Variant report

Variant	rs6780268
Chromosome Location	chr3:90166686-90166687
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 111 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs11128081	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11917293	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11918512	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11920640	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11924267	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11926877	1.00[EUR][1000 genomes]
rs12106840	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12107978	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12107987	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1402829	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1402830	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1402831	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1521801	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1521805	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1915788	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1996783	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1996784	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2204078	0.90[AFR][1000 genomes]
rs2204079	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs55719953	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs55726199	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56257056	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57237979	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57268246	1.00[EUR][1000 genomes]
rs57530512	1.00[EUR][1000 genomes]
rs57742239	1.00[EUR][1000 genomes]
rs57945456	1.00[EUR][1000 genomes]
rs57953580	1.00[EUR][1000 genomes]
rs58442773	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58444511	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58944054	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58977999	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59147897	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59297554	1.00[EUR][1000 genomes]
rs59437743	1.00[EUR][1000 genomes]
rs59649185	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59827615	1.00[EUR][1000 genomes]
rs60834002	1.00[EUR][1000 genomes]
rs61037499	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6551449	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6770945	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6772724	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6782153	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6787044	0.94[AFR][1000 genomes]
rs6789628	1.00[EUR][1000 genomes]
rs6789752	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6793888	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6798554	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6800191	0.90[AFR][1000 genomes]
rs6800705	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6804358	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72921826	1.00[EUR][1000 genomes]
rs72921827	1.00[EUR][1000 genomes]
rs72921828	1.00[EUR][1000 genomes]
rs72921836	0.83[AFR][1000 genomes]
rs72921847	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72921850	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72921853	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72921855	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72921864	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72921866	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72921873	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72921876	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72923735	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72923736	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72923737	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72923739	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72923741	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72923755	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72923757	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72923762	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72923764	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72923765	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72923767	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72923770	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72923771	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72923776	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72923777	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72923779	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72923781	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72923783	0.95[AFR][1000 genomes]
rs72923784	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72923786	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72923794	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72925705	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72925712	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73846008	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73849912	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7610765	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7619437	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7626330	0.95[AFR][1000 genomes]
rs7627792	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7637541	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7648089	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7648275	0.95[AFR][1000 genomes]
rs7648900	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs939741	0.89[AFR][1000 genomes]
rs9818065	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008018	chr3:89382031-90254063	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv536639	chr3:89382031-90254063	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1010932	chr3:89424428-90192503	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv530024	chr3:89548440-90304841	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1008130	chr3:89837442-90192503	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1010796	chr3:89870548-90192503	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1013598	chr3:89879377-90192503	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv536642	chr3:89879377-90192503	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv590966	chr3:89904882-90199759	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv590968	chr3:89979895-90199759	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv590970	chr3:89987871-90441306	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1010292	chr3:90057464-90192503	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv967037	chr3:90150991-90195660	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:90163200-90167800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:90164200-90167200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:90164200-90167800	Strong transcription	HUES6 Cell Line	embryonic stem cell
4	chr3:90166000-90169800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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