Variant report

Variant	esv3403829
Chromosome Location	chr12:56139035-56140433
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56135540..56139368-chr12:56208041..56213329,11	MCF-7	breast:
2	chr12:56131110..56132920-chr12:56139527..56141888,2	K562	blood:
3	chr12:56112563..56114483-chr12:56136186..56139060,2	K562	blood:
4	chr12:56137010..56139176-chr12:56366479..56369419,2	MCF-7	breast:
5	chr12:56135568..56140230-chr12:56496911..56501047,5	K562	blood:
6	chr12:56110287..56112074-chr12:56139458..56141706,2	K562	blood:
7	chr12:56136775..56139143-chr12:56214826..56217314,2	MCF-7	breast:
8	chr12:56135076..56139517-chr12:56332723..56335701,7	K562	blood:
9	chr12:56137294..56139429-chr12:56377696..56379845,2	K562	blood:
10	chr12:56112360..56117057-chr12:56137654..56141043,4	MCF-7	breast:
11	chr12:56136330..56139191-chr12:56511663..56513514,2	K562	blood:
12	chr12:56139474..56141266-chr12:56187183..56189811,2	MCF-7	breast:
13	chr12:56119392..56124555-chr12:56134719..56139155,10	MCF-7	breast:
14	chr12:56137714..56140365-chr12:56357823..56359746,2	K562	blood:
15	chr12:56117197..56125255-chr12:56135299..56142277,21	K562	blood:
16	chr12:56139597..56141342-chr12:56182890..56184805,2	MCF-7	breast:
17	chr12:56136481..56142183-chr12:56210043..56213312,6	K562	blood:
18	chr12:56135401..56138372-chr12:56138413..56141601,7	MCF-7	breast:
19	chr12:56107652..56112121-chr12:56134921..56139203,6	MCF-7	breast:
20	chr12:56118873..56123597-chr12:56135421..56141775,11	K562	blood:
21	chr12:56126916..56129373-chr12:56137804..56139318,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000135424	chromatin interactions
ENSG00000257390	chromatin interactions
ENSG00000258056	chromatin interactions
ENSG00000135404	chromatin interactions
ENSG00000135441	chromatin interactions
ENSG00000135437	chromatin interactions
ENSG00000139641	chromatin interactions
ENSG00000135482	chromatin interactions
ENSG00000185664	chromatin interactions
ENSG00000135414	chromatin interactions
ENSG00000205323	chromatin interactions
ENSG00000258311	chromatin interactions
ENSG00000123353	chromatin interactions
ENSG00000065357	chromatin interactions
ENSG00000170515	chromatin interactions
ENSG00000111540	chromatin interactions

Extended variants
information (count: 28 )
Associated
traits (count: 78 )

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs556624511	chr12:56139135-56139136	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	Chromatin interactive region	16 gene(s)	Overlapped CNVs	n/a
2	rs117839207	chr12:56139162-56139163	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	Chromatin interactive region	15 gene(s)	Overlapped CNVs	n/a
3	rs117721518	chr12:56139172-56139173	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	Chromatin interactive region	15 gene(s)	Overlapped CNVs	n/a
4	rs540234530	chr12:56139336-56139337	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers	Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
5	rs560522455	chr12:56139345-56139346	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers	Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
6	rs574416390	chr12:56139347-56139348	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers	Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
7	rs187599603	chr12:56139394-56139395	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers	Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
8	rs376820214	chr12:56139436-56139437	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
9	rs113834592	chr12:56139539-56139540	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
10	rs147208412	chr12:56139599-56139600	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
11	rs563423213	chr12:56139613-56139614	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
12	rs530775069	chr12:56139717-56139718	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
13	rs3782241	chr12:56139767-56139768	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
14	rs76584604	chr12:56139865-56139866	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
15	rs183418159	chr12:56139945-56139946	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
16	rs75178345	chr12:56139955-56139956	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
17	rs11829536	chr12:56140027-56140028	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	Chromatin interactive region	9 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
18	rs375821674	chr12:56140049-56140050	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
19	rs563782485	chr12:56140071-56140072	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
20	rs187746949	chr12:56140113-56140114	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
21	rs369047652	chr12:56140126-56140127	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
22	rs568032517	chr12:56140158-56140159	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
23	rs564687907	chr12:56140191-56140192	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
24	rs192214384	chr12:56140214-56140215	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
25	rs144893600	chr12:56140350-56140351	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
26	rs183358804	chr12:56140394-56140395	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
27	rs12422534	chr12:56140423-56140424	Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS	Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
28	rs532850941	chr12:56140425-56140426	Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS	Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:78)

Disease	PMID	Source
Seminomas	18059402	CNVD
Wilms tumour	21544195	CNVD
Esophageal cancer	21851588	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Ewing''s sarcoma	21437220	CNVD
Testicular germ cell tumor	18059402	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Neurodevelopmental disorder	22521361	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	18194544	CNVD
Breast cancer	21949216	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Acute myeloid leukemia	16864856	CNVD
Cancer	21637783	CNVD
Glioblastoma multiforme	21080181	CNVD
Renal cell carcinoma	19461508	CNVD
Burkitt''s lymphoma	18698080	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Hirschsprung''s Disease	21712996	CNVD
Lissencephaly	21572526	CNVD
Lung cancer	18438408	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Breast cancer	19602461	CNVD
Breast cancer	17899364	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	21364760	CNVD
Prostate cancer	18632612	CNVD
Follicular lymphoma	20505157	CNVD
Hepatocellular carcinoma	16750200	CNVD
Melanoma	18172304	CNVD
Metanephric adenoma	20802469	CNVD
Glioblastoma multiforme	17387387	CNVD
liposarcomas	17372913	CNVD
Non-small cell lung cancer	24170126	CNVD
Cancer	16751803	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Bladder cancer	21909424	CNVD
Intracranial aneurysm	16715129	CNVD
Breast cancer	17661082	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Breast cancer	21785460	CNVD
small cell lung cancer	20016488	CNVD
Hodgkin''s lymphoma	18179710	CNVD
Ewing''s sarcoma	17952124	CNVD
Autism	20531469	CNVD
Multiple myeloma	16616336	CNVD
Rhabdomyosarcoma	16790082	CNVD
Renal cell carcinoma	18765545	CNVD
Urothelial cell carcinoma	18451213	CNVD
Glioblastoma multiforme	21138945	CNVD
Glioblastoma multiforme	21569311	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Glioblastoma multiforme	19115005	CNVD
early-passage human iPS cells	21368824	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Liposarcoma	21253554	CNVD
Cancer	20164919	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:318 , 50 per page) page: 1 2 3 4 5 6 7

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56136200-56139800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:56136400-56140200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr12:56136600-56139200	Active TSS	Rectal Smooth Muscle	rectum
4	chr12:56136600-56139800	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr12:56136600-56140000	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr12:56136600-56140000	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr12:56136600-56140200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:56136600-56140600	Active TSS	Fetal Kidney	kidney
9	chr12:56137200-56139200	Flanking Active TSS	Fetal Muscle Leg	muscle
10	chr12:56137200-56140000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:56137400-56139200	Bivalent Enhancer	Stomach Mucosa	stomach
12	chr12:56137400-56139400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr12:56137400-56139400	Flanking Active TSS	Fetal Brain Female	brain
14	chr12:56137400-56139400	Flanking Active TSS	Fetal Muscle Trunk	muscle
15	chr12:56137400-56139800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:56137400-56140000	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr12:56137600-56139400	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr12:56137600-56139400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:56137600-56139400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr12:56137600-56139400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
21	chr12:56137600-56139400	Flanking Active TSS	Stomach Smooth Muscle	stomach
22	chr12:56137600-56140400	Enhancers	Fetal Brain Male	brain
23	chr12:56137800-56139200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr12:56137800-56139400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
25	chr12:56137800-56139400	Flanking Active TSS	Brain Anterior Caudate	brain
26	chr12:56137800-56139400	Flanking Active TSS	Brain Cingulate Gyrus	brain
27	chr12:56137800-56139400	Flanking Active TSS	Brain Hippocampus Middle	brain
28	chr12:56137800-56139400	Flanking Active TSS	Fetal Thymus	thymus
29	chr12:56137800-56139400	Flanking Active TSS	Dnd41	blood
30	chr12:56137800-56139400	Flanking Active TSS	GM12878-XiMat	blood
31	chr12:56137800-56139400	Flanking Active TSS	K562	blood
32	chr12:56137800-56139400	Flanking Active TSS	NH-A	brain
33	chr12:56137800-56139400	Flanking Active TSS	NHLF	lung
34	chr12:56137800-56140800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr12:56138000-56139400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:56138000-56139400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr12:56138000-56139400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr12:56138000-56139400	Enhancers	A549	lung
39	chr12:56138000-56140200	Flanking Active TSS	Brain Germinal Matrix	brain
40	chr12:56138000-56144800	Weak transcription	Liver	Liver
41	chr12:56138000-56144800	Weak transcription	Lung	lung
42	chr12:56138000-56145000	Weak transcription	Gastric	stomach
43	chr12:56138200-56139200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr12:56138200-56139200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr12:56138200-56139200	Enhancers	Spleen	Spleen
46	chr12:56138200-56139400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr12:56138200-56140000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr12:56138200-56140000	Enhancers	Primary T cells fromperipheralblood	blood
49	chr12:56138200-56140000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr12:56138200-56142400	Weak transcription	Aorta	Aorta

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