rs3656340 SNP Detail

Summary

• ID
  rs3656340
• Variation Type
  SNP
• Alleles
  A/G

• Created in dbSNP Build
  107
• Last Updated in dbSNP Build
  137
• Additional Resources
  JBrowse Genome Browser | Ensembl SNPView | UCSC Browser
  

Genome Location and Flanking Sequence

• Location
  Chr1:171076017 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              GTGGTCCCCA GAAAGTCAAG
  GCAGAGGCTT GGTCCCCTTA CCCTCTACAG CCACCTCTCC TTTTCTGGGC CTTTCTTCCT
  GAGATATAGT TTAAACACAA AATGTGGTGA TGATGGGAGG GGGGGTTCCT CATTTTTGTG
  TTAATCCATC CTATGTGAAG TCAAGACAGA CTCTAGCTTG CTTAGCCCTG GGGGTAGTTC
  R
  AGCAGGAACT GGGATGAGAA CTCTTGGGGG GCTACCTAGG ACACTGCATC TTTTGTGCCT
  TCTCCTTCTG CCAGCACCCC CCTCCCCACG TGCTGTAGCT GCCACTCTGT GGCCCTTTGT
  CTTTCACTGC TTAGTCACAC TCTTTGTTCT CAGCTCAGAT GGGGGGATGG AAAGGGGTAA
  TAAGAGTATC CTGGTGACAG                                            
  
  R = A/G
  

  
  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	C57BL/6J	CAST/EiJ	DBA/2J	FVB/NJ	KK/HlJ	LG/J	MOLF/EiJ	NOD/ShiLtJ	NZW/LacJ	PWD/PhJ	SM/J	WSB/EiJ
ss5032242	WI_WGS_1_172527009	WI	MOUSE	f	SNP	G							A
ss45060636	mCV23616715	ABI	CRAMUS_MOUSE	f	SNP		G	A					A		A
ss49750549	NES13032447	PERLEGEN	MM_PANEL2	f	SNP	G		A	A	G	A	G		A	A	A	A		A	A	A	A		G
ss146158261	ENSMUSSNP5673541	ENSEMBL	ENSEMBL_Sanger	f	SNP		G	A							A
ss320117552	CHEV_1_173178579	CHEVERUD	SCREENING_POP	f	SNP													G					A
SNP Consensus Information
SNP					Consensus Type	129S1/SvImJ	129X1/SvJ	A/J	AKR/J	BALB/cByJ	BTBR T<+> Itpr3/J	C3H/HeJ	C57BL/6J	CAST/EiJ	DBA/2J	FVB/NJ	KK/HlJ	LG/J	MOLF/EiJ	NOD/ShiLtJ	NZW/LacJ	PWD/PhJ	SM/J	WSB/EiJ
rs3656340					SNP	G	G	A	A	G	A	G	A	A	A	A	A	G	A	A	A	A	A	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
ss49750549	NES13032447	PERLEGEN	MM_PANEL	f	SNP	A/G

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr1:171076017 () rs orientation: forward

Symbol	Name	Function Class
Adamts4	ADAM metallopeptidase with thrombospondin type 1 motif 4	1973 bp upstream
Cpgi1016	CpG island 1016	928 bp distal
Gm71631	predicted gene, 71631	within coordinates
Ndufs2	NADH:ubiquinone oxidoreductase core subunit S2	within coordinates
Rr372446	regulatory region 372446	1 bp downstream
Rr423259	regulatory region 423259	836 bp distal
Rr423260	regulatory region 423260	1288 bp distal
Rr423261	regulatory region 423261	761 bp distal
Rr423262	regulatory region 423262	165 bp proximal
Rr423263	regulatory region 423263	1381 bp proximal
Rr423264	regulatory region 423264	1661 bp proximal
Rr423265	regulatory region 423265	1986 bp proximal
Tssr10000	transcription start site region 10000	1071 bp downstream
Tssr10001	transcription start site region 10001	1968 bp upstream
Tssr15023	transcription start site region 15023	1327 bp upstream