Variant report

Variant	esv3334089
Chromosome Location	chr9:117152193-117152424
allele	n/a
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	BHLHE40	chr9:117152277-117152690	GM12878	blood:	n/a	n/a
2	CEBPB	chr9:117152313-117152323	K562	blood:	n/a	n/a
3	CEBPB	chr9:117152226-117152426	HepG2	liver:	n/a	chr9:117152291-117152302
4	CHD1	chr9:117152409-117152727	GM12878	blood:	n/a	n/a
5	CHD2	chr9:117152329-117152792	GM12878	blood:	n/a	n/a
6	CTCF	chr9:117152412-117152686	GM12892	blood:	n/a	n/a
7	CTCF	chr9:117152420-117152570	GM12871	blood:	n/a	n/a
8	CTCF	chr9:117152420-117152570	GM12866	blood:	n/a	n/a
9	CTCF	chr9:117152420-117152570	GM12872	blood:	n/a	n/a
10	CTCF	chr9:117152404-117152700	GM19239	blood:	n/a	n/a
11	CTCF	chr9:117152346-117152743	GM12878	blood:	n/a	n/a
12	CTCF	chr9:117152380-117152530	BE2_C	brain:	n/a	n/a
13	CTCF	chr9:117152415-117152659	GM12891	blood:	n/a	n/a
14	CTCF	chr9:117152400-117152550	RPTEC	kidney:	n/a	n/a
15	CTCF	chr9:117152420-117152570	WERI-Rb-1	eye:	n/a	n/a
16	CTCF	chr9:117152420-117152570	GM12874	blood:	n/a	n/a
17	CTCF	chr9:117152400-117152550	GM12872	blood:	n/a	n/a
18	CTCF	chr9:117152220-117152370	GM12878	blood:	n/a	n/a
19	CTCF	chr9:117152400-117152550	GM12870	blood:	n/a	n/a
20	CTCF	chr9:117152380-117152530	GM12865	blood:	n/a	n/a
21	EBF1	chr9:117152171-117152704	GM12878	blood:	n/a	chr9:117152428-117152439
22	EBF1	chr9:117152256-117152561	GM12878	blood:	n/a	chr9:117152428-117152439
23	ESRRA	chr9:117150909-117154041	GM12878	blood:	n/a	chr9:117152085-117152097 chr9:117152091-117152100 chr9:117152311-117152324
24	MAX	chr9:117152401-117152716	GM12878	blood:	n/a	n/a
25	MAX	chr9:117152108-117152646	NB4	blood:	n/a	chr9:117152280-117152290
26	MAZ	chr9:117152211-117152724	GM12878	blood:	n/a	n/a
27	MTA3	chr9:117152081-117153182	GM12878	blood:	n/a	n/a
28	MXI1	chr9:117152121-117152823	GM12878	blood:	n/a	n/a
29	MYC	chr9:117152114-117152649	NB4	blood:	n/a	chr9:117152280-117152290
30	PAX5	chr9:117152269-117152718	GM12878	blood:	n/a	chr9:117152499-117152508
31	PAX5	chr9:117152194-117152821	GM12878	blood:	n/a	chr9:117152499-117152508
32	PAX5	chr9:117152374-117152573	GM12878	blood:	n/a	chr9:117152499-117152508
33	PAX5	chr9:117152250-117152699	GM12878	blood:	n/a	chr9:117152499-117152508
34	PBX3	chr9:117152174-117152457	GM12878	blood:	n/a	chr9:117152322-117152331
35	POLR2A	chr9:117151935-117152863	GM12878	blood:	n/a	n/a
36	POLR2A	chr9:117150579-117153681	K562	blood:	n/a	n/a
37	POLR2A	chr9:117152186-117153207	GM12892	blood:	n/a	n/a
38	POLR2A	chr9:117151975-117152907	GM12892	blood:	n/a	n/a
39	POLR2A	chr9:117152263-117152463	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr9:117144419-117153742	GM12878	blood:	n/a	n/a
41	POLR2A	chr9:117144250-117153778	GM12891	blood:	n/a	n/a
42	POLR2A	chr9:117152308-117152922	HepG2	liver:	n/a	n/a
43	POLR2A	chr9:117152376-117152965	GM12892	blood:	n/a	n/a
44	RAD21	chr9:117152358-117152706	GM12878	blood:	n/a	n/a
45	RAD21	chr9:117152335-117152690	GM12878	blood:	n/a	n/a
46	RAD21	chr9:117152383-117152649	GM12878	blood:	n/a	n/a
47	RAD21	chr9:117152336-117152679	H1-hESC	embryonic stem cell:	n/a	n/a
48	RUNX3	chr9:117152171-117152729	GM12878	blood:	n/a	n/a
49	RUNX3	chr9:117152263-117152723	GM12878	blood:	n/a	n/a
50	SIN3A	chr9:117152401-117152546	GM12878	blood:	n/a	chr9:117152450-117152460

No.	Distal block	Cell Line	Cell type
1	chr9:117148465..117156866-chr9:117157996..117162015,11	K562	blood:
2	chr9:117150472..117153242-chr9:117164215..117165923,2	K562	blood:
3	chr9:117148225..117150086-chr9:117151998..117154426,2	K562	blood:

Variant related genes	Relation type
AKNA	TF binding region
ENSG00000235119	chromatin interactions

Extended variants
information (count: 4 )
Associated
traits (count: 62 )

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	rs182889694	chr9:117152232-117152233	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs144096761	chr9:117152253-117152254	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs188661950	chr9:117152294-117152295	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs10982193	chr9:117152302-117152303	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:62)

Disease	PMID	Source
Acute lymphoblastic leukemia	22237106	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
Renal cell carcinoma	18592004	CNVD
Developmental delay	19490664	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
Medulloblastoma	21979893	CNVD
microdeletion syndrome	16199537	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Urothelial carcinoma	21177765	CNVD
Renal cell carcinoma	21668985	CNVD
Autism	22495311	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Cancer	16751803	CNVD
Myelofibrosis	22110671	CNVD
lymphocytic leukemia	21291569	CNVD
Leukemia	17361228	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Glioblastoma	16823260	CNVD
Non-small cell lung cancer	21044232	CNVD
Brain cancer	20823417	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Astrocytoma	17387387	CNVD
Glioblastoma multiforme	21080181	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Renal cell carcinoma	19461508	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Heart disease	21282601	CNVD
Lung cancer	18438408	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Breast cancer	17603634	CNVD
Acute myeloid leukemia	20729466	CNVD
Oral cancer	21386901	CNVD
Prostate cancer	18632612	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Gastric cancer	17908304	CNVD
small cell lung cancer	20016488	CNVD
Cardiac fibroma	18329553	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Testicular germ cell tumor	18059402	CNVD
Breast cancer	21364760	CNVD
Developmental delay	21147756	CNVD
Lung cancer	19147751	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Melanoma	18172304	CNVD
Colorectal cancer	16272173	CNVD
Bladder cancer	21909424	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	21509527	CNVD
Cancer	20164919	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Cervical cancer	16585170	CNVD
Ependymoma	19289631	CNVD
Melanoma	17363583	CNVD
Retinoblastoma	19183342	CNVD

Chromatin state (count:146 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117148800-117155000	Weak transcription	Hela-S3	cervix
2	chr9:117150200-117152600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr9:117150400-117152200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr9:117150400-117152200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr9:117150400-117152200	Enhancers	Placenta Amnion	Placenta Amnion
6	chr9:117150400-117152200	Flanking Active TSS	Dnd41	blood
7	chr9:117150400-117152400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
8	chr9:117150400-117152400	Flanking Active TSS	Fetal Thymus	thymus
9	chr9:117150400-117152600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
10	chr9:117150400-117152800	Flanking Active TSS	Primary T cells from cord blood	blood
11	chr9:117150400-117153000	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr9:117150400-117153000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
13	chr9:117150400-117154600	Weak transcription	Aorta	Aorta
14	chr9:117150400-117159800	Weak transcription	Psoas Muscle	Psoas
15	chr9:117150600-117152200	Weak transcription	Ovary	ovary
16	chr9:117150600-117152600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr9:117150600-117152600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr9:117150600-117152600	Enhancers	Placenta	Placenta
19	chr9:117150600-117152800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr9:117150600-117153000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr9:117150600-117153000	Genic enhancers	Spleen	Spleen
22	chr9:117150600-117156000	Enhancers	Stomach Mucosa	stomach
23	chr9:117150800-117152200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr9:117150800-117152200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr9:117150800-117152600	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr9:117150800-117152800	Enhancers	Brain Hippocampus Middle	brain
27	chr9:117150800-117153200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr9:117150800-117153200	Enhancers	Fetal Stomach	stomach
29	chr9:117150800-117153200	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr9:117150800-117153400	Enhancers	Liver	Liver
31	chr9:117150800-117153600	Enhancers	Fetal Muscle Leg	muscle
32	chr9:117150800-117153800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
33	chr9:117150800-117154000	Weak transcription	NH-A	brain
34	chr9:117150800-117154600	Weak transcription	Pancreas	Pancrea
35	chr9:117150800-117154800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr9:117150800-117157400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr9:117150800-117159200	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr9:117150800-117159400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr9:117150800-117159400	Genic enhancers	Primary B cells from peripheral blood	blood
40	chr9:117151000-117152200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr9:117151000-117152200	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr9:117151000-117152200	Weak transcription	Lung	lung
43	chr9:117151000-117152200	Enhancers	NHEK	skin
44	chr9:117151000-117152400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr9:117151000-117152400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr9:117151000-117152600	Weak transcription	Fetal Kidney	kidney
47	chr9:117151000-117152600	Weak transcription	Left Ventricle	heart
48	chr9:117151000-117152600	Weak transcription	NHDF-Ad	bronchial
49	chr9:117151000-117152800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr9:117151000-117152800	Weak transcription	Right Atrium	heart

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