Variant report

Variant	rs56999910
Chromosome Location	chr6:87857396-87857397
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:87856173..87858618-chr6:87861857..87866815,6	MCF-7	breast:
2	chr6:87855485..87860129-chr6:87863534..87866508,4	K562	blood:

Variant related genes	Relation type
ENSG00000188994	Chromatin interaction
ENSG00000272008	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10488045	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10498960	0.88[EUR][1000 genomes]
rs16878473	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16878570	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16878622	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16878638	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16878712	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16878713	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16878729	0.91[EUR][1000 genomes]
rs16878734	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs16878736	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs16878809	0.82[EUR][1000 genomes]
rs16878856	0.88[EUR][1000 genomes]
rs16878863	0.88[EUR][1000 genomes]
rs16878942	0.88[EUR][1000 genomes]
rs1925693	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs41273281	0.88[EUR][1000 genomes]
rs41273283	0.88[EUR][1000 genomes]
rs55647962	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs56096438	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56193950	0.88[EUR][1000 genomes]
rs56678817	0.88[EUR][1000 genomes]
rs56743579	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56847789	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56947685	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57043501	0.88[EUR][1000 genomes]
rs57116567	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57217108	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57421283	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57607342	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57962992	0.97[EUR][1000 genomes]
rs58032842	1.00[AMR][1000 genomes]
rs58124219	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58269367	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58327183	0.88[EUR][1000 genomes]
rs58474842	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58576901	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58731649	0.88[EUR][1000 genomes]
rs58735749	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58751410	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59034165	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59138817	0.88[EUR][1000 genomes]
rs59150116	0.88[EUR][1000 genomes]
rs59214037	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59344869	0.97[AFR][1000 genomes]
rs59495279	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59654654	0.87[EUR][1000 genomes]
rs59875769	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59964119	1.00[AMR][1000 genomes]
rs60074363	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60285195	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60544317	0.85[EUR][1000 genomes]
rs60746078	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60845773	0.88[EUR][1000 genomes]
rs60985818	0.94[EUR][1000 genomes]
rs60994855	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61047847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61379368	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61705669	0.88[EUR][1000 genomes]
rs73483720	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483728	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483743	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483749	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483752	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483758	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483760	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483765	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483769	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483771	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73483774	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483790	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483796	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73483799	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73485808	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73485811	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs73485813	0.94[EUR][1000 genomes]
rs73485815	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs73485820	0.88[EUR][1000 genomes]
rs73485826	0.88[EUR][1000 genomes]
rs73485828	0.88[EUR][1000 genomes]
rs73485831	0.88[EUR][1000 genomes]
rs73485848	0.88[EUR][1000 genomes]
rs73485849	0.88[EUR][1000 genomes]
rs73499768	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73499770	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73499771	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73499800	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73499802	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73501611	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73501620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73501623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73501629	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73501632	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73501636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73501638	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73501641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73501658	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73501662	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73751992	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024751	chr6:87433199-87908721	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv604114	chr6:87816905-87906053	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv2758067	chr6:87817883-87992957	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	esv2759453	chr6:87817883-87992957	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	esv3366503	chr6:87849282-87862940	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:87856400-87860800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr6:87856600-87860800	Weak transcription	GM12878-XiMat	blood

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