Variant report

Variant	rs6804377
Chromosome Location	chr3:89271087-89271088
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11128070	0.94[ASN][1000 genomes]
rs12494816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13077331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6551395	0.92[JPT][hapmap]
rs6551398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6551406	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6551408	1.00[GIH][hapmap]
rs6767230	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6779710	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6790662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6793981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6797343	0.91[JPT][hapmap]
rs6800287	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6807840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7373480	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7426466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7426527	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7427745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7427935	1.00[CEU][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7622368	1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7632543	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7633559	0.91[JPT][hapmap]
rs7651124	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.93[EUR][1000 genomes]
rs9310113	0.92[JPT][hapmap]
rs952815	0.82[MEX][hapmap]
rs9810701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9811026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9814718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9815137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9828822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9834135	0.81[ASN][1000 genomes]
rs9835264	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9859735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9860030	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9861649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9868041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[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:4 , 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	chr3:89270400-89271400	Enhancers	Fetal Brain Female	brain

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