Variant report

Variant	nsv558703
Chromosome Location	chr12:43015532-43025256
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	CHD2	chr12:43019491-43019597	K562	blood:	n/a	n/a
2	CTCF	chr12:43016180-43016330	NB4	blood:	n/a	n/a
3	EP300	chr12:43024204-43024416	K562	blood:	n/a	n/a
4	KAP1	chr12:43023782-43024522	U2OS	brain:	n/a	n/a
5	KAP1	chr12:43023607-43024511	HEK293	kidney:	n/a	n/a
6	MXI1	chr12:43018683-43018684	HepG2	liver:	n/a	n/a
7	NFIC	chr12:43019321-43019865	ECC-1	luminal epithelium:	n/a	n/a
8	NFYA	chr12:43019379-43019678	K562	blood:	n/a	chr12:43019530-43019548 chr12:43019554-43019572
9	NFYA	chr12:43019481-43019684	Hela-S3	cervix:	n/a	chr12:43019530-43019548 chr12:43019554-43019572
10	NFYB	chr12:43019303-43019703	K562	blood:	n/a	chr12:43019560-43019575 chr12:43019536-43019551 chr12:43019512-43019527
11	NFYB	chr12:43019379-43019617	GM12878	blood:	n/a	chr12:43019560-43019575 chr12:43019536-43019551 chr12:43019512-43019527
12	NFYB	chr12:43019394-43019613	Hela-S3	cervix:	n/a	chr12:43019560-43019575 chr12:43019536-43019551 chr12:43019512-43019527
13	POLR2A	chr12:43018918-43019033	GM12878	blood:	n/a	n/a
14	POLR2A	chr12:43023607-43023620	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr12:43023525-43023576	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:43019211-43019398	GM12878	blood:	n/a	n/a
17	RCOR1	chr12:43024116-43024461	K562	blood:	n/a	n/a
18	SETDB1	chr12:43023947-43024926	U2OS	brain:	n/a	n/a
19	TAL1	chr12:43024297-43024443	K562	blood:	n/a	n/a
20	TCF7L2	chr12:43023886-43024538	HEK293	kidney:	n/a	n/a
21	TEAD4	chr12:43024071-43024481	K562	blood:	n/a	n/a
22	ZNF384	chr12:43024570-43024588	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:43014304..43016802-chr12:43019715..43022401,2	MCF-7	breast:
2	chr12:43018191..43020196-chr12:43021950..43023568,2	K562	blood:
3	chr12:43018191..43020196-chr12:43021950..43023568,2	K562	blood:
4	chr12:43020347..43023127-chr12:43029388..43031746,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRICKLE1-1	chr12:43023263-43023488	ENSG00000257510

Variant related genes	Relation type
ENSG00000257687	TF binding region
ENSG00000257405	chromatin interactions
ENSG00000257687	chromatin interactions
POGZ	miRNA target sites

Extended variants
information (count: 409 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:409 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs12308577	chr12:43015532-43015533	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs115965432	chr12:43015544-43015545	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs535043943	chr12:43015573-43015574	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs118178290	chr12:43015582-43015583	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs141903360	chr12:43015583-43015584	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs568929507	chr12:43015599-43015600	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs150632038	chr12:43015628-43015629	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs561799102	chr12:43015638-43015639	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs192351656	chr12:43015705-43015706	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs547590709	chr12:43015728-43015729	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs74340883	chr12:43015770-43015771	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs140929072	chr12:43015794-43015795	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs57557308	chr12:43015795-43015796	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs184941948	chr12:43015797-43015798	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs77599095	chr12:43015799-43015800	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs7133172	chr12:43015863-43015864	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs147928842	chr12:43015924-43015925	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs140233654	chr12:43015926-43015927	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs554350181	chr12:43015948-43015949	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs7307159	chr12:43015964-43015965	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs555651018	chr12:43015992-43015993	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs540131977	chr12:43016037-43016038	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs558515553	chr12:43016072-43016073	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs150057045	chr12:43016114-43016115	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs2204906	chr12:43016128-43016129	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs145474476	chr12:43016131-43016132	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs75334863	chr12:43016195-43016196	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs572446880	chr12:43016213-43016214	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs540827535	chr12:43016221-43016222	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs374619450	chr12:43016313-43016314	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs559489877	chr12:43016337-43016338	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs7133774	chr12:43016361-43016362	Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs544882344	chr12:43016364-43016365	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs148817255	chr12:43016370-43016371	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs7133039	chr12:43016395-43016396	Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs143507711	chr12:43016420-43016421	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs531021228	chr12:43016421-43016422	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs76090554	chr12:43016450-43016451	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs547618877	chr12:43016453-43016454	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs564628109	chr12:43016463-43016464	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs566239553	chr12:43016479-43016480	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs540071601	chr12:43016515-43016516	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs7955064	chr12:43016527-43016528	Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs570383758	chr12:43016540-43016541	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs146442737	chr12:43016544-43016545	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs188932598	chr12:43016584-43016585	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs562022958	chr12:43016585-43016586	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs141013370	chr12:43016586-43016587	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs541119090	chr12:43016587-43016588	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs182061973	chr12:43016594-43016595	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:57)

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
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
Malignant peripheral nerve sheath tumor	18522746	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Breast cancer	19602461	CNVD
Breast cancer	17899364	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	21364760	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Cancer	20164919	CNVD
Breast cancer	22522925	CNVD
Acute lymphoblastic leukemia	21339820	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:43006000-43015800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:43008200-43016200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:43015800-43016400	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr12:43016000-43016400	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr12:43016000-43016400	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr12:43016000-43016600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:43016200-43017000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:43017000-43020800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:43018200-43019200	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr12:43018400-43019200	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr12:43020800-43021000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr12:43020800-43021200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr12:43021000-43021800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:43021400-43022000	Enhancers	Fetal Stomach	stomach
15	chr12:43024400-43026200	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr12:43024800-43026000	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr12:43025000-43026000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr12:43025200-43025600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:43025200-43026000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr12:43025200-43026600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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