rs28147109 SNP Detail

Summary

• ID
  rs28147109
• Variation Type
  SNP
• Alleles
  G/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
  Chr4:107226699 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                        TCCAGCCCCA GTTCCCTTGT CTTTTCTTGT TTTTCCTTTC
  CCTGCCATCC ATTTAAAATT GCAGATGGGA ATTGTGACTG GTATTAAAAA AAAAGTCTAA
  K
  CTAGCTAGTT GTAGCACATT CTTATAATCC AACTCTTAGG AGAGTGTAGC AAGAGGCTCC
  AGAGATCCTG GCTAGCCTGG GATACATATA GAGAAACTA                       
  
  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	129X1/SvJ	A/J	AKR/J	BALB/cByJ	BTBR T<+> Itpr3/J	C3H/HeJ	CAST/EiJ	DBA/2J	FVB/NJ	KK/HlJ	LG/J	MOLF/EiJ	NOD/ShiLtJ	NZW/LacJ	PWD/PhJ	SM/J	WSB/EiJ
ss38285733	NES09488759	PERLEGEN	MM_PANEL2	f	SNP	T		T	G	T	G	T	G	G	T	T		G	T	G	G		T
ss147178179	ENSMUSSNP4410367	ENSEMBL	ENSEMBL_Sanger	f	SNP		T	T						G
ss321247973	CHEV_4_107042107	CHEVERUD	SCREENING_POP	f	SNP												T					G
SNP Consensus Information
SNP					Consensus Type	129S1/SvImJ	129X1/SvJ	A/J	AKR/J	BALB/cByJ	BTBR T<+> Itpr3/J	C3H/HeJ	CAST/EiJ	DBA/2J	FVB/NJ	KK/HlJ	LG/J	MOLF/EiJ	NOD/ShiLtJ	NZW/LacJ	PWD/PhJ	SM/J	WSB/EiJ
rs28147109					SNP	T	T	T	G	T	G	T	G	G	T	T	T	G	T	G	G	G	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
ss38285733	NES09488759	PERLEGEN	MM_PANEL	f	SNP	G/T

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr4:107226699 () rs orientation: forward

Symbol	Name	Transcript	Protein	Function Class	Allele	Residue	Codon Position	AA Position
Cpgi14540	CpG island 14540			1109 bp distal
Ndc1	NDC1 transmembrane nucleoporin			Intron
				Noncoding-Transcript-Variant
Rr367664	regulatory region 367664			1615 bp downstream
Rr596979	regulatory region 596979			1708 bp distal
Rr596981	regulatory region 596981			823 bp distal
Rr596982	regulatory region 596982			1641 bp distal
Rr596983	regulatory region 596983			1197 bp distal
Tssr38245	transcription start site region 38245			1748 bp downstream
Tssr38246	transcription start site region 38246			1689 bp downstream
Tssr38247	transcription start site region 38247			1464 bp downstream
Tssr38248	transcription start site region 38248			1445 bp downstream
Tssr38249	transcription start site region 38249			1430 bp downstream
Tssr38250	transcription start site region 38250			1418 bp downstream
Tssr38251	transcription start site region 38251			1162 bp downstream