rs16805539 SNP Detail

Summary

• ID
  rs16805539
• Variation Type
  SNP
• Alleles
  C/T

• Created in dbSNP Build
  123
• Last Updated in dbSNP Build
  137
• Additional Resources
  JBrowse Genome Browser | Ensembl SNPView | UCSC Browser | Alliance Variant
  

Genome Location and Flanking Sequence

• Location
  Chr7:98305953 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                        GAGAAACGAG CACTCAAAAG CCTCCATTCT TCCTGTCCCT
  TTTCCTCTGC CTTTTGAAAG GAAAGGGCGG ACAACGCGGG TCCTAGTGGG AGTTGTAGTC
  Y
  GAGTCCAACC TCGCTCCTCT TTCTCTTGCT GCTTGCTGGT CACATGCGCA AGGAAGTCTG
  GGAGTGTAGT TCCTTTCGGC TTCTACATTA CCCTCCAGT                       
  
  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	129/Sv	129S1/SvImJ	A/HeJ	A/J	AKR/J	B10.D2-Hc<0> H2 H2-T18/oSnJ	BALB/cByJ	BALB/cJ	BTBR T<+> Itpr3/J	BUB	C3H/HeJ	C57BL/6J	CAST/EiJ	DBA/2J	FVB	FVB/NJ	KK/HlJ	LP/J	MOLF	MOLF/EiJ	MRL/MpJ	NOD/ShiLtJ	NZB/BlNJ	NZW/Lac	NZW/LacJ	PERA	PWD/PhJ	SM/J	SPRET/EiJ	WSB/EiJ
ss24760397	Emsy_JC10354_2	ROCHEBIO	RPAMM	f	SNP	C		C	C	C	C	C	C		C	T	C	T	T	C			C	T		C		C	C		T		C	C
ss61040536	NES16091015	PERLEGEN	MM_PANEL2	f	SNP		C		C	C		C		C		T		T	T		C	C			T		C			C		T			C
SNP Consensus Information
SNP					Consensus Type	129/Sv	129S1/SvImJ	A/HeJ	A/J	AKR/J	B10.D2-Hc<0> H2 H2-T18/oSnJ	BALB/cByJ	BALB/cJ	BTBR T<+> Itpr3/J	BUB	C3H/HeJ	C57BL/6J	CAST/EiJ	DBA/2J	FVB	FVB/NJ	KK/HlJ	LP/J	MOLF	MOLF/EiJ	MRL/MpJ	NOD/ShiLtJ	NZB/BlNJ	NZW/Lac	NZW/LacJ	PERA	PWD/PhJ	SM/J	SPRET/EiJ	WSB/EiJ
rs16805539					SNP	C	C	C	C	C	C	C	C	C	C	T	C	T	T	C	C	C	C	T	T	C	C	C	C	C	T	T	C	C	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
ss61040536	NES16091015	PERLEGEN	MM_PANEL	f	SNP	C/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr7:98305953 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
4930558N01Rik	RIKEN cDNA 4930558N01 gene			within coordinates
Emsy	EMSY, BRCA2-interacting transcriptional repressor			mRNA-UTR
				Noncoding-Transcript-Variant
Rr368380	regulatory region 368380			within coordinates
Rr651647	regulatory region 651647			585 bp distal
Rr651648	regulatory region 651648			211 bp distal
Rr651649	regulatory region 651649			403 bp distal
Rr651650	regulatory region 651650			within coordinates
Rr651651	regulatory region 651651			115 bp distal
Rr651652	regulatory region 651652			184 bp proximal
Tssr68028	transcription start site region 68028			893 bp downstream
Tssr68029	transcription start site region 68029			587 bp downstream
Tssr68030	transcription start site region 68030			545 bp downstream
Tssr68031	transcription start site region 68031			155 bp upstream
Tssr73641	transcription start site region 73641			222 bp upstream
Tssr73642	transcription start site region 73642			146 bp upstream
Tssr73643	transcription start site region 73643			46 bp downstream