Variant report

Variant	rs7870008
Chromosome Location	chr9:116225549-116225550
allele	C/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	MAX	chr9:116225523-116226508	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr9:116225521-116226639	ECC-1	luminal epithelium:	n/a	n/a
3	E2F6	chr9:116225348-116226497	H1-hESC	embryonic stem cell:	n/a	chr9:116225913-116225922 chr9:116225927-116225936 chr9:116225995-116226007
4	TCF12	chr9:116225474-116226324	A549	lung:	n/a	n/a
5	MAX	chr9:116225524-116226597	A549	lung:	n/a	n/a
6	E2F6	chr9:116225520-116226333	A549	lung:	n/a	chr9:116225913-116225922 chr9:116225927-116225936 chr9:116225995-116226007
7	MAX	chr9:116225492-116226652	MCF-7	breast:	n/a	n/a
8	MAX	chr9:116225448-116226909	HCT-116	colon:	n/a	n/a
9	CTCF	chr9:116225540-116225690	GM12865	blood:	n/a	n/a
10	ZNF263	chr9:116225413-116227501	HEK293-T-REx	kidney:	n/a	n/a
11	FOXM1	chr9:116225486-116226896	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr9:116225547-116225559	MCF-7	breast:	n/a	n/a
13	MAX	chr9:116225498-116226742	A549	lung:	n/a	n/a
14	FOXM1	chr9:116225446-116226440	ECC-1	luminal epithelium:	n/a	n/a
15	EP300	chr9:116225515-116226868	ECC-1	luminal epithelium:	n/a	chr9:116225854-116225863 chr9:116225857-116225866 chr9:116225855-116225864
16	MAX	chr9:116225269-116226626	MCF-7	breast:	n/a	n/a
17	MAX	chr9:116225449-116226666	ECC-1	luminal epithelium:	n/a	n/a
18	POLR2A	chr9:116225324-116226415	MCF-7	breast:	n/a	n/a
19	MAX	chr9:116225187-116226518	HepG2	liver:	n/a	n/a
20	HA-E2F1	chr9:116225519-116226544	MCF-7	breast:	n/a	chr9:116225980-116225991 chr9:116225913-116225922 chr9:116225927-116225936 chr9:116225995-116226006 chr9:116225995-116226007
21	POLR2A	chr9:116225420-116227223	Hela-S3	cervix:	n/a	n/a
22	TCF12	chr9:116225465-116226744	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:116224980..116228054-chr9:116260293..116265292,4	MCF-7	breast:
2	chr9:116222989..116229179-chr9:116341260..116348453,12	MCF-7	breast:
3	chr9:116223752..116229757-chr9:116340131..116348699,14	MCF-7	breast:
4	chr9:116223200..116229905-chr9:116240839..116245410,9	MCF-7	breast:
5	chr9:116206482..116208541-chr9:116225258..116228467,4	MCF-7	breast:
6	chr9:116224389..116227414-chr9:116412116..116415236,3	MCF-7	breast:
7	chr9:116223306..116225779-chr9:116227028..116228587,3	K562	blood:
8	chr9:116171440..116174451-chr9:116224493..116228672,6	MCF-7	breast:
9	chr9:116171540..116174931-chr9:116223597..116227370,5	MCF-7	breast:

Variant related genes	Relation type
RGS3	TF binding region
ENSG00000148229	Chromatin interaction
ENSG00000138835	Chromatin interaction
ENSG00000157653	Chromatin interaction
ENSG00000227482	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12346476	1.00[EUR][1000 genomes]
rs60969910	1.00[EUR][1000 genomes]
rs6478021	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7023224	1.00[EUR][1000 genomes]
rs7027261	1.00[EUR][1000 genomes]
rs7032245	1.00[EUR][1000 genomes]
rs7032414	1.00[EUR][1000 genomes]
rs7033489	1.00[EUR][1000 genomes]
rs7038258	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7042609	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73538901	1.00[EUR][1000 genomes]
rs73544687	1.00[EUR][1000 genomes]
rs73544688	1.00[EUR][1000 genomes]
rs7851265	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7853612	1.00[EUR][1000 genomes]
rs7856713	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7864169	1.00[EUR][1000 genomes]
rs7865642	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7866866	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7867017	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv893747	chr9:116214058-116386438	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS 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	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116218600-116229200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr9:116218800-116226000	Weak transcription	Fetal Kidney	kidney
3	chr9:116219400-116240000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr9:116223200-116225600	Enhancers	Fetal Heart	heart
5	chr9:116223400-116226000	Strong transcription	Primary hematopoietic stem cells	blood
6	chr9:116223600-116226800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr9:116224200-116225800	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr9:116224600-116225600	Enhancers	Fetal Brain Female	brain
9	chr9:116224600-116225600	Bivalent Enhancer	Fetal Muscle Leg	muscle
10	chr9:116224600-116226400	Bivalent Enhancer	Fetal Brain Male	brain
11	chr9:116224800-116225600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
12	chr9:116224800-116225600	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr9:116224800-116225800	Enhancers	Brain Hippocampus Middle	brain
14	chr9:116225000-116226400	Enhancers	Fetal Lung	lung
15	chr9:116225000-116226400	Enhancers	Placenta	Placenta
16	chr9:116225200-116225600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
17	chr9:116225200-116225600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
18	chr9:116225200-116225600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr9:116225200-116225600	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
20	chr9:116225200-116225600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr9:116225200-116225600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr9:116225200-116225600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr9:116225200-116225600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr9:116225200-116225600	Enhancers	Duodenum Mucosa	Duodenum
25	chr9:116225200-116225600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
26	chr9:116225200-116225600	Enhancers	Fetal Intestine Small	intestine
27	chr9:116225200-116225600	Bivalent Enhancer	Fetal Stomach	stomach
28	chr9:116225200-116225600	Enhancers	Right Ventricle	heart
29	chr9:116225200-116225600	Enhancers	Hela-S3	cervix
30	chr9:116225200-116225600	Enhancers	NHLF	lung
31	chr9:116225200-116225800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr9:116225200-116225800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr9:116225200-116225800	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr9:116225200-116225800	Enhancers	Adipose Nuclei	Adipose
35	chr9:116225200-116225800	Enhancers	Fetal Thymus	thymus
36	chr9:116225200-116225800	Flanking Active TSS	HepG2	liver
37	chr9:116225200-116226000	Enhancers	Liver	Liver
38	chr9:116225200-116226000	Enhancers	Left Ventricle	heart
39	chr9:116225200-116226000	Enhancers	Stomach Mucosa	stomach
40	chr9:116225400-116225600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr9:116225400-116225600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
42	chr9:116225400-116225600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
43	chr9:116225400-116225600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr9:116225400-116225600	Enhancers	Colonic Mucosa	Colon
45	chr9:116225400-116225600	Enhancers	Fetal Intestine Large	intestine
46	chr9:116225400-116225600	Enhancers	Pancreas	Pancrea
47	chr9:116225400-116225600	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr9:116225400-116225600	Weak transcription	Rectal Smooth Muscle	rectum
49	chr9:116225400-116225600	Enhancers	Right Atrium	heart
50	chr9:116225400-116225600	Enhancers	Sigmoid Colon	Sigmoid Colon

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