Variant report

Variant	rs73478129
Chromosome Location	chr9:86320454-86320455
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr9:86320374-86320806	GM12878	blood:	n/a	n/a
2	ZNF384	chr9:86319701-86321305	GM12878	blood:	n/a	n/a
3	RUNX3	chr9:86320231-86320712	GM12878	blood:	n/a	n/a
4	POLR2A	chr9:86320128-86320480	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:85832727..85836639-chr9:86319596..86323973,3	MCF-7	breast:
2	chr9:86319810..86324349-chr9:86592631..86598226,6	K562	blood:
3	chr9:86310182..86311687-chr9:86319047..86320880,2	K562	blood:
4	chr9:86320289..86324589-chr9:86593742..86599530,6	K562	blood:

Variant related genes	Relation type
ENSG00000254473	TF binding region
ENSG00000165119	Chromatin interaction
ENSG00000229109	Chromatin interaction
ENSG00000178966	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs57018109	1.00[AFR][1000 genomes]
rs57378362	0.93[AFR][1000 genomes]
rs60567720	0.93[AFR][1000 genomes]
rs60608689	0.93[AFR][1000 genomes]
rs73474390	1.00[AFR][1000 genomes]
rs73474395	1.00[AFR][1000 genomes]
rs73474399	1.00[AFR][1000 genomes]
rs73476304	1.00[AFR][1000 genomes]
rs73476308	0.85[AFR][1000 genomes]
rs73476315	1.00[AFR][1000 genomes]
rs73476323	1.00[AFR][1000 genomes]
rs73476326	1.00[AFR][1000 genomes]
rs73476336	1.00[AFR][1000 genomes]
rs73476338	1.00[AFR][1000 genomes]
rs73476342	0.93[AFR][1000 genomes]
rs73476345	0.85[AFR][1000 genomes]
rs73476376	1.00[AFR][1000 genomes]
rs73478135	0.93[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893512	chr9:86022215-86323309	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1044639	chr9:86252505-86412041	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv893513	chr9:86298632-86433459	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86289000-86321800	Weak transcription	Esophagus	oesophagus
2	chr9:86294000-86321800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:86296000-86320800	Weak transcription	Fetal Brain Female	brain
4	chr9:86297600-86321200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:86298800-86320800	Weak transcription	Fetal Thymus	thymus
6	chr9:86301000-86320800	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr9:86304400-86320800	Weak transcription	Brain Anterior Caudate	brain
8	chr9:86310400-86320600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr9:86311200-86320800	Weak transcription	Fetal Lung	lung
10	chr9:86311800-86321000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr9:86312800-86320800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr9:86313200-86320800	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr9:86313600-86321000	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr9:86314400-86320800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr9:86314600-86321400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr9:86314600-86321400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr9:86314600-86321400	Weak transcription	Gastric	stomach
18	chr9:86314600-86321800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr9:86315000-86320600	Weak transcription	Stomach Mucosa	stomach
20	chr9:86315200-86321400	Weak transcription	Aorta	Aorta
21	chr9:86315800-86320800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr9:86315800-86320800	Weak transcription	Brain Hippocampus Middle	brain
23	chr9:86316000-86320600	Weak transcription	Brain Substantia Nigra	brain
24	chr9:86316000-86321400	Weak transcription	Pancreas	Pancrea
25	chr9:86316000-86321800	Weak transcription	Lung	lung
26	chr9:86317000-86320600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr9:86317000-86320800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:86317000-86321000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr9:86317200-86320600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr9:86317200-86320600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr9:86317200-86320600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr9:86317200-86320600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr9:86317200-86320600	Weak transcription	Brain Angular Gyrus	brain
34	chr9:86317200-86320600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr9:86317200-86320600	Weak transcription	NH-A	brain
36	chr9:86317200-86320600	Weak transcription	Osteobl	bone
37	chr9:86317200-86320800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr9:86317200-86320800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr9:86317200-86320800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr9:86317200-86320800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr9:86317200-86320800	Weak transcription	Ovary	ovary
42	chr9:86317200-86320800	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr9:86317200-86320800	Weak transcription	Right Atrium	heart
44	chr9:86317200-86320800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr9:86317200-86321000	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr9:86317200-86321000	Weak transcription	Stomach Smooth Muscle	stomach
47	chr9:86317200-86321400	Weak transcription	Left Ventricle	heart
48	chr9:86317400-86320600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr9:86317400-86320800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr9:86317400-86321000	Weak transcription	HSMM	muscle

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