJ	BTBR T<+> Itpr3/J	CAST/EiJ	DBA/2J	FVB/NJ	KK/HlJ	MOLF/EiJ	NOD/ShiLtJ	NZW/LacJ	WSB/EiJ
rs39641947					SNP	A	A	A	A	A	G	A	A	A	A	A	A	A

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
ss51174926	NES13825888	PERLEGEN	MM_PANEL	f	SNP	A/G

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr5:87843754 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Csn2	casein beta			Intron
				Noncoding-Transcript-Variant
D5Mit12	DNA segment, Chr 5, Massachusetts Institute of Technology 12			1917 bp distal
D5Mit16	DNA segment, Chr 5, Massachusetts Institute of Technology 16			1877 bp distal
D5Mit16.1	DNA segment, Chr 5, Massachusetts Institute of Technology 16.1			1720 bp distal
Tssr1529	transcription start site region 1529			1334 bp downstream
Tssr46883	transcription start site region 46883			1384 bp downstream
Tssr46884	transcription start site region 46884			1369 bp downstream
Tssr46885	transcription start site region 46885			1348 bp downstream
Tssr46886	transcription start site region 46886			1318 bp downstream
Tssr46887	transcription start site region 46887			1301 bp downstream
Tssr46888	transcription start site region 46888			1195 bp downstream
Tssr46889	transcription start site region 46889			1176 bp downstream
Tssr46890	transcription start site region 46890			1143 bp downstream
Tssr46891	transcription start site region 46891			1130 bp downstream
Tssr46892	transcription start site region 46892			1101 bp downstream
Tssr46893	transcription start site region 46893			1075 bp downstream
Tssr46894	transcription start site region 46894			1030 bp downstream
Tssr46895	transcription start site region 46895			1010 bp downstream
Tssr46896	transcription start site region 46896			931 bp downstream
Tssr51618	transcription start site region 51618			1355 bp upstream
Tssr51619	transcription start site region 51619			1321 bp upstream
Tssr51620	transcription start site region 51620			1311 bp upstream
Tssr51621	transcription start site region 51621			1292 bp upstream
Tssr51622	transcription start site region 51622			1256 bp upstream
Tssr51623	transcription start site region 51623			1240 bp upstream
Tssr51624	transcription start site region 51624			1223 bp upstream
Tssr51625	transcription start site region 51625			1213 bp upstream
Tssr51626	transcription start site region 51626			1201 bp upstream
Tssr51627	transcription start site region 51627			1175 bp upstream
Tssr51628	transcription start site region 51628			1065 bp upstream
Tssr51629	transcription start site region 51629			971 bp upstream
Tssr51630	transcription start site region 51630			923 bp upstream
Tssr51631	transcription start site region 51631			884 bp upstream
Tssr51632	transcription start site region 51632			625 bp upstream
Tssr51633	transcription start site region 51633			158 bp downstream
Tssr51634	transcription start site region 51634			280 bp downstream
Tssr51635	transcription start site region 51635			1244 bp downstream
Tssr51636	transcription start site region 51636			1270 bp downstream
Tssr51637	transcription start site region 51637			1383 bp downstream