Variant report

Variant	rs58474842
Chromosome Location	chr6:87895618-87895619
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	chr6:87863892..87866785-chr6:87895133..87897742,3	MCF-7	breast:
2	chr6:87891478..87892996-chr6:87895079..87898075,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272008	Chromatin interaction
ENSG00000188994	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10488045	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10498960	0.94[EUR][1000 genomes]
rs16878473	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16878570	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16878622	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16878638	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16878712	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16878713	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16878729	0.97[EUR][1000 genomes]
rs16878734	1.00[EUR][1000 genomes]
rs16878736	1.00[EUR][1000 genomes]
rs16878809	0.88[EUR][1000 genomes]
rs16878856	0.94[EUR][1000 genomes]
rs16878863	0.94[EUR][1000 genomes]
rs16878942	0.94[EUR][1000 genomes]
rs1925693	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41273281	0.94[EUR][1000 genomes]
rs41273283	0.94[EUR][1000 genomes]
rs55647962	0.91[EUR][1000 genomes]
rs56096438	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56193950	0.94[EUR][1000 genomes]
rs56678817	0.94[EUR][1000 genomes]
rs56743579	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56847789	0.91[EUR][1000 genomes]
rs56947685	0.86[AMR][1000 genomes]
rs56999910	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57043501	0.94[EUR][1000 genomes]
rs57116567	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57217108	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57421283	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57607342	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57962992	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58032842	0.86[AMR][1000 genomes]
rs58124219	0.82[EUR][1000 genomes]
rs58269367	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58327183	0.94[EUR][1000 genomes]
rs58576901	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58731649	0.94[EUR][1000 genomes]
rs58735749	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58751410	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59034165	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59138817	0.94[EUR][1000 genomes]
rs59150116	0.94[EUR][1000 genomes]
rs59214037	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59495279	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59654654	0.94[EUR][1000 genomes]
rs59875769	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59964119	0.86[AMR][1000 genomes]
rs60074363	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60285195	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60544317	0.91[EUR][1000 genomes]
rs60746078	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs60845773	0.94[EUR][1000 genomes]
rs60985818	0.87[EUR][1000 genomes]
rs60994855	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61047847	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61379368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61705669	0.94[EUR][1000 genomes]
rs73483720	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73483728	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73483743	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73483749	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73483752	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73483758	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73483760	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73483765	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73483769	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73483771	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs73483774	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73483790	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73483796	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73483799	1.00[EUR][1000 genomes]
rs73485808	1.00[EUR][1000 genomes]
rs73485811	1.00[EUR][1000 genomes]
rs73485813	1.00[EUR][1000 genomes]
rs73485815	1.00[EUR][1000 genomes]
rs73485820	0.94[EUR][1000 genomes]
rs73485826	0.94[EUR][1000 genomes]
rs73485828	0.94[EUR][1000 genomes]
rs73485831	0.94[EUR][1000 genomes]
rs73485848	0.94[EUR][1000 genomes]
rs73485849	0.94[EUR][1000 genomes]
rs73499768	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73499770	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73499771	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73499800	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73499802	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73501611	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73501620	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73501623	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73501629	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73501632	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73501636	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73501638	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73501641	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73501658	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73501662	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73751992	0.83[AFR][1000 genomes];0.86[AMR][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	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

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:87867000-87915600	Weak transcription	NH-A	brain
2	chr6:87868000-87933000	Weak transcription	Hela-S3	cervix
3	chr6:87874400-87924200	Weak transcription	Fetal Kidney	kidney
4	chr6:87875000-87910400	Weak transcription	K562	blood
5	chr6:87879800-87923000	Weak transcription	Esophagus	oesophagus
6	chr6:87880600-87906000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:87881400-87926200	Weak transcription	Liver	Liver
8	chr6:87881800-87909400	Weak transcription	Fetal Brain Male	brain
9	chr6:87882000-87899400	Weak transcription	Duodenum Mucosa	Duodenum
10	chr6:87882200-87896400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:87883400-87926200	Weak transcription	Fetal Lung	lung
12	chr6:87883800-87897600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr6:87884000-87906000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:87884000-87964400	Weak transcription	NHEK	skin
15	chr6:87884600-87897600	Weak transcription	Colon Smooth Muscle	Colon
16	chr6:87884600-87899400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr6:87887800-87896800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:87888200-87964200	Weak transcription	HSMMtube	muscle
19	chr6:87889800-87926400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:87890200-87905800	Weak transcription	Brain Hippocampus Middle	brain
21	chr6:87890200-87906000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr6:87890200-87909400	Weak transcription	Brain Substantia Nigra	brain
23	chr6:87890400-87895800	Weak transcription	Brain Anterior Caudate	brain
24	chr6:87890400-87898400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr6:87890800-87909600	Weak transcription	Brain Germinal Matrix	brain
26	chr6:87890800-87910000	Weak transcription	Right Ventricle	heart
27	chr6:87890800-87933000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:87891000-87902800	Weak transcription	Pancreas	Pancrea
29	chr6:87891000-87920000	Weak transcription	Placenta	Placenta
30	chr6:87891000-87956000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:87891200-87895800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr6:87891200-87897400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr6:87891200-87897600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr6:87891200-87913000	Weak transcription	Lung	lung
35	chr6:87891200-87929200	Weak transcription	Thymus	Thymus
36	chr6:87891400-87912800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr6:87891400-87932600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:87892000-87896200	Weak transcription	Fetal Muscle Leg	muscle
39	chr6:87892000-87896400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr6:87892000-87897200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr6:87892000-87897400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr6:87892000-87923000	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr6:87892400-87899400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr6:87892800-87895800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr6:87892800-87896400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr6:87892800-87896400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
47	chr6:87892800-87896600	Strong transcription	Dnd41	blood
48	chr6:87892800-87901200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr6:87892800-87921600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr6:87893000-87896000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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