Variant report

Variant	rs7856713
Chromosome Location	chr9:116264957-116264958
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	POLR2A	chr9:116264680-116265022	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr9:116263262-116267925	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr9:116263135-116267750	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr9:116264711-116266689	HUVEC	blood vessel:	n/a	n/a
5	SPI1	chr9:116264946-116265447	GM12878	blood:	n/a	n/a
6	POLR2A	chr9:116263232-116266725	HUVEC	blood vessel:	n/a	n/a
7	SPI1	chr9:116264945-116265479	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:116264785..116266447-chr9:116267104..116270067,2	MCF-7	breast:
2	chr9:116224980..116228054-chr9:116260293..116265292,4	MCF-7	breast:

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

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10981835	0.87[YRI][hapmap]
rs12346476	1.00[EUR][1000 genomes]
rs60969910	1.00[EUR][1000 genomes]
rs6478021	1.00[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	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7042609	1.00[YRI][hapmap];1.00[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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7853612	1.00[EUR][1000 genomes]
rs7864169	1.00[EUR][1000 genomes]
rs7865642	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7866866	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7867017	1.00[EUR][1000 genomes]
rs7870008	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
3	nsv466508	chr9:116244982-116362738	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv615215	chr9:116244982-116362738	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv526579	chr9:116244982-116391162	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116242000-116266200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr9:116251600-116283800	Weak transcription	Hela-S3	cervix
3	chr9:116252400-116273200	Weak transcription	Pancreas	Pancrea
4	chr9:116255600-116265400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr9:116255600-116266600	Weak transcription	Stomach Mucosa	stomach
6	chr9:116255600-116269400	Weak transcription	Colon Smooth Muscle	Colon
7	chr9:116255600-116275800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr9:116257400-116270800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr9:116259200-116274000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr9:116259200-116274200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr9:116260200-116265400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr9:116262800-116266400	Weak transcription	A549	lung
13	chr9:116262800-116267400	Weak transcription	Aorta	Aorta
14	chr9:116262800-116274200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr9:116263000-116265200	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr9:116263200-116265000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
17	chr9:116263200-116265400	Active TSS	Left Ventricle	heart
18	chr9:116263200-116265400	Active TSS	Right Atrium	heart
19	chr9:116263200-116265400	Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr9:116263200-116266000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr9:116263200-116266200	Active TSS	Adipose Nuclei	Adipose
22	chr9:116263200-116267000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr9:116263400-116265400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr9:116263400-116265400	Active TSS	Right Ventricle	heart
25	chr9:116263400-116265600	Active TSS	Fetal Brain Female	brain
26	chr9:116263400-116266200	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
27	chr9:116263400-116266400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr9:116263400-116266400	Active TSS	Brain Anterior Caudate	brain
29	chr9:116263600-116265000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr9:116263600-116265200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr9:116263600-116265400	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr9:116263600-116266000	Active TSS	Brain Hippocampus Middle	brain
33	chr9:116263600-116266000	Active TSS	Psoas Muscle	Psoas
34	chr9:116263600-116266200	Active TSS	HUVEC	blood vessel
35	chr9:116263600-116266400	Active TSS	Fetal Muscle Leg	muscle
36	chr9:116263800-116265000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr9:116263800-116265200	Active TSS	Brain Cingulate Gyrus	brain
38	chr9:116263800-116265200	Enhancers	Brain Substantia Nigra	brain
39	chr9:116263800-116265200	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr9:116263800-116265400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr9:116263800-116265400	Active TSS	Fetal Muscle Trunk	muscle
42	chr9:116263800-116265600	Active TSS	Lung	lung
43	chr9:116263800-116265600	Active TSS	Ovary	ovary
44	chr9:116263800-116265800	Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr9:116263800-116265800	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr9:116263800-116266000	Active TSS	Esophagus	oesophagus
47	chr9:116263800-116266000	Flanking Active TSS	Placenta	Placenta
48	chr9:116263800-116266600	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr9:116263800-116266800	Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr9:116264000-116265000	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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