Variant report

Variant	esv3388339
Chromosome Location	chr12:40917344-40931738
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:64)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:40921093-40921125	GM13976	blood:	n/a	n/a
2	CTCF	chr12:40926900-40927050	WI-38	lung:	n/a	n/a
3	E2F4	chr12:40927953-40928008	MCF10A-Er-Src	breast:	n/a	n/a
4	E2F4	chr12:40931216-40931218	MCF10A-Er-Src	breast:	n/a	n/a
5	GABPA	chr12:40918691-40919382	HL-60	blood:	n/a	n/a
6	GATA3	chr12:40928411-40928509	SH-SY5Y	brain:	n/a	chr12:40928425-40928446
7	MAZ	chr12:40924770-40924774	HepG2	liver:	n/a	n/a
8	NANOG	chr12:40928651-40928972	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr12:40919298-40919520	K562	blood:	n/a	n/a
10	POLR2A	chr12:40926796-40926820	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr12:40919105-40919108	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr12:40929145-40929157	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr12:40922763-40923002	GM12878	blood:	n/a	n/a
14	SPI1	chr12:40918937-40919169	GM12878	blood:	n/a	n/a
15	SPI1	chr12:40918749-40919364	HL-60	blood:	n/a	n/a
16	SPI1	chr12:40918973-40919155	GM12891	blood:	n/a	n/a
17	SPI1	chr12:40918940-40919283	HL-60	blood:	n/a	n/a
18	SPI1	chr12:40918138-40918518	HL-60	blood:	n/a	n/a
19	TCF12	chr12:40928596-40928890	H1-hESC	embryonic stem cell:	n/a	n/a
20	TEAD4	chr12:40928616-40928951	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:64 , 50 per page) page: 1 2

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CNTN1-1	chr12:40927035-40927085	XLOC_009713
2	lnc-CNTN1-1	chr12:40927035-40927085	XLOC_009713
3	lnc-CNTN1-1	chr12:40925797-40925884	XLOC_009713
4	lnc-CNTN1-1	chr12:40921859-40921912	XLOC_009713
5	lnc-CNTN1-1	chr12:40931464-40931517	XLOC_009713
6	lnc-CNTN1-1	chr12:40929006-40929059	NONHSAT027736
7	lnc-CNTN1-1	chr12:40927035-40927085	NONHSAT027736
8	lnc-CNTN1-1	chr12:40926827-40926880	XLOC_009713
9	lnc-CNTN1-1	chr12:40927958-40928011	XLOC_009713
10	lnc-CNTN1-1	chr12:40921093-40921146	XLOC_009713
11	lnc-CNTN1-1	chr12:40924260-40924313	XLOC_009713
12	lnc-CNTN1-1	chr12:40928513-40928545	XLOC_009713
13	lnc-CNTN1-1	chr12:40924859-40926084	NONHSAT027733
14	lnc-CNTN1-1	chr12:40928815-40928868	XLOC_009713
15	lnc-CNTN1-1	chr12:40927958-40928011	XLOC_009713
16	lnc-CNTN1-1	chr12:40921859-40921912	NONHSAT027733
17	lnc-CNTN1-1	chr12:40917391-40917444	NONHSAT140068
18	lnc-CNTN1-1	chr12:40924260-40924313	NONHSAT027733
19	lnc-CNTN1-1	chr12:40931198-40931204	NONHSAT027736
20	lnc-CNTN1-1	chr12:40929006-40929059	XLOC_009713
21	lnc-CNTN1-1	chr12:40930242-40930286	NONHSAT027736
22	lnc-CNTN1-1	chr12:40924075-40924122	NONHSAT027733
23	lnc-CNTN1-1	chr12:40929708-40929761	NONHSAT027736
24	lnc-CNTN1-1	chr12:40926786-40926880	NONHSAT027736
25	lnc-CNTN1-1	chr12:40927958-40928011	NONHSAT027736
26	lnc-CNTN1-1	chr12:40926827-40926880	XLOC_009713
27	lnc-CNTN1-1	chr12:40922979-40923032	NONHSAT027733
28	lnc-CNTN1-1	chr12:40917391-40917444	NONHSAT027733
29	lnc-CNTN1-1	chr12:40918318-40919423	XLOC_009713
30	lnc-CNTN1-1	chr12:40928513-40928586	XLOC_009713
31	lnc-CNTN1-1	chr12:40917391-40917444	XLOC_009713
32	lnc-CNTN1-1	chr12:40931198-40931230	XLOC_009713
33	lnc-CNTN1-1	chr12:40919180-40919232	XLOC_009713
34	lnc-CNTN1-1	chr12:40928513-40928605	NONHSAT027733
35	lnc-CNTN1-1	chr12:40918318-40919423	NONHSAT027733
36	lnc-CNTN1-1	chr12:40919370-40919423	XLOC_009713
37	lnc-CNTN1-1	chr12:40921557-40921589	XLOC_009713
38	lnc-CNTN1-1	chr12:40929708-40929761	XLOC_009713
39	lnc-CNTN1-1	chr12:40929567-40929611	XLOC_009713
40	lnc-CNTN1-1	chr12:40924075-40924122	XLOC_009713
41	lnc-CNTN1-1	chr12:40928513-40928545	NONHSAT027736
42	lnc-CNTN1-1	chr12:40918318-40918368	XLOC_009713
43	lnc-CNTN1-1	chr12:40924859-40926084	XLOC_009713
44	lnc-CNTN1-1	chr12:40927958-40928011	NONHSAT027733
45	lnc-CNTN1-1	chr12:40930725-40930778	NONHSAT027736
46	lnc-CNTN1-1	chr12:40930242-40930286	XLOC_009713
47	lnc-CNTN1-1	chr12:40922979-40923032	XLOC_009713
48	lnc-CNTN1-1	chr12:40930725-40930778	XLOC_009713
49	lnc-CNTN1-1	chr12:40922059-40922111	XLOC_009713
50	lnc-CNTN1-1	chr12:40926827-40926880	NONHSAT027733

No data

Variant related genes	Relation type
MUC19	TF binding region
CALCOCO2	miRNA target sites
PROM1	miRNA target sites
YWHAG	miRNA target sites
FAM98A	miRNA target sites
ARHGAP12	miRNA target sites
CLIC4	miRNA target sites
ZEB1	miRNA target sites
ARNTL	miRNA target sites
RPE	miRNA target sites
PCMTD2	miRNA target sites
RRM2B	miRNA target sites
KIAA1191	miRNA target sites

Extended variants
information (count: 243 )
Associated
traits (count: 58 )

Variant overlapped rSNPs/rCNVs (count:243 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs184981268	chr12:40917375-40917376	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs376563034	chr12:40917399-40917400	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
3	rs560261370	chr12:40917403-40917404	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
4	rs11829565	chr12:40917416-40917417	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs556134928	chr12:40917418-40917419	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
6	rs201511068	chr12:40917432-40917433	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
7	rs190276413	chr12:40917456-40917457	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs2638890	chr12:40917474-40917475	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs2638891	chr12:40917486-40917487	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs137961271	chr12:40917506-40917507	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs201141559	chr12:40917533-40917534	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs542836303	chr12:40917534-40917535	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs181878865	chr12:40917536-40917537	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs572190115	chr12:40917542-40917543	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs545541214	chr12:40917551-40917552	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs73119906	chr12:40917571-40917572	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs576003048	chr12:40917590-40917591	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs149306898	chr12:40917601-40917602	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs543396479	chr12:40917626-40917627	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs530040331	chr12:40917641-40917642	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs73119908	chr12:40917664-40917665	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs149481208	chr12:40917693-40917694	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs184083435	chr12:40917791-40917792	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs374865515	chr12:40917793-40917794	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs188812634	chr12:40917872-40917873	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs111957740	chr12:40917897-40917898	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs552311393	chr12:40917957-40917958	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs143981812	chr12:40918006-40918007	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs111492511	chr12:40918008-40918009	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs148240749	chr12:40918012-40918013	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs555712514	chr12:40918028-40918029	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs1492318	chr12:40918031-40918032	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs142825324	chr12:40918189-40918190	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs571704881	chr12:40918268-40918269	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs2588397	chr12:40918271-40918272	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs561015154	chr12:40918294-40918295	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs1492319	chr12:40918345-40918346	Weak transcription	TF binding region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs567947286	chr12:40918386-40918387	Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
39	rs557608866	chr12:40918395-40918396	Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
40	rs536173422	chr12:40918414-40918415	Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
41	rs111226429	chr12:40918434-40918435	Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
42	rs73119913	chr12:40918443-40918444	Weak transcription	TF binding region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs575833209	chr12:40918510-40918511	Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
44	rs139791200	chr12:40918518-40918519	Weak transcription	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
45	rs557830970	chr12:40918521-40918522	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
46	rs73119915	chr12:40918678-40918679	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs540880988	chr12:40918713-40918714	Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
48	rs377310723	chr12:40918747-40918748	Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
49	rs559218611	chr12:40918762-40918763	Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
50	rs143787889	chr12:40918773-40918774	Weak transcription Enhancers	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:58)

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
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
Breast cancer	21364760	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40915600-40919400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:40918600-40919400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr12:40918800-40919200	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr12:40918800-40919400	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr12:40918800-40919400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr12:40919000-40919400	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr12:40919000-40919400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr12:40928400-40929200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:40928600-40929200	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr12:40928800-40929200	Enhancers	iPS-15b Cell Line	embryonic stem cell

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