rs39023990 SNP Detail

Summary

• ID
  rs39023990
• Variation Type
  SNP
• Alleles
  G/T

• 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
  Chr3:123028640 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                        TTCCAATACT GGCACAGAAT TCTACAGTTC CATGTTAACA
  TTTGATGAAA AGTTTTTTAC TTTCTTGCTT TCTAACTTCA TTTTAGCTGA ATGCCAGTTC
  K
  AATCTAAATG AGATTATGGG TATTATGCTA AACTGAAAAT CAATCTAATG TGACAAAGAT
  AAACAACGTA TTAAATAGCT ATTAGGTGCA CCAGAAAGC                       
  
  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	LG/J	MOLF/EiJ	MSM/Ms	NOD/ShiLtJ	NZW/LacJ	PWD/PhJ	SM/J	WSB/EiJ
ss51024636	NES13910109	PERLEGEN	MM_PANEL2	f	SNP	G	T	G	T	G	T	G	T	G	G		G		G	G	T		G
ss135760875	ENSMUSSNP4357815	ENSEMBL	ENSEMBL_Sanger	f	SNP		T											T
ss320918233	CHEV_3_122937909	CHEVERUD	SCREENING_POP	f	SNP											G						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	LG/J	MOLF/EiJ	MSM/Ms	NOD/ShiLtJ	NZW/LacJ	PWD/PhJ	SM/J	WSB/EiJ
rs39023990					SNP	G	T	G	T	G	T	G	T	G	G	G	G	T	G	G	T	T	G

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
ss51024636	NES13910109	PERLEGEN	MM_PANEL	f	SNP	G/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr3:123028640 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Cpgi13775	CpG island 13775			1001 bp proximal
Rr584473	regulatory region 584473			120 bp distal
Rr584474	regulatory region 584474			292 bp distal
Rr584475	regulatory region 584475			1095 bp proximal
Rr584476	regulatory region 584476			1929 bp proximal
Synpo2	synaptopodin 2			Intron
				Noncoding-Transcript-Variant
Tssr35497	transcription start site region 35497			1120 bp downstream
Tssr35498	transcription start site region 35498			1143 bp downstream