Variant report

Variant	nsv972977
Chromosome Location	chr12:29259810-29276403
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	CBX3	chr12:29265873-29266595	HCT-116	colon:	n/a	n/a
2	CHD1	chr12:29268769-29268795	GM12878	blood:	n/a	n/a
3	CTCF	chr12:29265460-29265610	HBMEC	blood vessel:	n/a	n/a
4	E2F4	chr12:29265027-29265093	MCF10A-Er-Src	breast:	n/a	n/a
5	EP300	chr12:29263771-29263876	GM12878	blood:	n/a	n/a
6	FOS	chr12:29266030-29266449	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr12:29266009-29266468	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr12:29266139-29266427	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr12:29266123-29266418	MCF10A-Er-Src	breast:	n/a	n/a
10	FOSL1	chr12:29265953-29266935	HCT-116	colon:	n/a	n/a
11	FOSL2	chr12:29266111-29266417	SK-N-SH	brain:	n/a	n/a
12	GATA3	chr12:29271048-29271157	SH-SY5Y	brain:	n/a	chr12:29271112-29271122
13	JUND	chr12:29265904-29266601	HCT-116	colon:	n/a	n/a
14	JUND	chr12:29265903-29266975	HCT-116	colon:	n/a	n/a
15	MAX	chr12:29271192-29271269	NB4	blood:	n/a	n/a
16	MYC	chr12:29266230-29266413	MCF10A-Er-Src	breast:	n/a	n/a
17	MYC	chr12:29263769-29263774	MCF10A-Er-Src	breast:	n/a	n/a
18	MYC	chr12:29265493-29265565	H1-hESC	embryonic stem cell:	n/a	n/a
19	NFYB	chr12:29267866-29268453	K562	blood:	n/a	n/a
20	NFYB	chr12:29267942-29268190	GM12878	blood:	n/a	n/a
21	POLR2A	chr12:29265439-29265631	A549	lung:	n/a	n/a
22	POLR2A	chr12:29271232-29271255	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr12:29266081-29266408	HCT-116	colon:	n/a	n/a
24	RUNX3	chr12:29263698-29264066	GM12878	blood:	n/a	chr12:29263891-29263906
25	SETDB1	chr12:29263952-29264594	U2OS	brain:	n/a	n/a
26	SP1	chr12:29265944-29266636	HCT-116	colon:	n/a	n/a
27	SP1	chr12:29265810-29267098	HCT-116	colon:	n/a	n/a
28	SPI1	chr12:29263704-29264129	GM12891	blood:	n/a	n/a
29	SPI1	chr12:29263789-29264077	HL-60	blood:	n/a	n/a
30	SPI1	chr12:29263834-29264045	GM12878	blood:	n/a	n/a
31	SPI1	chr12:29263725-29264105	GM12878	blood:	n/a	n/a
32	SPI1	chr12:29263819-29264136	GM12891	blood:	n/a	n/a
33	STAT3	chr12:29273520-29273608	MCF10A-Er-Src	breast:	n/a	n/a
34	STAT3	chr12:29264505-29264641	MCF10A-Er-Src	breast:	n/a	n/a
35	STAT3	chr12:29266011-29266399	MCF10A-Er-Src	breast:	n/a	n/a
36	STAT3	chr12:29266072-29266393	MCF10A-Er-Src	breast:	n/a	n/a
37	STAT3	chr12:29260145-29260345	MCF10A-Er-Src	breast:	n/a	n/a
38	STAT3	chr12:29266144-29266344	MCF10A-Er-Src	breast:	n/a	n/a
39	TEAD4	chr12:29265907-29266431	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:29274504..29277462-chr12:29319528..29321413,2	K562	blood:
2	chr12:29255547..29258096-chr12:29276125..29278955,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000222481	TF binding region

Extended variants
information (count: 484 )
Associated
traits (count: 62 )

Variant overlapped rSNPs/rCNVs (count:484 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs149784878	chr12:29260005-29260006	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs575748164	chr12:29260014-29260015	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs77178870	chr12:29260046-29260047	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs535983823	chr12:29260059-29260060	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs557800837	chr12:29260077-29260078	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs187019679	chr12:29260096-29260097	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs144654957	chr12:29260099-29260100	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs12227313	chr12:29260114-29260115	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs76363402	chr12:29260154-29260155	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs12231262	chr12:29260157-29260158	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs562648219	chr12:29260164-29260165	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs139764672	chr12:29260165-29260166	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs551310807	chr12:29260170-29260171	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs559000121	chr12:29263622-29263623	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
15	rs112627141	chr12:29263627-29263628	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
16	rs112830322	chr12:29263629-29263630	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
17	rs557107467	chr12:29263631-29263632	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
18	rs11559799	chr12:29263637-29263638	ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs7315912	chr12:29263649-29263650	ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs7316030	chr12:29263676-29263677	ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs551613913	chr12:29263677-29263678	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
22	rs139484957	chr12:29263707-29263708	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
23	rs56283843	chr12:29263717-29263718	ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs374134028	chr12:29263739-29263740	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
25	rs11531008	chr12:29263752-29263753	ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs11537408	chr12:29263756-29263757	ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs550077508	chr12:29263775-29263776	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
28	rs12314772	chr12:29263776-29263777	ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs142742541	chr12:29263784-29263785	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
30	rs374349350	chr12:29263814-29263815	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
31	rs184968725	chr12:29263947-29263948	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
32	rs541207963	chr12:29264000-29264001	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
33	rs61481716	chr12:29265205-29265206	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs546857809	chr12:29265220-29265221	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs568684689	chr12:29265232-29265233	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs553455653	chr12:29265320-29265321	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs3940535	chr12:29265329-29265330	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs545469605	chr12:29265347-29265348	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs544227970	chr12:29265457-29265458	Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
40	rs7139208	chr12:29265458-29265459	Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
41	rs189285565	chr12:29265461-29265462	Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
42	rs575290160	chr12:29265481-29265482	Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
43	rs562880840	chr12:29265537-29265538	Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
44	rs980851	chr12:29265540-29265541	Enhancers ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs557891748	chr12:29265584-29265585	Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
46	rs572841944	chr12:29265585-29265586	Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
47	rs540253735	chr12:29265615-29265616	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
48	rs533208821	chr12:29265643-29265644	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
49	rs142547504	chr12:29265649-29265650	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
50	rs147582161	chr12:29265671-29265672	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:62)

Disease	PMID	Source
Melanoma	18172304	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Myxofibrosarcoma	16751306	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Wilms tumour	21544195	CNVD
Squamous cell cancer	21044232	CNVD
Acute myeloid leukemia	16864856	CNVD
T-cell acute lymphoblastic leukemia	20065082	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Endometrial cancer	22040021	CNVD
Colorectal cancer	20709793	CNVD
Breast cancer	21264507	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Testicular cancer	18059402	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Seminomas	18059402	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
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
Acute lymphoblastic leukemia	21248843	CNVD
Ewing''s sarcoma	17952124	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	21858162	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Myelodysplastic syndrome	21251322	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Cancer	20164919	CNVD
Acute myeloid leukemia	21251322	CNVD
Acute myeloid leukemia	20729466	CNVD
small cell lung cancer	20016488	CNVD
Neurodevelopmental disorder	22521361	CNVD
Breast cancer	21509527	CNVD
Autism	22102821	CNVD
Follicular lymphoma	18703704	CNVD
Lung cancer	18438408	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Breast cancer	17133270	CNVD
Breast cancer	21364760	CNVD
Cancer	21129771	CNVD
Hepatocellular carcinoma	16750200	CNVD
Breast cancer	17899364	CNVD
Myelofibrosis	22110671	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29260000-29260200	Enhancers	Gastric	stomach
2	chr12:29263600-29264000	ZNF genes & repeats	Dnd41	blood
3	chr12:29265200-29266800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:29265200-29267000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:29265200-29267000	Enhancers	HMEC	breast
6	chr12:29265200-29267000	Enhancers	NHEK	skin
7	chr12:29265400-29265800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr12:29265400-29266200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:29265400-29266400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:29265400-29266800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:29265600-29265800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:29265600-29266200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr12:29265600-29266200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:29265600-29266200	Enhancers	Brain Anterior Caudate	brain
15	chr12:29265600-29266200	Enhancers	Placenta	Placenta
16	chr12:29265800-29267800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr12:29266200-29266400	ZNF genes & repeats	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr12:29266400-29286400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr12:29267800-29268000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr12:29268600-29269200	Enhancers	Fetal Kidney	kidney
21	chr12:29269200-29269600	Weak transcription	Fetal Kidney	kidney
22	chr12:29269600-29270200	Enhancers	Fetal Kidney	kidney
23	chr12:29271000-29271600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:29271200-29271600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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