Variant report

Variant	esv3428528
Chromosome Location	chr22:29653712-29654071
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:29653510-29654782	GM12891	blood:	n/a	n/a
2	POLR2A	chr22:29654053-29654635	HL-60	blood:	n/a	n/a
3	POLR2A	chr22:29653791-29654045	GM12878	blood:	n/a	n/a
4	POLR2A	chr22:29653559-29657623	GM12892	blood:	n/a	n/a
5	POLR2A	chr22:29653662-29653963	K562	blood:	n/a	n/a
6	POLR2A	chr22:29653588-29656022	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr22:29653527-29654524	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr22:29653728-29654407	GM12891	blood:	n/a	n/a
9	POLR2A	chr22:29653767-29654134	MCF-7	breast:	n/a	n/a
10	POLR2A	chr22:29653540-29657993	SK-N-MC	brain:	n/a	n/a
11	POLR2A	chr22:29653774-29654178	HepG2	liver:	n/a	n/a
12	POLR2A	chr22:29654048-29654126	GM12878	blood:	n/a	n/a
13	POLR2A	chr22:29653655-29655844	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr22:29653683-29657301	GM12878	blood:	n/a	n/a
15	POLR2A	chr22:29653421-29654121	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr22:29653458-29653804	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr22:29653561-29653948	GM12878	blood:	n/a	n/a
18	POLR2A	chr22:29654018-29654465	GM12878	blood:	n/a	n/a
19	POLR2A	chr22:29653602-29657482	GM12891	blood:	n/a	n/a
20	POLR2A	chr22:29653724-29654185	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr22:29653486-29657933	GM12892	blood:	n/a	n/a
22	POLR2A	chr22:29654068-29655286	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr22:29653621-29654814	GM12892	blood:	n/a	n/a
24	POLR2A	chr22:29652410-29657525	GM12878	blood:	n/a	n/a
25	POLR2A	chr22:29653526-29658915	K562	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29638508..29640700-chr22:29653710..29656559,2	K562	blood:
2	chr22:29609413..29611410-chr22:29651943..29654586,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000237015	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 69 )

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs558388414	chr22:29653727-29653728	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs80070388	chr22:29653746-29653747	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs540812639	chr22:29653750-29653751	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs562292605	chr22:29653755-29653756	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs568710359	chr22:29653756-29653757	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs529574502	chr22:29653829-29653830	Weak transcription Strong transcription Enhancers Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs544295718	chr22:29653830-29653831	Weak transcription Strong transcription Enhancers Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs188117832	chr22:29653841-29653842	Weak transcription Strong transcription Enhancers Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs140192539	chr22:29653868-29653869	Weak transcription Strong transcription Enhancers Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs115675426	chr22:29653875-29653876	Weak transcription Strong transcription Enhancers Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs554646843	chr22:29653879-29653880	Weak transcription Strong transcription Enhancers Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs143851200	chr22:29653893-29653894	Weak transcription Strong transcription Enhancers Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs146366517	chr22:29653913-29653914	Weak transcription Strong transcription Enhancers Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs762817	chr22:29653929-29653930	Weak transcription Strong transcription Enhancers Bivalent Enhancer	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs567485608	chr22:29653959-29653960	Weak transcription Strong transcription Enhancers Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs909798	chr22:29654004-29654005	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
17	rs549826710	chr22:29654007-29654008	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs139681149	chr22:29654020-29654021	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs538749349	chr22:29654025-29654026	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs113253459	chr22:29654027-29654028	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs553950502	chr22:29654033-29654034	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs572169599	chr22:29654044-29654045	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs553810328	chr22:29654046-29654047	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:69)

Disease	PMID	Source
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	21080181	CNVD
Velocardiofacial syndrome	20111667	CNVD
Medulloblastoma	21979893	CNVD
sporadic solitary meningiomas	19589153	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Autism	22495311	CNVD
Chordoma	21602918	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Congenital heart defect	22511896	CNVD
Breast cancer	17603634	CNVD
Endometrial cancer	22040021	CNVD
Burkitt''s lymphoma	18698080	CNVD
Acute myeloid leukemia	16864856	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	17387387	CNVD
Seminomas	18059402	CNVD
Cancer	16751803	CNVD
Metanephric adenoma	20802469	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Colorectal cancer	19359472	CNVD
Metachromatic leukodystrophy	18421352	CNVD
Basal cell lymphoma	17170743	CNVD
Gastrointestinal stromal cancer	19259404	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Gastrointestinal stromal cancer	17535989	CNVD
Paraganglioma	17535989	CNVD
Pulmonary chondroma	17535989	CNVD
Breast cancer	21858162	CNVD
Myelodysplastic syndrome	21251322	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	16608533	CNVD
Melanoma	18172304	CNVD
Ovarian cancer	22174824	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Wilms tumour	21544195	CNVD
Acute myeloid leukemia	21251322	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Medullary thyroid carcinoma	18765511	CNVD
Lung cancer	18438408	CNVD
Pancreatic endocrine tumor	17639061	CNVD
abnormal development	18461090	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
small cell lung cancer	20016488	CNVD
Cancer	21183584	CNVD
Renal cell carcinoma	18765545	CNVD
Schizophrenia	19521646	CNVD
Schizophrenia	18990708	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Hepatocellular carcinoma	16750200	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Myelofibrosis	22110671	CNVD
Non-small cell lung cancer	21829676	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Autism	17322880	CNVD
Breast cancer	20409316	CNVD
Neurofibromatosis type 2	19566914	CNVD
Autism	19384346	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29622000-29655200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr22:29622000-29655800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr22:29622400-29656600	Weak transcription	Colonic Mucosa	Colon
4	chr22:29629000-29659400	Weak transcription	Brain Anterior Caudate	brain
5	chr22:29629600-29655400	Weak transcription	Liver	Liver
6	chr22:29629600-29655400	Weak transcription	Gastric	stomach
7	chr22:29633600-29654400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr22:29634600-29655200	Weak transcription	Brain Angular Gyrus	brain
9	chr22:29638400-29655200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr22:29639000-29655200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr22:29639400-29654200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr22:29639800-29656400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr22:29641600-29655600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr22:29641600-29659800	Weak transcription	Ovary	ovary
15	chr22:29641600-29661800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr22:29641800-29657800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr22:29642000-29659600	Weak transcription	Colon Smooth Muscle	Colon
18	chr22:29642200-29659800	Weak transcription	Duodenum Mucosa	Duodenum
19	chr22:29642600-29662400	Strong transcription	Fetal Intestine Small	intestine
20	chr22:29643600-29660400	Weak transcription	Fetal Kidney	kidney
21	chr22:29644600-29659800	Weak transcription	Brain Substantia Nigra	brain
22	chr22:29647400-29662000	Strong transcription	Fetal Stomach	stomach
23	chr22:29648000-29653800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr22:29648400-29657400	Strong transcription	Fetal Intestine Large	intestine
25	chr22:29648800-29655400	Weak transcription	Brain Hippocampus Middle	brain
26	chr22:29649000-29654000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr22:29649000-29662400	Weak transcription	Fetal Brain Male	brain
28	chr22:29649800-29655200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr22:29649800-29656000	Strong transcription	Spleen	Spleen
30	chr22:29649800-29657400	Strong transcription	Fetal Brain Female	brain
31	chr22:29650000-29655000	Weak transcription	Esophagus	oesophagus
32	chr22:29650200-29653800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr22:29650200-29653800	Weak transcription	Fetal Muscle Trunk	muscle
34	chr22:29650200-29654600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr22:29650200-29655400	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr22:29650200-29655400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr22:29650200-29657200	Strong transcription	Brain Germinal Matrix	brain
38	chr22:29650200-29662600	Weak transcription	Stomach Mucosa	stomach
39	chr22:29650400-29655200	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr22:29650400-29655600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr22:29650600-29655200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr22:29650600-29659800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr22:29650600-29660000	Weak transcription	Primary T cells from cord blood	blood
44	chr22:29650600-29660200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr22:29650800-29659800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr22:29651000-29659600	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr22:29651000-29660000	Weak transcription	HepG2	liver
48	chr22:29651200-29654000	Weak transcription	Fetal Thymus	thymus
49	chr22:29651200-29654200	Weak transcription	Placenta	Placenta
50	chr22:29651200-29654800	Weak transcription	Thymus	Thymus

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