Variant report

Variant	nsv1047639
Chromosome Location	chr12:40774370-40804386
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:5)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:31 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr12:40791302-40791514	A549	lung:	n/a	n/a
2	CEBPB	chr12:40791310-40791585	HepG2	liver:	n/a	n/a
3	CTCF	chr12:40799240-40799390	GM12875	blood:	n/a	n/a
4	CTCF	chr12:40785540-40785690	AG04450	lung:	n/a	n/a
5	E2F4	chr12:40799614-40799739	MCF10A-Er-Src	breast:	n/a	n/a
6	FOSL2	chr12:40781274-40781632	HepG2	liver:	n/a	n/a
7	FOXA1	chr12:40786846-40787160	T-47D	breast:	n/a	n/a
8	FOXA1	chr12:40781148-40781337	T-47D	breast:	n/a	n/a
9	FOXA1	chr12:40786733-40787173	T-47D	breast:	n/a	n/a
10	FOXA1	chr12:40781088-40781346	T-47D	breast:	n/a	n/a
11	FOXA2	chr12:40786844-40787220	A549	lung:	n/a	n/a
12	GATA3	chr12:40781075-40781450	T-47D	breast:	n/a	n/a
13	GATA3	chr12:40795759-40795893	SH-SY5Y	brain:	n/a	n/a
14	JUN	chr12:40790722-40790871	HepG2	liver:	n/a	chr12:40790815-40790824 chr12:40790811-40790824
15	JUND	chr12:40790683-40790938	HepG2	liver:	n/a	chr12:40790815-40790824
16	JUND	chr12:40781425-40781603	HepG2	liver:	n/a	n/a
17	JUND	chr12:40781369-40781620	HepG2	liver:	n/a	n/a
18	MAZ	chr12:40788734-40788856	HepG2	liver:	n/a	n/a
19	MXI1	chr12:40800876-40800985	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr12:40798535-40798714	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr12:40791118-40791161	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr12:40803454-40803476	A549	lung:	n/a	n/a
23	POLR2A	chr12:40791713-40791801	GM12878	blood:	n/a	n/a
24	POLR2A	chr12:40782989-40783018	Gliobla	brain:	n/a	n/a
25	POLR2A	chr12:40797752-40797951	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr12:40803385-40803422	A549	lung:	n/a	n/a
27	POLR2A	chr12:40800166-40800213	MCF10A-Er-Src	breast:	n/a	n/a
28	STAT3	chr12:40785243-40785467	MCF10A-Er-Src	breast:	n/a	n/a
29	USF1	chr12:40799199-40799531	H1-hESC	embryonic stem cell:	n/a	n/a
30	USF1	chr12:40799222-40799506	H1-hESC	embryonic stem cell:	n/a	n/a
31	USF2	chr12:40799316-40799549	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40803393..40806032-chr12:40844478..40846629,2	K562	blood:
2	chr12:40802735..40804254-chr12:40811941..40814562,2	K562	blood:
3	12:40793507-40812339..12:40836437-40839614	H1-hESC	embryonic stem cell:	embryo
4	chr12:40802843..40805068-chr12:40806902..40808859,2	K562	blood:
5	chr12:40768243..40769926-chr12:40782774..40784277,2	K562	blood:

(count:5 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC2A13-3	chr12:40792362-40792466	ENSG00000258167.1
2	lnc-SLC2A13-3	chr12:40789655-40789788	ENSG00000258167.1
3	lnc-MUC19-1	chr12:40791681-40791713	NONHSAT027728
4	lnc-MUC19-1	chr12:40787197-40787301	NONHSAT027728
5	lnc-SLC2A13-3	chr12:40789712-40789790	XLOC_010054

No data

Variant related genes	Relation type
MUC19	TF binding region
ENSG00000205592	chromatin interactions
ENSG00000258167	chromatin interactions
SLC25A37	miRNA target sites

Extended variants
information (count: 1054 )
Associated
traits (count: 58 )

Variant overlapped rSNPs/rCNVs (count:1054 , 50 per page) page: 1 2 3 4 5 6 7 ... 22

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs577476244	chr12:40776204-40776205	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs11176362	chr12:40776221-40776222	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs369436533	chr12:40776255-40776256	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs563123948	chr12:40776270-40776271	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs575390093	chr12:40776277-40776278	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs373208749	chr12:40776297-40776298	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs542780085	chr12:40776353-40776354	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs201486773	chr12:40776362-40776363	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs561056129	chr12:40776395-40776396	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs199922348	chr12:40776407-40776408	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs528049560	chr12:40776423-40776424	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs546581763	chr12:40776448-40776449	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs142260097	chr12:40776449-40776450	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs73277585	chr12:40776457-40776458	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs73107149	chr12:40776460-40776461	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs568737480	chr12:40776473-40776474	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs536330175	chr12:40776519-40776520	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs185843625	chr12:40776541-40776542	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs566977382	chr12:40776574-40776575	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs533894317	chr12:40776577-40776578	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs530963533	chr12:40778816-40778817	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs549173249	chr12:40778850-40778851	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs192620246	chr12:40778858-40778859	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs148420677	chr12:40778867-40778868	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs73277591	chr12:40778919-40778920	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs565577265	chr12:40778921-40778922	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs10878496	chr12:40778957-40778958	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs73277595	chr12:40778979-40778980	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs10784575	chr12:40779003-40779004	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs374051487	chr12:40779026-40779027	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs555314871	chr12:40779028-40779029	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs574076889	chr12:40779057-40779058	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs7957611	chr12:40779073-40779074	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs112052514	chr12:40779097-40779098	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs200379390	chr12:40779122-40779123	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs546164968	chr12:40779125-40779126	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs185082691	chr12:40779154-40779155	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs371327833	chr12:40779162-40779163	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs190325210	chr12:40779185-40779186	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs373494133	chr12:40779188-40779189	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs564685314	chr12:40779211-40779212	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs563597212	chr12:40779213-40779214	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs531147505	chr12:40779214-40779215	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs192583957	chr12:40779265-40779266	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs561347868	chr12:40779278-40779279	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs7957905	chr12:40779292-40779293	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs547145578	chr12:40779293-40779294	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs112066936	chr12:40779295-40779296	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs184924980	chr12:40779346-40779347	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs187969474	chr12:40779348-40779349	Weak transcription	n/a	n/a	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
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40776200-40776600	Enhancers	Fetal Heart	heart
2	chr12:40778800-40779200	Enhancers	Placenta	Placenta
3	chr12:40779200-40779600	Weak transcription	Placenta	Placenta
4	chr12:40779600-40781200	Enhancers	Placenta	Placenta
5	chr12:40781200-40781600	Weak transcription	Placenta	Placenta
6	chr12:40781600-40782000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:40781600-40783400	Enhancers	Placenta	Placenta
8	chr12:40782000-40783600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:40784400-40785400	Enhancers	Liver	Liver
10	chr12:40785200-40786400	Enhancers	A549	lung
11	chr12:40787000-40787200	ZNF genes & repeats	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr12:40787200-40799200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr12:40793600-40793800	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr12:40793800-40799400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr12:40796800-40797000	Enhancers	Spleen	Spleen
16	chr12:40799000-40799800	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr12:40799200-40799600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr12:40799200-40799600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:40799200-40799600	Enhancers	H9 Cell Line	embryonic stem cell
20	chr12:40799400-40799800	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr12:40799400-40799800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:40799400-40800200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:40799600-40800000	Enhancers	HMEC	breast
24	chr12:40799600-40813200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr12:40799800-40801800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr12:40803400-40805600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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