Variant report

Variant	rs10516787
Chromosome Location	chr4:87920334-87920335
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87853540..87856355-chr4:87919742..87922210,3	MCF-7	breast:
2	chr4:87918478..87926067-chr4:87926181..87931063,13	MCF-7	breast:
3	chr4:87852916..87856061-chr4:87919493..87922700,3	K562	blood:
4	chr4:87858278..87859821-chr4:87918030..87920940,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163633	Chromatin interaction
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10015508	0.94[CEU][hapmap]
rs10489044	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13109968	1.00[AFR][1000 genomes]
rs13110344	1.00[AFR][1000 genomes]
rs13120839	0.94[CEU][hapmap]
rs13136338	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13136465	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13140610	0.83[AFR][1000 genomes]
rs13141697	0.89[CEU][hapmap]
rs17012114	0.88[CEU][hapmap]
rs17012130	0.88[CEU][hapmap]
rs17702203	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs33983129	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34140562	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34227282	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34709431	1.00[AFR][1000 genomes]
rs34745873	1.00[AFR][1000 genomes]
rs35182728	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35245331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35653846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35812445	1.00[AFR][1000 genomes]
rs35849753	0.83[AFR][1000 genomes]
rs35886751	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41525049	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs431836	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62305658	1.00[AFR][1000 genomes]
rs62306466	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs62306480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62306505	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62306508	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62306509	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62306510	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62306511	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62306514	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6811350	0.94[CEU][hapmap]
rs6853425	0.83[AFR][1000 genomes]
rs727143	0.94[CEU][hapmap]
rs767314	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv999098	chr4:87899091-88016048	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv537167	chr4:87899091-88016048	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87872600-87926200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr4:87892400-87920600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr4:87894600-87921000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr4:87899000-87920600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr4:87899000-87921200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:87899200-87920800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr4:87899200-87922800	Weak transcription	Osteobl	bone
8	chr4:87899200-87925800	Weak transcription	Hela-S3	cervix
9	chr4:87899200-87926600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:87900000-87924400	Weak transcription	NHEK	skin
11	chr4:87900200-87920800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:87903200-87926200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr4:87903600-87921000	Weak transcription	Primary T cells from cord blood	blood
14	chr4:87904200-87926200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr4:87904600-87921000	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr4:87910000-87921200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr4:87912800-87920600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr4:87914200-87927400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:87915800-87920600	Weak transcription	Brain Anterior Caudate	brain
20	chr4:87915800-87921000	Weak transcription	Small Intestine	intestine
21	chr4:87916000-87920600	Weak transcription	Ovary	ovary
22	chr4:87916000-87921000	Weak transcription	Stomach Mucosa	stomach
23	chr4:87916000-87926200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:87916200-87920800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr4:87916200-87921000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr4:87916200-87922800	Weak transcription	Lung	lung
27	chr4:87916200-87927200	Weak transcription	Esophagus	oesophagus
28	chr4:87916400-87920800	Weak transcription	Pancreas	Pancrea
29	chr4:87916400-87926200	Weak transcription	Fetal Intestine Large	intestine
30	chr4:87916400-87927200	Weak transcription	Gastric	stomach
31	chr4:87917800-87921600	Enhancers	Primary B cells from cord blood	blood
32	chr4:87917800-87921800	Enhancers	Primary B cells from peripheral blood	blood
33	chr4:87918000-87925400	Enhancers	Placenta	Placenta
34	chr4:87918600-87920600	Weak transcription	Fetal Intestine Small	intestine
35	chr4:87918800-87921600	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr4:87919000-87921200	Enhancers	Left Ventricle	heart
37	chr4:87919000-87921600	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr4:87919000-87921600	Enhancers	H1 Cell Line	embryonic stem cell
39	chr4:87919000-87927000	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr4:87919200-87921600	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr4:87919200-87921800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr4:87919200-87922000	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr4:87919200-87922200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr4:87919200-87927400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr4:87919400-87921600	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr4:87919400-87921600	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr4:87919400-87923000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr4:87919400-87925400	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr4:87919600-87920600	Weak transcription	Adipose Nuclei	Adipose
50	chr4:87919600-87920800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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