rs6380539 SNP Detail

Summary

• ID
  rs6380539
• Variation Type
  SNP
• Alleles
  C/T

• Created in dbSNP Build
  116
• Last Updated in dbSNP Build
  137
• Additional Resources
  JBrowse Genome Browser | Ensembl SNPView | UCSC Browser
  

Genome Location and Flanking Sequence

• Location
  Chr2:102490787 (GRCm39)
• SNP Orientation to the Genome
  forward

• SNP Reference Flanking Sequence

                                              TCCTTGGTTC TGGCATTTTC
  TGGGGGCATG TTTAATAGAA ATCAAACTCC GCCAACTTTC GGTGAGGTGG TGGGTGGTGA
  GTGGAAAGAT GGTGTTTAAA GCCAGACATC GAGATTCCAA CCTCAGACAA AGAAAATACG
  TCTAAATCTG CCCATCTTCA TCCAAGAGAA AGAACCTATT CATCTATTTC TCTCATCCCA
  Y
  GAATCTTTCC AAACATGCCT CGCATCTTGT CTGACATAAA ATTTCTTCAC ATTGCTTATT
  TACCAGTGTG GACCTTTGGA GTGGTTACTT ATCAGAAAAG GTGCTCTACT TTGGTGCTTG
  TGTGCAAGGA AGGCAGTATC ATGTGCTCAA ACATATCTCT AGAATTACAT ATTAGGAGCC
  CACATGACTT AACATCAGCA                                            
  
  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	A/J	C57BL/6J	CZECHII/EiJ	LG/J	SM/J
ss8786693	WI_WGS_2_103482800	WI	MOUSE	f	SNP		C	T
ss45346853	mCV23733510	ABI	CRAMUS_MOUSE	f	SNP	T	C
ss147119793	ENSMUSSNP5097463	ENSEMBL	ENSEMBL_Sanger	f	SNP	T
ss320439909	CHEV_2_102500599	CHEVERUD	SCREENING_POP	f	SNP				T	C
SNP Consensus Information
SNP					Consensus Type	A/J	C57BL/6J	CZECHII/EiJ	LG/J	SM/J
rs6380539					SNP	T	C	T	T	C

Gene/Marker
Associations
and
Function
Classes

MGI genes/markers associated with the SNP

Location: Chr2:102490787 () rs orientation: forward

Symbol	Name	Function Class
Cpgi11978	CpG island 11978	687 bp distal
Gm57687	predicted gene, 57687	within coordinates
Rr561713	regulatory region 561713	1773 bp distal
Rr561714	regulatory region 561714	1630 bp distal
Rr561715	regulatory region 561715	1151 bp distal
Rr561716	regulatory region 561716	366 bp distal
Rr561717	regulatory region 561717	1855 bp proximal
Slc1a2	solute carrier family 1 (glial high affinity glutamate transporter), member 2	within coordinates
Tssr19100	transcription start site region 19100	1862 bp downstream
Tssr19101	transcription start site region 19101	1773 bp downstream
Tssr19102	transcription start site region 19102	1747 bp downstream
Tssr19103	transcription start site region 19103	1700 bp downstream
Tssr19104	transcription start site region 19104	1678 bp downstream
Tssr19105	transcription start site region 19105	1608 bp downstream
Tssr19106	transcription start site region 19106	1590 bp downstream
Tssr19107	transcription start site region 19107	1570 bp downstream
Tssr19108	transcription start site region 19108	1534 bp downstream
Tssr19109	transcription start site region 19109	1492 bp downstream
Tssr19110	transcription start site region 19110	1210 bp downstream