Variant report

Variant	rs7853377
Chromosome Location	chr9:86552205-86552206
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:86551919..86553846-chr9:86578831..86580851,2	K562	blood:
2	chr9:86551370..86553240-chr9:86557554..86559080,2	MCF-7	breast:
3	chr9:86548981..86555040-chr9:86588754..86596573,13	MCF-7	breast:
4	chr9:86550607..86552795-chr9:86930808..86933198,2	MCF-7	breast:
5	chr9:86551814..86552501-chr9:86930023..86930750,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165119	Chromatin interaction
ENSG00000178966	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10114889	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs10115699	0.81[EUR][1000 genomes]
rs10780645	0.86[CEU][hapmap]
rs12682981	0.83[CEU][hapmap]
rs13289566	0.82[EUR][1000 genomes]
rs13290882	0.82[CEU][hapmap]
rs13295313	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13296528	0.83[CEU][hapmap]
rs167203	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1831757	0.82[CEU][hapmap]
rs1982151	0.87[CEU][hapmap]
rs2576362	0.82[CEU][hapmap]
rs2780103	0.82[CEU][hapmap]
rs28521174	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs296886	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs296887	0.88[CEU][hapmap]
rs296888	0.87[CEU][hapmap]
rs296889	0.87[CEU][hapmap]
rs296893	0.88[CEU][hapmap]
rs296894	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs3180887	0.82[CEU][hapmap]
rs4147132	0.82[CEU][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4147133	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs4535826	0.81[AFR][1000 genomes]
rs6559742	0.93[CEU][hapmap]
rs6559751	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs7020300	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs7033292	0.88[CEU][hapmap]
rs7853235	0.92[CEU][hapmap]
rs7855177	0.93[CEU][hapmap]
rs7861065	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7869321	0.83[CEU][hapmap]
rs930340	0.93[CEU][hapmap]
rs963459	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469859	chr9:86398152-86587957	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv482641	chr9:86398152-86587957	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	esv2758192	chr9:86414024-86603602	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2759701	chr9:86414024-86603602	Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv8541	chr9:86469723-86593758	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv831644	chr9:86534310-86704395	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
7	esv3366490	chr9:86541369-86608868	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
8	nsv1043703	chr9:86545917-86603545	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Height	20881960	GWAS catalog

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86536600-86571000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:86537000-86553600	Weak transcription	Fetal Intestine Small	intestine
3	chr9:86537000-86553600	Weak transcription	Thymus	Thymus
4	chr9:86543000-86571000	Weak transcription	Esophagus	oesophagus
5	chr9:86544000-86552400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr9:86546800-86553400	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr9:86546800-86553600	Weak transcription	Fetal Thymus	thymus
8	chr9:86547200-86553600	Weak transcription	Primary T cells from cord blood	blood
9	chr9:86547200-86553800	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr9:86547200-86570200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr9:86547800-86554200	Weak transcription	Dnd41	blood
12	chr9:86548000-86567000	Weak transcription	GM12878-XiMat	blood
13	chr9:86548600-86552600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr9:86548600-86552600	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr9:86548600-86553000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr9:86548800-86554400	Weak transcription	Small Intestine	intestine
17	chr9:86549000-86553800	Weak transcription	Pancreas	Pancrea
18	chr9:86549000-86570200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr9:86549400-86553000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr9:86549600-86552400	Weak transcription	Fetal Brain Female	brain
21	chr9:86549600-86553600	Weak transcription	Liver	Liver
22	chr9:86549600-86553600	Weak transcription	Fetal Stomach	stomach
23	chr9:86549600-86553600	Weak transcription	Left Ventricle	heart
24	chr9:86549600-86557000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr9:86550000-86552800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr9:86550200-86552400	Weak transcription	Adipose Nuclei	Adipose
27	chr9:86550200-86552400	Weak transcription	Fetal Intestine Large	intestine
28	chr9:86550200-86552400	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr9:86550200-86552600	Enhancers	Hela-S3	cervix
30	chr9:86550200-86552800	Weak transcription	HepG2	liver
31	chr9:86550200-86553400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr9:86550200-86553600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr9:86550200-86553600	Weak transcription	Colon Smooth Muscle	Colon
34	chr9:86550200-86553800	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr9:86550200-86553800	Weak transcription	Ovary	ovary
36	chr9:86550200-86553800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr9:86550200-86554000	Weak transcription	Lung	lung
38	chr9:86550200-86554000	Weak transcription	Right Ventricle	heart
39	chr9:86550200-86554400	Weak transcription	HSMMtube	muscle
40	chr9:86550200-86555000	Weak transcription	A549	lung
41	chr9:86550200-86555600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr9:86550200-86557000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr9:86550200-86557200	Weak transcription	Rectal Smooth Muscle	rectum
44	chr9:86550200-86559200	Weak transcription	Brain Anterior Caudate	brain
45	chr9:86550200-86570400	Weak transcription	Aorta	Aorta
46	chr9:86550400-86552400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr9:86550400-86553000	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr9:86550400-86553600	Weak transcription	Brain Cingulate Gyrus	brain
49	chr9:86550400-86553600	Weak transcription	Fetal Muscle Leg	muscle
50	chr9:86550400-86554200	Weak transcription	Placenta	Placenta

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