rs49990716 SNP Detail

Summary

• ID
  rs49990716
• Variation Type
  SNP
• Alleles
  G/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
  Chr3:90521413 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              TGAGTAGCCC CTGTCCCGGT
  TCCCCCTCCT GCCTCTCATC TGAGTGGCAT TTAATCACAG TTCCTGATCT TACTTCCTGT
  GGAGGGATGC TCGTATGCCT CCATGCTGCC CTGTCCCCTG AGGGAGGAGC AGGGGCTGAG
  GAGAGTAAAT CAAGGTAAAC CCAAGCTGAA GGCCCATCTT TGGTCCCAAC GAGCACTTGT
  K
  TGAGAGAGGA CTTCCAGGGA AGGGGTAAGG AATCTAGGGT GTTGGCCACC ACTGAGTGTG
  GACTTCTCCT TCTTAATGTA TTAGAAGCTG CAGGATGCTG AAATTGCAAG GCTGATGGAT
  GATCTGGACC GTAACAAGGA TCAGGAAGTA AACTTCCAGG AGTATGTCGC CTTCCTGGGG
  GCCTTGGCTT TGATCTACAA                                            
  
  K = G/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	MOLF/EiJ	NOD/ShiLtJ	NZW/LacJ	PWD/PhJ	WSB/EiJ
ss60424266	NES15923483	PERLEGEN	MM_PANEL2	f	SNP	T	T	T	T	T	T	G	T	T	T	T	T	T	T	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	MOLF/EiJ	NOD/ShiLtJ	NZW/LacJ	PWD/PhJ	WSB/EiJ
rs49990716					SNP	T	T	T	T	T	T	G	T	T	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
ss60424266	NES15923483	PERLEGEN	MM_PANEL	f	SNP	G/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr3:90521413 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Cpgi13468	CpG island 13468			740 bp distal
Gm57853	predicted gene, 57853			Intron
				Noncoding-Transcript-Variant
Rr397814	regulatory region 397814			1315 bp upstream
Rr580416	regulatory region 580416			1723 bp distal
Rr580417	regulatory region 580417			791 bp distal
Rr580418	regulatory region 580418			1297 bp distal
Rr580419	regulatory region 580419			1476 bp proximal
S100a6	S100 calcium binding protein A6 (calcyclin)			Intron
				Noncoding-Transcript-Variant
Tssr30242	transcription start site region 30242			1810 bp downstream
Tssr30243	transcription start site region 30243			1241 bp downstream
Tssr30244	transcription start site region 30244			1225 bp downstream
Tssr30245	transcription start site region 30245			1127 bp downstream
Tssr30246	transcription start site region 30246			949 bp downstream
Tssr30247	transcription start site region 30247			914 bp downstream
Tssr30248	transcription start site region 30248			814 bp downstream
Tssr30249	transcription start site region 30249			570 bp downstream
Tssr30250	transcription start site region 30250			337 bp downstream
Tssr30251	transcription start site region 30251			253 bp downstream
Tssr30252	transcription start site region 30252			240 bp upstream
Tssr30253	transcription start site region 30253			264 bp upstream
Tssr34246	transcription start site region 34246			305 bp downstream