Variant report

Variant	esv3408790
Chromosome Location	chr22:28999302-29001500
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:28996007..28999960-chr22:29194026..29197947,6	MCF-7	breast:
2	chr22:28997050..28999545-chr22:28999902..29002703,2	MCF-7	breast:
3	chr22:28997050..28999545-chr22:28999902..29002703,2	MCF-7	breast:
4	chr22:29001462..29003738-chr22:29195242..29198224,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100219	chromatin interactions
ENSG00000226471	chromatin interactions

Extended variants
information (count: 78 )
Associated
traits (count: 69 )

Variant overlapped rSNPs/rCNVs (count:78 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs185190742	chr22:28999322-28999323	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs538025629	chr22:28999363-28999364	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs9613654	chr22:28999369-28999370	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs554358871	chr22:28999371-28999372	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs79755375	chr22:28999374-28999375	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs139484975	chr22:28999375-28999376	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs372822109	chr22:28999382-28999383	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs5752763	chr22:28999402-28999403	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs556822307	chr22:28999490-28999491	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs578097602	chr22:28999501-28999502	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs34323251	chr22:28999524-28999525	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs553606630	chr22:28999576-28999577	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs572060215	chr22:28999633-28999634	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs542224307	chr22:28999662-28999663	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs12166129	chr22:28999668-28999669	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs5762712	chr22:28999721-28999722	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs543291302	chr22:28999725-28999726	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs564206055	chr22:28999751-28999752	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs532224408	chr22:28999755-28999756	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs576023071	chr22:28999789-28999790	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs368676044	chr22:28999790-28999791	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs541427795	chr22:28999830-28999831	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs189226473	chr22:28999850-28999851	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs374125895	chr22:28999870-28999871	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs181924592	chr22:28999878-28999879	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs12166245	chr22:28999890-28999891	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs538571325	chr22:28999900-28999901	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs540838260	chr22:28999928-28999929	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs571880439	chr22:28999935-28999936	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs538859303	chr22:28999961-28999962	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs186814333	chr22:28999987-28999988	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs536117716	chr22:29000018-29000019	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs12166363	chr22:29000057-29000058	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs542311929	chr22:29000081-29000082	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs191594754	chr22:29000082-29000083	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs570005833	chr22:29000193-29000194	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs375751470	chr22:29000214-29000215	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs183844762	chr22:29000249-29000250	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs556762814	chr22:29000286-29000287	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs575617536	chr22:29000292-29000293	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs71275602	chr22:29000310-29000311	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs186315440	chr22:29000346-29000347	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs565055834	chr22:29000370-29000371	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs190375869	chr22:29000435-29000436	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs540880693	chr22:29000441-29000442	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs559493723	chr22:29000463-29000464	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs368240929	chr22:29000484-29000485	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs151223836	chr22:29000587-29000588	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs577634925	chr22:29000589-29000590	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs549480478	chr22:29000671-29000672	Weak transcription Enhancers	n/a	n/a	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
Breast cancer	21509527	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
Ovine squamous-cell carcinoma	17599052	CNVD
Cat eye syndrome	16708226	CNVD
Olfactory neuroblastoma	18408657	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
Ovarian clear cell carcinoma	21343371	CNVD
Schizophrenia	21346763	CNVD

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28991400-29000800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr22:28991400-29001000	Weak transcription	Fetal Lung	lung
3	chr22:28991400-29003600	Weak transcription	NHLF	lung
4	chr22:28991400-29004200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr22:28991800-29007600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr22:28996200-29002800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr22:28997000-29000600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr22:28998200-29004000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr22:28999400-28999600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr22:28999800-29000000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr22:29000000-29000800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr22:29000600-29002000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr22:29000800-29001600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr22:29000800-29001600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr22:29000800-29001600	Enhancers	HUVEC	blood vessel
16	chr22:29001000-29001400	Enhancers	Brain Hippocampus Middle	brain
17	chr22:29001000-29001600	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr22:29001000-29001600	Enhancers	Fetal Lung	lung
19	chr22:29001000-29001800	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr22:29001000-29001800	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr22:29001200-29001600	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr22:29001200-29001600	Enhancers	iPS-18 Cell Line	embryonic stem cell

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