Variant report

Variant	nsv559668
Chromosome Location	chr12:86416212-86432115
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr12:86420707-86420864	IMR90	lung:	n/a	n/a
2	CTCF	chr12:86431666-86431796	Spleen_OC	spleen:	n/a	n/a
3	GATA3	chr12:86422367-86422546	SH-SY5Y	brain:	n/a	n/a
4	MAFK	chr12:86425111-86425311	HepG2	liver:	n/a	chr12:86425189-86425200 chr12:86425189-86425205 chr12:86425188-86425202 chr12:86425189-86425204 chr12:86425151-86425166
5	MAFK	chr12:86425136-86425256	HepG2	liver:	n/a	chr12:86425189-86425200 chr12:86425189-86425205 chr12:86425188-86425202 chr12:86425189-86425204 chr12:86425151-86425166
6	POLR2A	chr12:86420956-86421007	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr12:86416807-86416896	MCF10A-Er-Src	breast:	n/a	n/a
8	SPI1	chr12:86429973-86430139	K562	blood:	n/a	n/a
9	SPI1	chr12:86429930-86430151	GM12891	blood:	n/a	n/a
10	SPI1	chr12:86429878-86430157	GM12891	blood:	n/a	n/a
11	SPI1	chr12:86429901-86430203	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:86416679..86418710-chr12:86418948..86421586,2	MCF-7	breast:
2	chr12:86416679..86418710-chr12:86418948..86421586,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MGAT4C-1	chr12:86421882-86421982	NONHSAT029760

Variant related genes	Relation type
MGAT4C	TF binding region

Extended variants
information (count: 76 )
Associated
traits (count: 63 )

Variant overlapped rSNPs/rCNVs (count:76 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs543297194	chr12:86421920-86421921	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
2	rs564862144	chr12:86421945-86421946	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
3	rs576006353	chr12:86422368-86422369	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs543432178	chr12:86422395-86422396	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs376993319	chr12:86422434-86422435	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs138359405	chr12:86422510-86422511	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs115131380	chr12:86425149-86425150	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs143793026	chr12:86425157-86425158	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs557798771	chr12:86425198-86425199	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs572860266	chr12:86425241-86425242	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs554714263	chr12:86425305-86425306	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs369083148	chr12:86430816-86430817	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs539198270	chr12:86430852-86430853	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs12818675	chr12:86430891-86430892	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs553203707	chr12:86430917-86430918	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs189855329	chr12:86430920-86430921	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs142059879	chr12:86430922-86430923	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs536646990	chr12:86430990-86430991	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs530488824	chr12:86430997-86430998	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs374603397	chr12:86431043-86431044	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs144714172	chr12:86431053-86431054	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs565524623	chr12:86431071-86431072	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs532689506	chr12:86431116-86431117	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs547723851	chr12:86431132-86431133	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs565917887	chr12:86431157-86431158	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs530258821	chr12:86431192-86431193	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs548249144	chr12:86431195-86431196	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs570067143	chr12:86431222-86431223	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs373339654	chr12:86431255-86431256	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs537413339	chr12:86431257-86431258	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs558684953	chr12:86431296-86431297	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs555441313	chr12:86431297-86431298	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs192796381	chr12:86431326-86431327	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs534944386	chr12:86431336-86431337	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs386764957	chr12:86431363-86431364	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs6539937	chr12:86431374-86431375	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs184846227	chr12:86431395-86431396	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs542058565	chr12:86431406-86431407	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs556973693	chr12:86431412-86431413	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs569528678	chr12:86431416-86431417	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs61931120	chr12:86431417-86431418	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs189290492	chr12:86431457-86431458	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs139858882	chr12:86431467-86431468	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs528104286	chr12:86431514-86431515	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs541310985	chr12:86431516-86431517	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs559636357	chr12:86431535-86431536	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs530204642	chr12:86431542-86431543	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs548500639	chr12:86431544-86431545	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs563761202	chr12:86431550-86431551	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs530898755	chr12:86431570-86431571	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:63)

Disease	PMID	Source
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
Autism	22495311	CNVD
T-cell prolymphocytic leukemia	19278963	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
Lung cancer	18438408	CNVD
Breast cancer	17899364	CNVD
Cancer	16751803	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
small cell lung cancer	20016488	CNVD
Melanoma	18172304	CNVD
Glioblastoma multiforme	21390271	CNVD
Cancer	20164919	CNVD
Metanephric adenoma	20802469	CNVD
Acute myeloid leukemia	21251322	CNVD
Prostate cancer	18632612	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Breast cancer	22032731	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Ovarian cancer	21720365	CNVD
Acute myeloid leukemia	20729466	CNVD
Myelofibrosis	22110671	CNVD
Colorectal cancer	16272173	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Renal cell carcinoma	18194544	CNVD
lymphocytic leukemia	21291569	CNVD
Breast cancer	21364760	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:86430800-86433800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:86431600-86431800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell

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