rs29872040 SNP Detail

Summary

• ID
  rs29872040
• 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
  Chr6:52204436 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              ATGGGGAAAA TCGCCAGTCA
  ACATCAAGAG GTGTTTGTCT TGCTGAGGGG TCACCTCGCC TAGTTTCTGG GCCCTGTATG
  AACCGCTCTG GTATCCTTCC CTCTTCTGTT TTTTCCTCCT ATTCCTCTAT CACCCCACTT
  TTTTTCCCCT TCCTTCCCAT TCCCCTTTTC CTTCTTTTGT TACTCCCCTC CCTCCCTTCC
  Y
  CTCTTTCCCC CCCGCCCCCA TCTCCAGCGC CCCTGCCTTG GTTATCCTTG AAACAGAACA
  ACAGAGATCC CATAGTCAAA CTACAGCTCA AGTCCAGTGC TACAAATTAA CCCGGGAGGA
  ACACTGGACA TTGACTTTAA TCTCATCCTT TGGTCAAATG GAGGATGTTA TTTTTCACCC
  CTTAGAATCT TTGGGAATAA                                            
  
  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	129X1/SvJ	A/J	DBA/2J
ss45871923	mCV22669414	ABI	CRAMUS_MOUSE	f	SNP	C	T	T
ss133191098	ENSMUSSNP3597470	ENSEMBL	ENSEMBL_Sanger	f	SNP	C	T	T
SNP Consensus Information
SNP					Consensus Type	129X1/SvJ	A/J	DBA/2J
rs29872040					SNP	C	T	T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr6:52204436 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Cpgi17431	CpG island 17431			1077 bp distal
Cpgi17432	CpG island 17432			1528 bp proximal
Gm57855	predicted gene, 57855			Intron
				Noncoding-Transcript-Variant
Gm68361	predicted gene, 68361			within coordinates
Hoxa9	homeobox A9			Intron
				Noncoding-Transcript-Variant
Rr630377	regulatory region 630377			777 bp distal
Rr630378	regulatory region 630378			255 bp distal
Rr630379	regulatory region 630379			97 bp distal
Rr630380	regulatory region 630380			within coordinates
Rr630381	regulatory region 630381			1963 bp proximal
Tssr61009	transcription start site region 61009			1592 bp upstream
Tssr61010	transcription start site region 61010			1500 bp upstream
Tssr61011	transcription start site region 61011			1294 bp upstream
Tssr61012	transcription start site region 61012			1260 bp upstream