Variant report

Variant	esv3388136
Chromosome Location	chr1:228916429-228919727
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:228913388..228915243-chr1:228916401..228917971,2	MCF-7	breast:

Extended variants
information (count: 138 )
Associated
traits (count: 90 )

Variant overlapped rSNPs/rCNVs (count:138 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs372055221	chr1:228916449-228916450	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs73099554	chr1:228916459-228916460	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs185061021	chr1:228916460-228916461	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs137919112	chr1:228916461-228916462	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs543193320	chr1:228916488-228916489	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs376558090	chr1:228916492-228916493	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs563115945	chr1:228916504-228916505	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs140825384	chr1:228916579-228916580	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs73099555	chr1:228916604-228916605	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs559324341	chr1:228916614-228916615	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
11	rs241324	chr1:228916634-228916635	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
12	rs548433323	chr1:228916660-228916661	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
13	rs371667632	chr1:228916667-228916668	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
14	rs571895268	chr1:228916689-228916690	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
15	rs531038745	chr1:228916708-228916709	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
16	rs560314919	chr1:228916722-228916723	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
17	rs374399103	chr1:228916723-228916724	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
18	rs201386474	chr1:228916724-228916725	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
19	rs143827835	chr1:228916725-228916726	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
20	rs551216193	chr1:228916726-228916727	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
21	rs571020556	chr1:228916728-228916729	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
22	rs540144183	chr1:228916731-228916732	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
23	rs112283785	chr1:228916734-228916735	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
24	rs34154277	chr1:228916768-228916769	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
25	rs538540268	chr1:228916820-228916821	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs141837517	chr1:228916844-228916845	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs565583314	chr1:228916854-228916855	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs150783301	chr1:228916883-228916884	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs554398023	chr1:228916892-228916893	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs574498019	chr1:228916908-228916909	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs536715078	chr1:228916941-228916942	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs368359677	chr1:228916965-228916966	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs556747791	chr1:228916996-228916997	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs189373735	chr1:228917045-228917046	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
35	rs241323	chr1:228917051-228917052	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
36	rs112204069	chr1:228917099-228917100	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
37	rs180940569	chr1:228917154-228917155	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
38	rs369136618	chr1:228917163-228917164	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
39	rs183506037	chr1:228917199-228917200	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
40	rs113409554	chr1:228917299-228917300	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
41	rs372762410	chr1:228917325-228917326	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
42	rs241322	chr1:228917346-228917347	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
43	rs241321	chr1:228917406-228917407	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
44	rs551051933	chr1:228917453-228917454	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
45	rs189407244	chr1:228917536-228917537	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
46	rs533558790	chr1:228917559-228917560	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
47	rs181966294	chr1:228917562-228917563	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
48	rs543169234	chr1:228917567-228917568	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
49	rs552844170	chr1:228917572-228917573	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
50	rs372277360	chr1:228917573-228917574	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:90)

Disease	PMID	Source
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Autism	22495311	CNVD
Melanoma	18172304	CNVD
Rett syndrome	21593744	CNVD
Medulloblastoma	21979893	CNVD
Cancer	20164919	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	CNVD
Non-small cell lung cancer	21044232	CNVD
Cervical cancer	21063398	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	20632083	CNVD
Endometrial cancer	22040021	CNVD
Ewing''s sarcoma	21437220	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Medulloblastoma	21292688	CNVD
Phyllodes tumor	17334353	CNVD
Breast cancer	21264507	CNVD
Liposarcoma	21253554	CNVD
Multiple myeloma	21628407	CNVD
Cancer	16751803	CNVD
Prostate cancer	16705090	CNVD
Neuroblastoma	19435921	CNVD
Breast cancer	17850661	CNVD
Breast cancer	16461572	CNVD
Intracranial tumor	16823260	CNVD
Medulloblastoma	18056178	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	21899760	CNVD
Breast cancer	21858162	CNVD
Non-small cell lung cancer	21385341	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	16608533	CNVD
Ewing''s sarcoma	22429812	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Acute myeloid leukemia	21251322	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Testicular germ cell tumor	18059402	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Breast cancer	21509527	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Urothelial carcinoma	21177765	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Chordoma	18071362	CNVD
T-cell lymphomas	19863542	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hepatocellular carcinoma	18803288	CNVD
Urothelial tumor	18831757	CNVD
Lung cancer	18438408	CNVD
Medulloblastoma	16783165	CNVD
Basal cell lymphoma	17170743	CNVD
Mental retardation	19951919	CNVD
Non-syndromic sensorineural hearing loss	17873649	CNVD
Basal cell lymphoma	17053054	CNVD
Autism	14699429	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Congenital abnormalities	21549014	CNVD
Developmental delay	21549014	CNVD
Mental retardation	21549014	CNVD
small cell lung cancer	20016488	CNVD
Glioblastoma multiforme	21138945	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Cancer	20164920	CNVD
Cancer	17060936	CNVD
abnormal development	18461090	CNVD
Breast cancer	21364760	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Myelofibrosis	22110671	CNVD
Ovarian clear cell carcinoma	19293255	CNVD
Pancreatic cancer	17952125	CNVD
early-passage human iPS cells	21368824	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:141 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228906200-228917000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:228912600-228920800	Weak transcription	Fetal Thymus	thymus
3	chr1:228915200-228916600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:228915400-228916600	Weak transcription	Placenta	Placenta
5	chr1:228915400-228917000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:228915400-228921200	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr1:228915600-228919200	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr1:228916400-228916800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:228916400-228916800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr1:228916400-228917800	Enhancers	Fetal Lung	lung
11	chr1:228916400-228918400	Enhancers	HepG2	liver
12	chr1:228916400-228919600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:228916600-228916800	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:228916600-228917000	Enhancers	Right Atrium	heart
15	chr1:228916600-228917000	Enhancers	Right Ventricle	heart
16	chr1:228916600-228917600	Enhancers	Brain Substantia Nigra	brain
17	chr1:228916600-228917800	Enhancers	Placenta	Placenta
18	chr1:228916600-228917800	Enhancers	Fetal Stomach	stomach
19	chr1:228916600-228920600	Enhancers	Placenta Amnion	Placenta Amnion
20	chr1:228916800-228917000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:228916800-228917000	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr1:228916800-228917000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:228916800-228917200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:228916800-228917400	Enhancers	Brain Hippocampus Middle	brain
25	chr1:228916800-228917600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:228916800-228917800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr1:228916800-228918000	Enhancers	Brain Cingulate Gyrus	brain
28	chr1:228916800-228919200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:228916800-228921000	Enhancers	Fetal Intestine Small	intestine
30	chr1:228917000-228917200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:228917000-228917200	Enhancers	H9 Cell Line	embryonic stem cell
32	chr1:228917000-228917200	Enhancers	Fetal Kidney	kidney
33	chr1:228917000-228917200	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr1:228917000-228917400	Flanking Active TSS	Brain Anterior Caudate	brain
35	chr1:228917000-228917400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
36	chr1:228917000-228917400	Active TSS	Fetal Brain Male	brain
37	chr1:228917000-228917400	Weak transcription	Right Atrium	heart
38	chr1:228917000-228917400	Weak transcription	Right Ventricle	heart
39	chr1:228917000-228917600	Enhancers	Brain Angular Gyrus	brain
40	chr1:228917000-228917600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr1:228917000-228917800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:228917000-228917800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:228917000-228917800	Enhancers	Adipose Nuclei	Adipose
44	chr1:228917000-228917800	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr1:228917000-228918000	Bivalent Enhancer	Fetal Heart	heart
46	chr1:228917000-228918000	Enhancers	Ovary	ovary
47	chr1:228917000-228918800	Enhancers	NHDF-Ad	bronchial
48	chr1:228917000-228919200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:228917000-228919200	Enhancers	Psoas Muscle	Psoas
50	chr1:228917000-228921000	Enhancers	Fetal Intestine Large	intestine

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