Variant report

Variant	rs7866396
Chromosome Location	chr9:97806270-97806271
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr9:97806209-97806463	K562	blood:	n/a	n/a
2	MYC	chr9:97806167-97806439	K562	blood:	n/a	n/a
3	POLR2A	chr9:97806219-97806453	MCF-7	breast:	n/a	n/a
4	FOXA2	chr9:97805971-97806465	A549	lung:	n/a	n/a
5	FOXA1	chr9:97806014-97806531	HepG2	liver:	n/a	n/a
6	MAX	chr9:97806107-97806586	HepG2	liver:	n/a	n/a
7	BCL3	chr9:97805869-97809192	A549	lung:	n/a	chr9:97807640-97807649
8	FOXA1	chr9:97806030-97806490	HepG2	liver:	n/a	n/a
9	MAX	chr9:97806263-97806407	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr9:97806119-97806483	K562	blood:	n/a	n/a
11	FOXA1	chr9:97806029-97806436	HepG2	liver:	n/a	n/a
12	FOXA2	chr9:97806119-97806465	HepG2	liver:	n/a	n/a
13	POLR2A	chr9:97806063-97806394	A549	lung:	n/a	n/a
14	MYC	chr9:97806199-97806458	K562	blood:	n/a	n/a
15	MAX	chr9:97806209-97806411	K562	blood:	n/a	n/a
16	MAX	chr9:97805913-97806593	A549	lung:	n/a	n/a
17	FOXA1	chr9:97806100-97806489	HepG2	liver:	n/a	n/a
18	FOXA2	chr9:97806044-97806512	A549	lung:	n/a	n/a
19	MAX	chr9:97806003-97806496	A549	lung:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:97805704..97807873-chr9:97845688..97847934,2	MCF-7	breast:
2	chr9:97680454..97683100-chr9:97804978..97806982,2	MCF-7	breast:
3	chr9:97805422..97807754-chr9:97822770..97825763,2	MCF-7	breast:
4	chr9:97799418..97802536-chr9:97804091..97807017,3	MCF-7	breast:
5	chr9:97804859..97806414-chr9:97808670..97810361,2	MCF-7	breast:
6	chr9:97803206..97809214-chr9:97809347..97813672,8	MCF-7	breast:
7	chr9:97763979..97769403-chr9:97805439..97812937,10	MCF-7	breast:
8	chr9:97805980..97807545-chr9:97820488..97822005,2	MCF-7	breast:
9	chr9:97804181..97807973-chr9:97809683..97813710,4	K562	blood:
10	chr9:97806251..97809142-chr9:97810861..97813740,3	MCF-7	breast:

No data

Variant related genes	Relation type
C9orf3	TF binding region
ENSG00000207864	Chromatin interaction
ENSG00000207563	Chromatin interaction
ENSG00000148120	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs356660	0.82[YRI][hapmap]
rs356685	0.82[YRI][hapmap]
rs4647513	0.82[YRI][hapmap]
rs4647559	0.91[YRI][hapmap]
rs4744443	0.91[YRI][hapmap]
rs55934897	0.93[AFR][1000 genomes]
rs57477477	0.93[AFR][1000 genomes]
rs58436835	0.93[AFR][1000 genomes]
rs640628	0.84[YRI][hapmap]
rs7033294	0.82[YRI][hapmap]
rs73654503	0.93[AFR][1000 genomes]
rs73657019	0.93[AFR][1000 genomes]
rs73657021	0.90[AFR][1000 genomes]
rs73657023	0.90[AFR][1000 genomes]
rs73657030	0.96[AFR][1000 genomes]
rs73657033	1.00[AFR][1000 genomes]
rs73657034	1.00[AFR][1000 genomes]
rs73657046	0.87[AFR][1000 genomes]
rs73657047	0.93[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
2	nsv1038106	chr9:97793038-97881416	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
3	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
4	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97770800-97810000	Weak transcription	Primary T cells from cord blood	blood
2	chr9:97793400-97810400	Weak transcription	HUVEC	blood vessel
3	chr9:97794200-97807000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:97795000-97810400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr9:97795600-97808600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr9:97797000-97807800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr9:97798200-97808600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr9:97799400-97807600	Weak transcription	Thymus	Thymus
9	chr9:97799400-97810000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr9:97799800-97806800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr9:97800000-97808600	Genic enhancers	Liver	Liver
12	chr9:97801400-97807000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr9:97801600-97810000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr9:97801800-97806800	Weak transcription	HMEC	breast
15	chr9:97801800-97807000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr9:97802200-97807600	Strong transcription	HSMM	muscle
17	chr9:97802400-97807200	Strong transcription	HSMMtube	muscle
18	chr9:97803000-97806600	Weak transcription	Spleen	Spleen
19	chr9:97803000-97810800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr9:97803200-97806600	Weak transcription	Esophagus	oesophagus
21	chr9:97803400-97807600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr9:97803600-97806600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr9:97803800-97806600	Weak transcription	Stomach Mucosa	stomach
24	chr9:97804000-97807200	Enhancers	Pancreas	Pancrea
25	chr9:97804000-97808800	Weak transcription	Fetal Kidney	kidney
26	chr9:97804000-97810400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr9:97804200-97806800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr9:97804200-97806800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr9:97804200-97807000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr9:97804200-97807000	Weak transcription	Colonic Mucosa	Colon
31	chr9:97804200-97807800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr9:97804400-97806800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr9:97804400-97806800	Weak transcription	Right Ventricle	heart
34	chr9:97804400-97810400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr9:97804400-97810800	Weak transcription	K562	blood
36	chr9:97804600-97807000	Enhancers	Fetal Heart	heart
37	chr9:97804600-97807200	Genic enhancers	HepG2	liver
38	chr9:97804800-97808200	Strong transcription	NH-A	brain
39	chr9:97804800-97808200	Strong transcription	NHLF	lung
40	chr9:97805000-97806400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr9:97805000-97810000	Weak transcription	Brain Anterior Caudate	brain
42	chr9:97805200-97807200	Strong transcription	Hela-S3	cervix
43	chr9:97805200-97808400	Genic enhancers	Fetal Intestine Small	intestine
44	chr9:97805200-97810400	Weak transcription	Brain Angular Gyrus	brain
45	chr9:97805400-97806600	Weak transcription	Psoas Muscle	Psoas
46	chr9:97805400-97807000	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr9:97805400-97807200	Weak transcription	Aorta	Aorta
48	chr9:97805400-97810600	Weak transcription	Small Intestine	intestine
49	chr9:97805600-97810800	Weak transcription	GM12878-XiMat	blood
50	chr9:97805800-97806800	Enhancers	Pancreatic Islets	Pancreatic Islet

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