Variant report

Variant	esv9779
Chromosome Location	chr3:28392059-28393315
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:28388560-28395839	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr3:28387839-28396035	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr3:28389421-28392084	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:28388762-28392516	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:28279814..28285757-chr3:28388127..28392208,14	K562	blood:
2	chr3:28360111..28361698-chr3:28390791..28393091,2	K562	blood:
3	chr3:28391232..28393248-chr3:28418194..28419782,2	K562	blood:
4	chr3:28279814..28284603-chr3:28388127..28392296,9	K562	blood:
5	chr3:23957644..23960053-chr3:28390990..28393934,2	K562	blood:
6	chr3:28390959..28393888-chr3:28439197..28440878,2	K562	blood:
7	chr3:28388985..28391534-chr3:28392522..28395411,2	MCF-7	breast:

No data

Variant related genes	Relation type
AZI2	TF binding region
ENSG00000197885	chromatin interactions
ENSG00000206559	chromatin interactions
ENSG00000174748	chromatin interactions
ENSG00000163512	chromatin interactions
ENSG00000187118	chromatin interactions

Extended variants
information (count: 41 )
Associated
traits (count: 74 )

Variant overlapped rSNPs/rCNVs (count:41 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs142497099	chr3:28392060-28392061	Active TSS Weak transcription Flanking Active TSS Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
2	rs35702956	chr3:28392084-28392085	Active TSS Weak transcription Flanking Active TSS Enhancers	TF binding region Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs76148927	chr3:28392096-28392097	Active TSS Weak transcription Flanking Active TSS Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
4	rs554833124	chr3:28392112-28392113	Active TSS Weak transcription Flanking Active TSS Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
5	rs559569202	chr3:28392194-28392195	Active TSS Weak transcription Flanking Active TSS Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
6	rs545576568	chr3:28392285-28392286	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
7	rs540689358	chr3:28392288-28392289	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
8	rs528421934	chr3:28392293-28392294	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
9	rs17021381	chr3:28392313-28392314	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs190646463	chr3:28392321-28392322	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
11	rs551212355	chr3:28392363-28392364	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
12	rs115488228	chr3:28392385-28392386	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
13	rs147588690	chr3:28392418-28392419	Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
14	rs149044084	chr3:28392451-28392452	Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
15	rs557100665	chr3:28392471-28392472	Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
16	rs183169577	chr3:28392485-28392486	Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
17	rs558762407	chr3:28392488-28392489	Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
18	rs565915359	chr3:28392501-28392502	Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
19	rs143020078	chr3:28392554-28392555	Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
20	rs6763313	chr3:28392598-28392599	Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	5 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs368057663	chr3:28392627-28392628	Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
22	rs187851008	chr3:28392635-28392636	Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
23	rs554809749	chr3:28392647-28392648	Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
24	rs574106559	chr3:28392666-28392667	Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
25	rs546091754	chr3:28392712-28392713	Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
26	rs189571922	chr3:28392713-28392714	Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
27	rs536599150	chr3:28392742-28392743	Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
28	rs556903814	chr3:28392744-28392745	Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
29	rs182604517	chr3:28392746-28392747	Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
30	rs559340781	chr3:28392788-28392789	Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
31	rs576897827	chr3:28392837-28392838	Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
32	rs545859429	chr3:28392862-28392863	Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
33	rs559608302	chr3:28392889-28392890	Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
34	rs188064247	chr3:28392890-28392891	Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
35	rs573039354	chr3:28392892-28392893	Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
36	rs200231974	chr3:28392945-28392946	Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
37	rs572472327	chr3:28392977-28392978	Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
38	rs542154461	chr3:28393045-28393046	Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
39	rs192690114	chr3:28393063-28393064	Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
40	rs530831299	chr3:28393075-28393076	Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
41	rs549948355	chr3:28393285-28393286	Weak transcription ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:74)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	17327916	CNVD
Glioblastoma multiforme	21080181	CNVD
Neuroblastoma	18923191	CNVD
Colorectal cancer	21297112	CNVD
Lynch syndrome	18415027	CNVD
Renal cell carcinoma	18592004	CNVD
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
lymphocytic leukemia	21291569	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Esophageal cancer	20955586	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Squamous cell cancer	20885788	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Melanoma	20688739	CNVD
Acute myeloid leukemia	21251322	CNVD
Myelofibrosis	22110671	CNVD
Lung cancer	16618734	CNVD
Cancer	20164919	CNVD
Developmental delay	21147756	CNVD
Schizophrenia	18511947	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28387600-28392200	Active TSS	Right Atrium	heart
2	chr3:28388400-28392200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:28389200-28392200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:28391000-28392200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr3:28391000-28394400	Weak transcription	Spleen	Spleen
6	chr3:28391200-28393600	Weak transcription	Gastric	stomach
7	chr3:28391200-28395200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:28391400-28392200	Enhancers	Brain Anterior Caudate	brain
9	chr3:28391400-28392400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:28391400-28392800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr3:28391400-28393200	Weak transcription	Primary B cells from peripheral blood	blood
12	chr3:28391400-28393200	Weak transcription	Fetal Kidney	kidney
13	chr3:28391400-28393200	Weak transcription	Ovary	ovary
14	chr3:28391400-28393600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:28391400-28393600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:28391400-28393600	Weak transcription	Aorta	Aorta
17	chr3:28391400-28393600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr3:28391400-28393600	Weak transcription	Pancreas	Pancrea
19	chr3:28391400-28393600	Weak transcription	HSMM	muscle
20	chr3:28391400-28394000	Weak transcription	Brain Substantia Nigra	brain
21	chr3:28391400-28394200	Weak transcription	Left Ventricle	heart
22	chr3:28391400-28394400	Weak transcription	Placenta	Placenta
23	chr3:28391400-28394400	Weak transcription	Fetal Stomach	stomach
24	chr3:28391400-28395200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:28391400-28395200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr3:28391400-28396000	Weak transcription	Colonic Mucosa	Colon
27	chr3:28391600-28392200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:28391600-28392200	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr3:28391600-28392200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:28391600-28392200	Enhancers	HepG2	liver
31	chr3:28391600-28392400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr3:28391600-28392400	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr3:28391600-28392600	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr3:28391600-28392600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr3:28391600-28392600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr3:28391600-28392800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:28391600-28392800	Weak transcription	Fetal Lung	lung
38	chr3:28391600-28392800	Weak transcription	Psoas Muscle	Psoas
39	chr3:28391600-28393200	Weak transcription	Primary B cells from cord blood	blood
40	chr3:28391600-28393400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr3:28391600-28394600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:28391600-28395400	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr3:28391600-28395400	Weak transcription	Brain Hippocampus Middle	brain
44	chr3:28391600-28397800	Weak transcription	Stomach Smooth Muscle	stomach
45	chr3:28391600-28398600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr3:28391800-28392200	Enhancers	Primary T cells from cord blood	blood
47	chr3:28391800-28392200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:28391800-28392200	Enhancers	Pancreatic Islets	Pancreatic Islet
49	chr3:28391800-28392400	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr3:28391800-28392400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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