Variant report

Variant	esv1950723
Chromosome Location	chr6:45389143-45389144
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	CHD1	chr6:45388363-45391883	IMR90	lung:	n/a	chr6:45391066-45391076 chr6:45391635-45391645
2	CTCF	chr6:45389120-45389270	HAc	cerebellar:	n/a	n/a
3	EBF1	chr6:45389071-45389370	GM12878	blood:	n/a	chr6:45389199-45389212 chr6:45389201-45389210 chr6:45389200-45389211 chr6:45389201-45389210 chr6:45389200-45389210
4	EBF1	chr6:45389095-45389284	GM12878	blood:	n/a	chr6:45389199-45389212 chr6:45389201-45389210 chr6:45389200-45389211 chr6:45389201-45389210 chr6:45389200-45389210
5	GTF2F1	chr6:45389137-45389753	Hela-S3	cervix:	n/a	n/a
6	MAX	chr6:45389076-45389699	SK-N-SH	brain:	n/a	chr6:45389137-45389147
7	MAZ	chr6:45389048-45392554	IMR90	lung:	n/a	chr6:45391434-45391444 chr6:45389137-45389147
8	MAZ	chr6:45389117-45390768	Hela-S3	cervix:	n/a	chr6:45389137-45389147
9	MAZ	chr6:45389116-45390826	K562	blood:	n/a	chr6:45389137-45389147
10	MXI1	chr6:45387978-45389214	IMR90	lung:	n/a	chr6:45388578-45388587
11	MYC	chr6:45388403-45390078	K562	blood:	n/a	chr6:45388578-45388589 chr6:45388578-45388588 chr6:45388579-45388588 chr6:45388580-45388587 chr6:45389137-45389147 chr6:45388579-45388589
12	POLR2A	chr6:45388936-45390689	H1-neurons	neurons:	n/a	n/a
13	POLR2A	chr6:45389134-45390316	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr6:45388973-45389841	H1-neurons	neurons:	n/a	n/a
15	RAD21	chr6:45388419-45392074	IMR90	lung:	n/a	chr6:45391794-45391808 chr6:45392039-45392052 chr6:45390904-45390916 chr6:45390740-45390753 chr6:45391581-45391591 chr6:45388466-45388478
16	RAD21	chr6:45389075-45390508	HCT-116	colon:	n/a	n/a
17	RAD21	chr6:45389127-45390166	Hela-S3	cervix:	n/a	n/a
18	SIN3A	chr6:45389123-45390301	H1-hESC	embryonic stem cell:	n/a	n/a
19	SMC3	chr6:45389042-45390791	Hela-S3	cervix:	n/a	n/a
20	ZBTB7A	chr6:45389125-45389721	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:45387795..45389727-chr6:45621998..45623537,2	MCF-7	breast:
2	chr6:45343131..45346998-chr6:45386286..45389886,4	MCF-7	breast:
3	chr6:45343194..45347445-chr6:45386856..45389425,4	MCF-7	breast:
4	chr6:45388588..45389630-chr6:45682064..45682718,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SUPT3H-2	chr6:45388816-45389742	ENSG00000271857.1

Variant related genes	Relation type
RUNX2	TF binding region
ENSG00000196284	chromatin interactions

Extended variants
information (count: 1 )
Associated
traits (count: 88 )

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	rs372049131	chr6:45389143-45389144	Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:88)

Disease	PMID	Source
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Leukemia	21518781	CNVD
Cancer	21637783	CNVD
Facial dysmorphism	22105932	CNVD
Medulloblastoma	21979893	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Endometrial cancer	22040021	CNVD
Acute myeloid leukemia	16864856	CNVD
Breast cancer	21264507	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Bladder cancer	19088036	CNVD
Wilms tumour	21544195	CNVD
Uveal melanoma	21693616	CNVD
Biliary cancer	19435499	CNVD
Malaria	21533027	CNVD
Retinoblastoma	19183342	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	21858162	CNVD
Ewing''s sarcoma	17952124	CNVD
Autism	21448237	CNVD
Melanoma	18172304	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Hepatocellular carcinoma	16750200	CNVD
Autism	22495311	CNVD
Cancer	16790693	CNVD
Systemic lupus erythematosus	17503323	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Urothelial carcinoma	18382360	CNVD
Cancer	21183584	CNVD
Hodgkin''s lymphoma	17606441	CNVD
small cell lung cancer	20016488	CNVD
Gastric cancer	17908304	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Neuroblastoma	16790693	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Osteosarcoma	16790693	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Lung cancer	18438408	CNVD
Ovarian cancer	21720365	CNVD
Osteosarcoma	21197465	CNVD
Gastric cancer	24379144	CNVD
Neuroblastoma	18923191	CNVD
abnormal development	18461090	CNVD
Breast cancer	17603634	CNVD
Breast cancer	21364760	CNVD
Colorectal cancer	16790693	CNVD
Congenital adrenal hyperplasia	18478071	CNVD
Congenital anomalies of the kidney and urinary tract	18316590	CNVD
Systemic lupus erythematosus	19287148	CNVD
Colorectal cancer	19359472	CNVD
Multiple myeloma	16616336	CNVD
Chordoma	18071362	CNVD
Follicular lymphoma	16790693	CNVD
Osteosarcoma	19286668	CNVD
Neurocytoma	17123091	CNVD
lymphocytic leukemia	21291569	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Cancer	20164919	CNVD
Breast cancer	22522925	CNVD
Schizophrenia	23813976	CNVD
Myelofibrosis	22110671	CNVD
Heart disease	21282601	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Breast cancer	16608533	CNVD
early-passage human iPS cells	21368824	CNVD

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45386800-45389400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr6:45386800-45389400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr6:45387000-45389400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
4	chr6:45387000-45389800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr6:45387000-45391800	Bivalent Enhancer	Fetal Brain Male	brain
6	chr6:45387000-45392200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr6:45387200-45389200	Bivalent Enhancer	Brain Germinal Matrix	brain
8	chr6:45387200-45389400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:45387200-45389400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
10	chr6:45387200-45389600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
11	chr6:45387200-45389600	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
12	chr6:45387200-45390800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
13	chr6:45387400-45389200	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
14	chr6:45387400-45389400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
15	chr6:45387400-45389600	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:45387400-45391000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
17	chr6:45387600-45389200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
18	chr6:45387600-45389200	Bivalent Enhancer	Fetal Muscle Leg	muscle
19	chr6:45387600-45389200	Bivalent Enhancer	Placenta	Placenta
20	chr6:45387600-45389200	Bivalent Enhancer	Fetal Stomach	stomach
21	chr6:45387600-45389600	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
22	chr6:45387800-45389200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
23	chr6:45387800-45389200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:45387800-45389200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
25	chr6:45387800-45389200	Bivalent Enhancer	Fetal Lung	lung
26	chr6:45387800-45389200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
27	chr6:45387800-45389400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:45387800-45389400	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
29	chr6:45387800-45389400	Bivalent Enhancer	HUVEC	blood vessel
30	chr6:45387800-45389600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
31	chr6:45387800-45390000	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr6:45388000-45389200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
33	chr6:45388000-45389200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:45388000-45389200	Flanking Active TSS	Brain Substantia Nigra	brain
35	chr6:45388200-45389200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr6:45388200-45389200	Bivalent/Poised TSS	Left Ventricle	heart
37	chr6:45388200-45389200	Weak transcription	Lung	lung
38	chr6:45388200-45389200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
39	chr6:45388200-45389200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
40	chr6:45388200-45389200	Weak transcription	Spleen	Spleen
41	chr6:45388200-45389400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:45388200-45389400	Bivalent/Poised TSS	Aorta	Aorta
43	chr6:45388200-45389400	Weak transcription	Gastric	stomach
44	chr6:45388200-45389400	Weak transcription	Pancreas	Pancrea
45	chr6:45388200-45389400	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
46	chr6:45388200-45389600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr6:45388200-45390800	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
48	chr6:45388200-45391800	Active TSS	Ovary	ovary
49	chr6:45388200-45392000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:45388200-45392000	Active TSS	NHDF-Ad	bronchial

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