Variant report

Variant	rs6551408
Chromosome Location	chr3:89270738-89270739
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11128070	0.83[AMR][1000 genomes]
rs12494816	0.83[AMR][1000 genomes]
rs6551398	0.83[AMR][1000 genomes]
rs6551399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6551405	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap]
rs6767230	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes]
rs6779710	1.00[GIH][hapmap]
rs6790662	0.83[AMR][1000 genomes]
rs6793981	0.83[AMR][1000 genomes]
rs6800287	0.83[AMR][1000 genomes]
rs6804377	1.00[GIH][hapmap]
rs6807840	0.83[AMR][1000 genomes]
rs7426466	0.83[AMR][1000 genomes]
rs7632543	0.83[AMR][1000 genomes]
rs7636079	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7640398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7652840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9310108	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9810701	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes]
rs9811026	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes]
rs9814718	0.83[AMR][1000 genomes]
rs9828822	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes]
rs9829805	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9839955	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9859735	1.00[ASW][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes]
rs9860030	1.00[ASW][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9861649	0.83[TSI][hapmap];0.83[AMR][1000 genomes]
rs9868041	0.83[AMR][1000 genomes]
rs9883722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834760	chr3:89085529-89299398	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv997874	chr3:89188275-89279573	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv437866	chr3:89247881-89480265	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv2757001	chr3:89260495-89271087	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
5	esv2759160	chr3:89260495-89271087	Weak transcription Flanking Active TSS Enhancers Active TSS	n/a	n/a	inside rSNPs	diseases
6	esv3379291	chr3:89270662-89272710	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89263600-89277000	Weak transcription	Brain Germinal Matrix	brain
2	chr3:89266200-89272200	Weak transcription	Fetal Brain Male	brain
3	chr3:89266400-89277800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:89270200-89270800	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr3:89270400-89271400	Enhancers	Fetal Brain Female	brain

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