Variant report

Variant	rs9489698
Chromosome Location	chr6:119703776-119703777
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1112369	0.84[ASN][1000 genomes]
rs11153828	0.84[ASN][1000 genomes]
rs12660903	0.81[ASN][1000 genomes]
rs12661049	0.81[ASN][1000 genomes]
rs12665340	0.81[ASN][1000 genomes]
rs12665378	0.95[ASN][1000 genomes]
rs1288080	0.86[ASN][1000 genomes]
rs1288081	0.86[ASN][1000 genomes]
rs1318271	0.84[ASN][1000 genomes]
rs1341490	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs1353864	0.84[ASN][1000 genomes]
rs1392090	0.84[ASN][1000 genomes]
rs1499569	0.84[ASN][1000 genomes]
rs1553171	0.83[ASN][1000 genomes]
rs17081283	0.84[ASN][1000 genomes]
rs17081375	0.81[ASN][1000 genomes]
rs17081423	0.89[ASW][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs1813894	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1875056	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1963055	0.84[ASN][1000 genomes]
rs2036256	0.81[ASN][1000 genomes]
rs2066353	0.84[ASN][1000 genomes]
rs2153823	0.95[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap]
rs2185752	0.84[ASN][1000 genomes]
rs2185754	0.83[ASN][1000 genomes]
rs3891962	0.90[ASN][1000 genomes]
rs4142250	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4142806	0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs4551205	0.81[ASN][1000 genomes]
rs4613849	0.81[ASN][1000 genomes]
rs4945637	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4945640	0.84[ASN][1000 genomes]
rs4945642	0.82[ASN][1000 genomes]
rs4946417	0.90[ASN][1000 genomes]
rs4946419	0.81[ASN][1000 genomes]
rs4946420	0.84[ASN][1000 genomes]
rs4946423	0.83[ASN][1000 genomes]
rs4946424	0.81[ASN][1000 genomes]
rs4946426	0.81[ASN][1000 genomes]
rs4946427	0.94[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs55901595	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56081039	0.81[ASN][1000 genomes]
rs56091753	0.83[ASN][1000 genomes]
rs56346325	0.81[ASN][1000 genomes]
rs6913097	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs6918211	0.84[ASN][1000 genomes]
rs6923080	0.84[ASN][1000 genomes]
rs6935310	0.85[ASN][1000 genomes]
rs6940248	0.81[ASN][1000 genomes]
rs742962	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7452780	0.81[ASN][1000 genomes]
rs7745025	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs7757317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7768102	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9320694	0.89[ASW][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs9385073	0.84[ASN][1000 genomes]
rs9387652	0.84[ASN][1000 genomes]
rs9481911	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9481922	0.87[ASN][1000 genomes]
rs9481924	0.90[ASN][1000 genomes]
rs9481927	0.90[ASN][1000 genomes]
rs9481929	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9481930	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9481931	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9481933	0.84[ASN][1000 genomes]
rs9481936	0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.81[ASN][1000 genomes]
rs9489709	0.85[ASN][1000 genomes]
rs9489710	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9489714	0.90[ASN][1000 genomes]
rs9489715	0.90[ASN][1000 genomes]
rs9489716	0.90[ASN][1000 genomes]
rs9489717	0.90[ASN][1000 genomes]
rs9489718	0.87[ASN][1000 genomes]
rs9489719	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9489720	0.84[ASN][1000 genomes]
rs9489723	0.83[ASN][1000 genomes]
rs9489724	0.83[ASN][1000 genomes]
rs9489725	0.81[ASN][1000 genomes]
rs9489727	0.81[ASN][1000 genomes]
rs9489728	0.81[ASN][1000 genomes]
rs9489729	0.81[ASN][1000 genomes]
rs9489731	0.81[ASN][1000 genomes]
rs9489733	0.95[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs9885803	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025995	chr6:119407742-119709548	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv3447598	chr6:119558591-120119384	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv3389526	chr6:119558598-120190087	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9489698	PLXND1	trans	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119689600-119720600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:119703000-119709400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr6:119703400-119703800	Enhancers	HepG2	liver
4	chr6:119703600-119704000	ZNF genes & repeats	Primary B cells from cord blood	blood

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