Variant report

Variant	rs73540089
Chromosome Location	chr9:97765376-97765377
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	RFX5	chr9:97764166-97767012	SK-N-SH	brain:	n/a	chr9:97764370-97764385 chr9:97764370-97764385
2	POLR2A	chr9:97764929-97765436	ProgFib	skin:	n/a	n/a
3	SP1	chr9:97764959-97765636	A549	lung:	n/a	n/a
4	SP1	chr9:97765002-97765652	A549	lung:	n/a	n/a
5	TCF12	chr9:97764876-97765682	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:97728899..97731372-chr9:97764520..97766152,2	MCF-7	breast:
2	chr9:97671639..97694679-chr9:97760418..97786060,142	MCF-7	breast:
3	chr9:97763979..97769403-chr9:97805439..97812937,10	MCF-7	breast:
4	chr9:97692878..97695081-chr9:97763307..97765405,2	MCF-7	breast:
5	chr9:97674991..97691307-chr9:97751911..97773298,151	MCF-7	breast:
6	chr9:97763635..97773461-chr9:97847821..97861280,36	MCF-7	breast:

Variant related genes	Relation type
C9orf3	TF binding region
ENSG00000148120	Chromatin interaction
ENSG00000207617	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs60553517	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60856972	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7037239	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73524654	1.00[AMR][1000 genomes]
rs73526528	1.00[AMR][1000 genomes]
rs73526540	1.00[AMR][1000 genomes]
rs73526548	1.00[AMR][1000 genomes]
rs73526572	1.00[AMR][1000 genomes]
rs73528441	1.00[AMR][1000 genomes]
rs73532355	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73534109	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73534113	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73534154	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73534159	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73536042	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73536067	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73536074	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73538140	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73538152	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73540059	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73540062	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73540077	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97670600-97766000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr9:97736600-97766200	Weak transcription	Right Ventricle	heart
3	chr9:97755200-97766400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:97758400-97766000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr9:97758400-97766400	Weak transcription	Gastric	stomach
6	chr9:97758600-97766400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr9:97759200-97766200	Weak transcription	Brain Angular Gyrus	brain
8	chr9:97759200-97766200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr9:97759400-97766000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr9:97759400-97766000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr9:97759400-97766200	Weak transcription	Stomach Mucosa	stomach
12	chr9:97762200-97766200	Weak transcription	Placenta	Placenta
13	chr9:97763000-97766000	Enhancers	Fetal Stomach	stomach
14	chr9:97763400-97766400	Weak transcription	Lung	lung
15	chr9:97763600-97765800	Weak transcription	Osteobl	bone
16	chr9:97763600-97766000	Weak transcription	HMEC	breast
17	chr9:97763600-97766200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr9:97763600-97766200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr9:97763600-97766200	Weak transcription	Right Atrium	heart
20	chr9:97763600-97766400	Weak transcription	Psoas Muscle	Psoas
21	chr9:97763800-97765400	Enhancers	Ovary	ovary
22	chr9:97763800-97765600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr9:97764600-97766000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr9:97764600-97766000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr9:97764600-97766000	Enhancers	Muscle Satellite Cultured Cells	--
26	chr9:97764600-97766000	Enhancers	Fetal Lung	lung
27	chr9:97764800-97765400	Flanking Active TSS	Liver	Liver
28	chr9:97764800-97765600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr9:97764800-97765800	Flanking Active TSS	A549	lung
30	chr9:97765000-97765400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:97765000-97765400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr9:97765000-97765400	Bivalent Enhancer	Fetal Muscle Leg	muscle
33	chr9:97765000-97765400	Enhancers	Left Ventricle	heart
34	chr9:97765000-97765400	Enhancers	Pancreas	Pancrea
35	chr9:97765000-97765400	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr9:97765000-97765400	Flanking Active TSS	HSMM	muscle
37	chr9:97765000-97765400	Flanking Active TSS	HSMMtube	muscle
38	chr9:97765000-97765600	Bivalent Enhancer	Small Intestine	intestine
39	chr9:97765000-97765800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr9:97765000-97765800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr9:97765000-97765800	Enhancers	Colonic Mucosa	Colon
42	chr9:97765000-97766000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr9:97765000-97766000	Enhancers	Duodenum Mucosa	Duodenum
44	chr9:97765000-97766000	Enhancers	Fetal Heart	heart
45	chr9:97765000-97766000	Enhancers	Fetal Intestine Large	intestine
46	chr9:97765000-97766000	Enhancers	Fetal Kidney	kidney
47	chr9:97765000-97766000	Enhancers	Hela-S3	cervix
48	chr9:97765000-97766000	Enhancers	HepG2	liver
49	chr9:97765000-97766000	Enhancers	NHDF-Ad	bronchial
50	chr9:97765000-97766000	Enhancers	NHLF	lung

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