Variant report

Variant	rs9990553
Chromosome Location	chr4:62707491-62707492
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10004644	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10021525	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10021694	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10446786	0.89[CHB][hapmap]
rs12641643	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12651006	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1376307	0.84[JPT][hapmap]
rs1551096	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17292058	0.94[CEU][hapmap];0.80[GIH][hapmap];0.88[TSI][hapmap]
rs1839614	0.90[EUR][1000 genomes]
rs1868789	0.90[EUR][1000 genomes]
rs2013374	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2122641	0.91[EUR][1000 genomes]
rs2122642	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2345041	1.00[CEU][hapmap];0.95[GIH][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs34764145	0.88[EUR][1000 genomes]
rs35946366	0.91[EUR][1000 genomes]
rs3860623	0.89[CEU][hapmap];0.80[GIH][hapmap];0.88[TSI][hapmap]
rs4493573	0.84[JPT][hapmap]
rs4860436	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6551658	0.91[EUR][1000 genomes]
rs6551659	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6551660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6832443	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6845019	1.00[CEU][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs7437698	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7656882	0.84[JPT][hapmap]
rs7665141	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7695134	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs990640	1.00[CEU][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461377	chr4:62368762-62883431	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv594328	chr4:62368762-62883431	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv829949	chr4:62615637-62761629	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv428760	chr4:62649399-62824542	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:62706400-62707800	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr4:62706400-62708000	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr4:62706600-62707800	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr4:62706600-62708600	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr4:62706600-62708800	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr4:62706800-62707800	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr4:62706800-62708200	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr4:62707000-62707800	Enhancers	H1 Cell Line	embryonic stem cell
9	chr4:62707000-62708800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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