Variant report

Variant	esv3430509
Chromosome Location	chr4:22459366-22459574
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	GATA3	chr4:22459403-22459654	SH-SY5Y	brain:	n/a	n/a
2	GATA3	chr4:22459004-22459904	SK-N-SH	brain:	n/a	chr4:22459682-22459693

No.	Distal block	Cell Line	Cell type
1	chr4:22457536..22463707-chr4:22514115..22518559,7	MCF-7	breast:
2	chr4:22449726..22452368-chr4:22458347..22461364,3	MCF-7	breast:
3	chr4:22452403..22454410-chr4:22458067..22459809,2	MCF-7	breast:

Variant related genes	Relation type
GPR125	TF binding region
ENSG00000152990	chromatin interactions

Extended variants
information (count: 11 )
Associated
traits (count: 59 )

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs137992137	chr4:22459373-22459374	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs142676589	chr4:22459383-22459384	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs1903781	chr4:22459401-22459402	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs6448158	chr4:22459437-22459438	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs533483865	chr4:22459453-22459454	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs35926750	chr4:22459476-22459477	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs563591092	chr4:22459506-22459507	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs531033180	chr4:22459537-22459538	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs369873466	chr4:22459539-22459540	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs112554018	chr4:22459548-22459549	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs549521912	chr4:22459550-22459551	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:59)

Disease	PMID	Source
Breast cancer	17603634	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	17533364	CNVD
Oral squamous cell carcinoma	17134496	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Cancer	21637783	CNVD
Melanoma	21693616	CNVD
Squamous cell cancer	21044232	CNVD
Colorectal cancer	20709793	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Non-small cell lung cancer	21044232	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	17387387	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Cervical cancer	21062161	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Neuroblastoma	18923191	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21785460	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Lung cancer	18438408	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	21858162	CNVD
small cell lung cancer	20016488	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Cancer	21183584	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Gastric cancer	21586687	CNVD
Breast cancer	17133270	CNVD
lymphocytic leukemia	21291569	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	16608533	CNVD
Non-small cell lung cancer	21829676	CNVD
Melanoma	22183965	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Olfactory neuroblastoma	18408657	CNVD
Burkitt''s lymphoma	20823134	CNVD
Burkitt''s lymphoma	19759907	CNVD
Myelofibrosis	22110671	CNVD
Colorectal cancer	16774939	CNVD
Cancer	22183965	CNVD
Gastric cancer	16891809	CNVD
Pancreatic cancer	17952125	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:22388400-22473600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr4:22388800-22469600	Weak transcription	Colonic Mucosa	Colon
3	chr4:22389200-22473600	Weak transcription	Fetal Brain Male	brain
4	chr4:22390600-22459800	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr4:22393600-22459800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:22400800-22461800	Weak transcription	Gastric	stomach
7	chr4:22419200-22476200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:22419400-22465800	Weak transcription	HUVEC	blood vessel
9	chr4:22420600-22488000	Weak transcription	Aorta	Aorta
10	chr4:22426000-22461800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr4:22428600-22460600	Weak transcription	Placenta	Placenta
12	chr4:22432400-22460400	Weak transcription	Small Intestine	intestine
13	chr4:22433800-22479200	Weak transcription	Brain Hippocampus Middle	brain
14	chr4:22434000-22461200	Weak transcription	Brain Anterior Caudate	brain
15	chr4:22437400-22476400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr4:22437800-22459600	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr4:22437800-22465000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr4:22443400-22471200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr4:22443400-22472400	Weak transcription	Ovary	ovary
20	chr4:22443400-22473600	Weak transcription	Fetal Brain Female	brain
21	chr4:22443600-22470800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr4:22443600-22476200	Weak transcription	A549	lung
23	chr4:22443800-22474600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:22444000-22470800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr4:22447200-22467600	Weak transcription	Thymus	Thymus
26	chr4:22447200-22473800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr4:22447200-22475000	Weak transcription	NHLF	lung
28	chr4:22447800-22473400	Weak transcription	Brain Germinal Matrix	brain
29	chr4:22448000-22461400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr4:22448600-22472600	Weak transcription	Primary T cells from cord blood	blood
31	chr4:22450200-22459600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr4:22450200-22471000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr4:22450200-22473800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr4:22450200-22473800	Weak transcription	NH-A	brain
35	chr4:22450400-22460200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr4:22450400-22461800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr4:22450400-22474800	Weak transcription	Adipose Nuclei	Adipose
38	chr4:22450400-22476000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr4:22450400-22484000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr4:22450400-22493200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:22450800-22464200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr4:22451200-22459600	Weak transcription	Liver	Liver
43	chr4:22451400-22464000	Weak transcription	Fetal Stomach	stomach
44	chr4:22453400-22460800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr4:22453800-22460000	Weak transcription	Psoas Muscle	Psoas
46	chr4:22454400-22462200	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr4:22455600-22474200	Weak transcription	Fetal Thymus	thymus
48	chr4:22456400-22459800	Weak transcription	HSMMtube	muscle
49	chr4:22456400-22461600	Weak transcription	HMEC	breast
50	chr4:22456400-22476200	Weak transcription	H9 Cell Line	embryonic stem cell

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