Variant report

Variant	esv2753350
Chromosome Location	chr12:39617233-39669533
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:38722084..38722866-chr12:39667246..39667987,2	MCF-7	breast:
2	chr12:39300107..39301045-chr12:39666439..39667709,7	MCF-7	breast:
3	chr12:38532568..38533113-chr12:39666750..39667387,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C12orf40-4	chr12:39667587-39667691	NONHSAT027698
2	lnc-C12orf40-4	chr12:39667024-39667150	NONHSAT027698

Variant related genes	Relation type
ENSG00000257718	chromatin interactions

Extended variants
information (count: 783 )
Associated
traits (count: 59 )

Variant overlapped rSNPs/rCNVs (count:783 , 50 per page) page: 1 2 3 4 5 6 7 ... 16

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs77807322	chr12:39620807-39620808	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs145714825	chr12:39620828-39620829	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs140462177	chr12:39620914-39620915	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs533345670	chr12:39620969-39620970	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs559604507	chr12:39620970-39620971	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs533473733	chr12:39620974-39620975	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs370409234	chr12:39621054-39621055	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs551729149	chr12:39621091-39621092	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs117915737	chr12:39621133-39621134	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs189686559	chr12:39621169-39621170	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs73266458	chr12:39621277-39621278	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs549852816	chr12:39621278-39621279	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs4403835	chr12:39621324-39621325	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs7350605	chr12:39621331-39621332	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs78162718	chr12:39621335-39621336	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs572346355	chr12:39621358-39621359	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs145584968	chr12:39621441-39621442	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs558147827	chr12:39621488-39621489	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs146507287	chr12:39621519-39621520	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs77470244	chr12:39621521-39621522	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs75821956	chr12:39621538-39621539	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs181226968	chr12:39621544-39621545	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs375070526	chr12:39621549-39621550	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs141045680	chr12:39621557-39621558	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs559543438	chr12:39621558-39621559	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs533413174	chr12:39621569-39621570	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs143119845	chr12:39621570-39621571	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs563881486	chr12:39621589-39621590	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs549853790	chr12:39621718-39621719	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs539599962	chr12:39621719-39621720	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs76650065	chr12:39621729-39621730	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs531336531	chr12:39621730-39621731	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs372966760	chr12:39621745-39621746	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs4768669	chr12:39621747-39621748	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs186208522	chr12:39621766-39621767	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs148232174	chr12:39621791-39621792	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs572863438	chr12:39621796-39621797	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs549028854	chr12:39621808-39621809	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs191956987	chr12:39621877-39621878	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs547583542	chr12:39621891-39621892	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs141198042	chr12:39621931-39621932	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs368320021	chr12:39621942-39621943	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs181452332	chr12:39621961-39621962	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs576305595	chr12:39621977-39621978	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs537443181	chr12:39622032-39622033	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs17126974	chr12:39622094-39622095	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs186472084	chr12:39622106-39622107	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs541144743	chr12:39622120-39622121	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs553111077	chr12:39622168-39622169	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs191011027	chr12:39622182-39622183	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:59)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
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
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Ewing''s sarcoma	17952124	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Cancer	20164919	CNVD
Neurodevelopmental disorder	22521361	CNVD
Breast cancer	21509527	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
T-cell prolymphocytic leukemia	17713554	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
Myelofibrosis	22110671	CNVD
Breast cancer	17603634	CNVD
Cancer	21183584	CNVD
Hirschsprung''s Disease	21712996	CNVD
Lissencephaly	21572526	CNVD
Lung cancer	18438408	CNVD
Acute myeloid leukemia	21251322	CNVD
small cell lung cancer	20016488	CNVD
Autism	20858243	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Breast cancer	19602461	CNVD
Breast cancer	17899364	CNVD
Cancer	20164920	CNVD
Colorectal cancer	16272173	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39620800-39622000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:39621000-39621400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:39621000-39621600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:39621200-39621400	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr12:39622000-39624000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:39624000-39624600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:39624600-39629600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:39629400-39630200	Enhancers	Colon Smooth Muscle	Colon
9	chr12:39629600-39631400	Enhancers	NH-A	brain
10	chr12:39629600-39635000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:39629800-39630000	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr12:39629800-39630400	Enhancers	A549	lung
13	chr12:39629800-39631200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:39630000-39634000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr12:39630200-39631200	Enhancers	Hela-S3	cervix
16	chr12:39630200-39631400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:39630200-39631400	Enhancers	Muscle Satellite Cultured Cells	--
18	chr12:39630400-39631200	Flanking Active TSS	A549	lung
19	chr12:39630600-39631000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:39630600-39631000	Enhancers	HSMMtube	muscle
21	chr12:39630800-39631200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:39630800-39631600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr12:39631200-39631400	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr12:39631200-39631400	Enhancers	A549	lung
25	chr12:39631200-39632600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:39631200-39632600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:39631400-39632600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr12:39631400-39633200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:39631600-39632200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr12:39632200-39632800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr12:39632200-39632800	Bivalent Enhancer	A549	lung
32	chr12:39632400-39632800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr12:39632600-39632800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr12:39632600-39633400	Enhancers	Rectal Mucosa Donor 29	rectum
35	chr12:39632600-39633800	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr12:39632600-39634200	Enhancers	Fetal Intestine Large	intestine
37	chr12:39632600-39634400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr12:39632600-39634800	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr12:39632600-39635000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr12:39632800-39633200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr12:39632800-39633400	Enhancers	Brain Substantia Nigra	brain
42	chr12:39632800-39634200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr12:39633200-39634000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr12:39633200-39634200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:39633400-39633800	Enhancers	HepG2	liver
46	chr12:39633400-39634000	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr12:39633400-39634400	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr12:39633400-39634600	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr12:39633400-39634800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr12:39633800-39634600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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