Variant report

Variant	nsv558599
Chromosome Location	chr12:40790698-40814452
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:15)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr12:40791310-40791585	HepG2	liver:	n/a	n/a
2	CEBPB	chr12:40791302-40791514	A549	lung:	n/a	n/a
3	CTCF	chr12:40805024-40805091	LNCaP	prostate:	n/a	n/a
4	CTCF	chr12:40799240-40799390	GM12875	blood:	n/a	n/a
5	E2F4	chr12:40799614-40799739	MCF10A-Er-Src	breast:	n/a	n/a
6	GATA3	chr12:40795759-40795893	SH-SY5Y	brain:	n/a	n/a
7	GATA3	chr12:40810161-40810625	MCF-7	breast:	n/a	n/a
8	JUN	chr12:40790722-40790871	HepG2	liver:	n/a	chr12:40790815-40790824 chr12:40790811-40790824
9	JUND	chr12:40790683-40790938	HepG2	liver:	n/a	chr12:40790815-40790824
10	MAFK	chr12:40811655-40811801	HepG2	liver:	n/a	n/a
11	MXI1	chr12:40800876-40800985	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr12:40806369-40806465	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr12:40803454-40803476	A549	lung:	n/a	n/a
14	POLR2A	chr12:40803385-40803422	A549	lung:	n/a	n/a
15	POLR2A	chr12:40798535-40798714	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr12:40800166-40800213	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr12:40791713-40791801	GM12878	blood:	n/a	n/a
18	POLR2A	chr12:40797752-40797951	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr12:40791118-40791161	MCF10A-Er-Src	breast:	n/a	n/a
20	STAT3	chr12:40806038-40806113	MCF10A-Er-Src	breast:	n/a	n/a
21	STAT3	chr12:40813810-40814010	MCF10A-Er-Src	breast:	n/a	n/a
22	STAT3	chr12:40808552-40808706	MCF10A-Er-Src	breast:	n/a	n/a
23	STAT3	chr12:40809708-40809713	MCF10A-Er-Src	breast:	n/a	n/a
24	USF1	chr12:40799199-40799531	H1-hESC	embryonic stem cell:	n/a	n/a
25	USF1	chr12:40799222-40799506	H1-hESC	embryonic stem cell:	n/a	n/a
26	USF2	chr12:40808250-40808281	H1-hESC	embryonic stem cell:	n/a	n/a
27	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	chr12:40802735..40804254-chr12:40811941..40814562,2	K562	blood:
2	chr12:40802843..40805068-chr12:40806902..40808859,2	K562	blood:
3	chr12:40803393..40806032-chr12:40844478..40846629,2	K562	blood:
4	12:40793507-40812339..12:40836437-40839614	H1-hESC	embryonic stem cell:	embryo
5	chr12:40802843..40805068-chr12:40806902..40808859,2	K562	blood:

(count:15 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC2A13-3	chr12:40814022-40814113	XLOC_010054
2	lnc-SLC2A13-3	chr12:40810103-40810240	XLOC_010054
3	lnc-MUC19-1	chr12:40811932-40811982	NONHSAT027728
4	lnc-MUC19-1	chr12:40791681-40791713	NONHSAT027728
5	lnc-SLC2A13-3	chr12:40814022-40814118	XLOC_010054
6	lnc-MUC19-1	chr12:40814009-40814237	NONHSAT027728
7	lnc-MUC19-1	chr12:40805835-40805984	NONHSAT027728
8	lnc-SLC2A13-3	chr12:40814022-40814113	ENSG00000258167.1
9	lnc-SLC2A13-3	chr12:40807837-40807921	XLOC_010054
10	lnc-SLC2A13-3	chr12:40810105-40810240	XLOC_010054
11	lnc-SLC2A13-3	chr12:40792362-40792466	ENSG00000258167.1
12	lnc-SLC2A13-3	chr12:40814022-40814118	XLOC_010054
13	lnc-MUC19-1	chr12:40805409-40805429	NONHSAT027728
14	lnc-MUC19-1	chr12:40812976-40813035	NONHSAT027728
15	lnc-SLC2A13-3	chr12:40810105-40810240	XLOC_010054

No data

Variant related genes	Relation type
MUC19	TF binding region
ENSG00000258167	chromatin interactions
ENSG00000205592	chromatin interactions
MORF4L1	miRNA target sites
SEC23IP	miRNA target sites
BLOC1S3	miRNA target sites
STXBP3	miRNA target sites

Extended variants
information (count: 967 )
Associated
traits (count: 58 )

Variant overlapped rSNPs/rCNVs (count:967 , 50 per page) page: 1 2 3 4 5 6 7 ... 20

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs11564263	chr12:40790698-40790699	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs139528704	chr12:40790740-40790741	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs144227830	chr12:40790758-40790759	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs377143771	chr12:40790764-40790765	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs528594244	chr12:40790782-40790783	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs546791918	chr12:40790856-40790857	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs570826780	chr12:40790909-40790910	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs563146465	chr12:40790911-40790912	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs11564262	chr12:40790924-40790925	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs192116672	chr12:40790925-40790926	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs11564261	chr12:40790930-40790931	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs1549562	chr12:40790940-40790941	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs536836639	chr12:40790965-40790966	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs555230701	chr12:40791012-40791013	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs35297383	chr12:40791044-40791045	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs11564105	chr12:40791058-40791059	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs554381533	chr12:40791078-40791079	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs148750738	chr12:40791085-40791086	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs527657929	chr12:40791113-40791114	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs10784589	chr12:40791214-40791215	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs375613030	chr12:40791224-40791225	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs577522784	chr12:40791229-40791230	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs544690531	chr12:40791237-40791238	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs11564260	chr12:40791245-40791246	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs575187469	chr12:40791248-40791249	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs554465448	chr12:40791283-40791284	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs542395577	chr12:40791352-40791353	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs370028993	chr12:40791364-40791365	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs117929583	chr12:40791407-40791408	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs76485602	chr12:40791410-40791411	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs547025715	chr12:40791421-40791422	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs558144263	chr12:40791466-40791467	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs532527848	chr12:40791513-40791514	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs56852472	chr12:40791539-40791540	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs569550886	chr12:40791571-40791572	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs536979436	chr12:40791591-40791592	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs548915221	chr12:40791592-40791593	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs199515917	chr12:40791656-40791657	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs567044536	chr12:40791658-40791659	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs74079640	chr12:40791689-40791690	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs35069108	chr12:40791701-40791702	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
42	rs577707699	chr12:40791702-40791703	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
43	rs538604763	chr12:40791712-40791713	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
44	rs556714676	chr12:40791749-40791750	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs574906949	chr12:40791768-40791769	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs559953448	chr12:40791795-40791796	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs145665119	chr12:40791852-40791853	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs560851600	chr12:40791859-40791860	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs34057894	chr12:40791866-40791867	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs572660875	chr12:40791912-40791913	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:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40787200-40799200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:40793600-40793800	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr12:40793800-40799400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr12:40796800-40797000	Enhancers	Spleen	Spleen
5	chr12:40799000-40799800	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr12:40799200-40799600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:40799200-40799600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:40799200-40799600	Enhancers	H9 Cell Line	embryonic stem cell
9	chr12:40799400-40799800	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr12:40799400-40799800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:40799400-40800200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:40799600-40800000	Enhancers	HMEC	breast
13	chr12:40799600-40813200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr12:40799800-40801800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr12:40803400-40805600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr12:40805600-40806200	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr12:40806200-40807600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr12:40807800-40808000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr12:40813200-40813400	ZNF genes & repeats	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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