Variant report

Variant	nsv826532
Chromosome Location	chr12:123744177-123746143
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:25)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:10)
Mature miRNA
region (count: 0)
miRNA target
sites (count:1)

(count:25 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CBX3	chr12:123744876-123745233	K562	blood:	n/a	n/a
2	CTCF	chr12:123745220-123745370	HCPEpiC	choroid plexus:	n/a	n/a
3	FOXA1	chr12:123744589-123744979	T-47D	breast:	n/a	n/a
4	FOXA1	chr12:123744561-123745042	T-47D	breast:	n/a	n/a
5	GATA3	chr12:123744539-123744973	T-47D	breast:	n/a	n/a
6	GATA3	chr12:123744603-123744895	T-47D	breast:	n/a	n/a
7	GATA3	chr12:123745766-123745839	SH-SY5Y	brain:	n/a	n/a
8	POLR2A	chr12:123745645-123745693	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr12:123744409-123744578	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr12:123744491-123744881	HepG2	liver:	n/a	n/a
11	POLR2A	chr12:123745953-123746020	HepG2	liver:	n/a	n/a
12	POLR2A	chr12:123744402-123744407	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr12:123742464-123744201	PFSK-1	brain:	n/a	n/a
14	POLR2A	chr12:123745400-123745495	ProgFib	skin:	n/a	n/a
15	POLR2A	chr12:123743980-123744315	HepG2	liver:	n/a	n/a
16	POLR2A	chr12:123744209-123744285	K562	blood:	n/a	n/a
17	POLR2A	chr12:123744573-123744707	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr12:123744896-123744897	HepG2	liver:	n/a	n/a
19	POLR2A	chr12:123745231-123745247	MCF-7	breast:	n/a	n/a
20	POLR2A	chr12:123745537-123745579	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr12:123744362-123744646	HepG2	liver:	n/a	n/a
22	POLR2A	chr12:123744337-123744534	GM12878	blood:	n/a	n/a
23	POLR2A	chr12:123742720-123744190	PANC-1	pancreas:	n/a	n/a
24	SETDB1	chr12:123744957-123745325	U2OS	brain:	n/a	n/a
25	SP1	chr12:123745563-123745933	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123740880..123744807-chr12:123747455..123750621,4	MCF-7	breast:
2	chr12:123735647..123738456-chr12:123742871..123745926,3	K562	blood:
3	chr12:123716155..123719079-chr12:123740733..123744668,4	K562	blood:
4	chr12:123733838..123737944-chr12:123742344..123746385,6	MCF-7	breast:
5	chr12:123716188..123719079-chr12:123740733..123744668,4	K562	blood:
6	chr12:123735701..123738592-chr12:123744837..123746422,2	MCF-7	breast:

(count:10 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CDK2AP1-1	chr12:123745373-123745490	ENSG00000235423.3
2	lnc-CDK2AP1-1	chr12:123745373-123745766	ENSG00000235423.3
3	lnc-CDK2AP1-1	chr12:123745676-123746030	ENSG00000235423.4
4	lnc-CDK2AP1-1	chr12:123744821-123744994	ENSG00000235423.3
5	lnc-CDK2AP1-1	chr12:123744821-123745050	ENSG00000235423.3
6	lnc-CDK2AP1-1	chr12:123744821-123745050	ENSG00000235423.3
7	lnc-CDK2AP1-1	chr12:123744821-123745050	ENSG00000235423.3
8	lnc-CDK2AP1-1	chr12:123744821-123745050	ENSG00000235423.4
9	lnc-CDK2AP1-1	chr12:123745676-123746030	ENSG00000235423.3
10	lnc-CDK2AP1-1	chr12:123745373-123745490	ENSG00000235423.4

No data

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

No.	miRNA target gene	miRNA name	Chromosome Location	mirBase accession
1	CDK2AP1	hsa-miR-21-5p	chr12:123745913-123745934

Variant related genes	Relation type
ENSG00000269980	TF binding region
ENSG00000235423	TF binding region
ENSG00000130921	chromatin interactions
ENSG00000051825	chromatin interactions
MED13L	miRNA target sites
MIB1	miRNA target sites
ZNF644	miRNA target sites

Extended variants
information (count: 69 )
Associated
traits (count: 70 )

Variant overlapped rSNPs/rCNVs (count:69 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs565584042	chr12:123744239-123744240	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
2	rs532651488	chr12:123744263-123744264	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
3	rs550585481	chr12:123744315-123744316	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
4	rs77972844	chr12:123744342-123744343	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
5	rs568878983	chr12:123744354-123744355	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
6	rs62729361	chr12:123744359-123744360	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
7	rs147533589	chr12:123744361-123744362	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
8	rs76462748	chr12:123744362-123744363	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
9	rs78644143	chr12:123744363-123744364	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
10	rs60247869	chr12:123744364-123744365	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
11	rs398021461	chr12:123744367-123744368	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
12	rs369216597	chr12:123744368-123744369	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
13	rs372502660	chr12:123744370-123744371	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
14	rs536231142	chr12:123744443-123744444	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
15	rs548305381	chr12:123744465-123744466	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
16	rs566622725	chr12:123744683-123744684	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs7961303	chr12:123744746-123744747	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs112226101	chr12:123744758-123744759	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs186181116	chr12:123744768-123744769	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs138275196	chr12:123744854-123744855	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
21	rs369737479	chr12:123744886-123744887	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
22	rs115685320	chr12:123744924-123744925	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
23	rs557009847	chr12:123744936-123744937	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
24	rs1980251	chr12:123744955-123744956	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
25	rs567419572	chr12:123745004-123745005	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
26	rs191051293	chr12:123745017-123745018	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
27	rs561009885	chr12:123745048-123745049	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
28	rs549099956	chr12:123745054-123745055	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
29	rs572813162	chr12:123745108-123745109	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
30	rs540827066	chr12:123745120-123745121	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
31	rs78197735	chr12:123745149-123745150	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
32	rs143402852	chr12:123745174-123745175	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
33	rs1980252	chr12:123745178-123745179	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
34	rs181236777	chr12:123745186-123745187	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
35	rs147425448	chr12:123745220-123745221	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
36	rs530083224	chr12:123745241-123745242	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
37	rs57020427	chr12:123745256-123745257	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
38	rs137869895	chr12:123745284-123745285	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
39	rs2337934	chr12:123745359-123745360	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
40	rs185686418	chr12:123745362-123745363	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
41	rs527736374	chr12:123745383-123745384	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
42	rs546793545	chr12:123745411-123745412	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
43	rs377174629	chr12:123745515-123745516	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
44	rs541697640	chr12:123745705-123745706	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
45	rs6633	chr12:123745809-123745810	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
46	rs530731159	chr12:123745819-123745820	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
47	rs190688259	chr12:123745828-123745829	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
48	rs41276694	chr12:123745829-123745830	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
49	rs569168383	chr12:123745853-123745854	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
50	rs536266194	chr12:123745854-123745855	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:70)

Disease	PMID	Source
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
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
small cell lung cancer	20016488	CNVD
Glioblastoma multiforme	21390271	CNVD
Cancer	20164919	CNVD
Cancer	16751803	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
Wilms tumour	21544195	CNVD
Ovarian cancer	21720365	CNVD
Colorectal cancer	16272173	CNVD
lymphocytic leukemia	21291569	CNVD
Breast cancer	16397240	CNVD
Breast cancer	17133270	CNVD
Breast cancer	17603634	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Schizophrenia	18923514	CNVD
Schizophrenia	22241247	CNVD
Cryptorchidism	21048976	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Neuroblastoma	18923191	CNVD
Medulloblastoma	16783165	CNVD
Breast cancer	21806811	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
Prostate cancer	18632612	CNVD
Myelofibrosis	22110671	CNVD
Beckwith-Wiedemann syndrome	20648245	CNVD
Developmental delay	21457577	CNVD
dysmorphic	21457577	CNVD
Ovine squamous-cell carcinoma	17599052	CNVD
Olfactory neuroblastoma	18408657	CNVD
Chordoma	18071362	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Recurrent pregnancy loss	19789632	CNVD

Chromatin state (count:165 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123725800-123746400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:123733400-123745000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:123734600-123753200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:123735200-123751800	Strong transcription	Fetal Stomach	stomach
5	chr12:123735400-123745400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr12:123735600-123752400	Strong transcription	Thymus	Thymus
7	chr12:123736000-123745400	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr12:123736000-123747800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:123736000-123748000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:123736000-123752200	Strong transcription	Dnd41	blood
11	chr12:123736200-123744200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:123736200-123751400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr12:123736400-123750600	Strong transcription	Fetal Lung	lung
14	chr12:123736400-123752200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:123736400-123752600	Strong transcription	NHLF	lung
16	chr12:123737000-123753000	Strong transcription	Fetal Intestine Small	intestine
17	chr12:123737200-123752000	Strong transcription	A549	lung
18	chr12:123737400-123749000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:123737800-123745000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:123737800-123745600	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr12:123737800-123746800	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr12:123738000-123744600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr12:123738000-123745200	Strong transcription	Spleen	Spleen
24	chr12:123738000-123746000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr12:123738000-123746200	Strong transcription	H9 Cell Line	embryonic stem cell
26	chr12:123738000-123746200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr12:123738000-123746600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr12:123738000-123748200	Strong transcription	Primary T cells from cord blood	blood
29	chr12:123738000-123749200	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr12:123738000-123749200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr12:123738000-123749600	Strong transcription	Fetal Muscle Leg	muscle
32	chr12:123738000-123749600	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr12:123738000-123750400	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr12:123738000-123751000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr12:123738000-123751200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:123738000-123751800	Strong transcription	Liver	Liver
37	chr12:123738000-123751800	Strong transcription	Fetal Intestine Large	intestine
38	chr12:123738000-123752000	Strong transcription	Duodenum Mucosa	Duodenum
39	chr12:123738000-123752000	Strong transcription	HUVEC	blood vessel
40	chr12:123738000-123752600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr12:123738000-123752800	Strong transcription	Placenta Amnion	Placenta Amnion
42	chr12:123738200-123748400	Strong transcription	Primary hematopoietic stem cells	blood
43	chr12:123738200-123751800	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr12:123738200-123752000	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr12:123738400-123748400	Strong transcription	NH-A	brain
46	chr12:123738600-123746200	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr12:123738600-123752200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr12:123738800-123749800	Strong transcription	HSMMtube	muscle
49	chr12:123739000-123748600	Strong transcription	HSMM	muscle
50	chr12:123739000-123749400	Strong transcription	Fetal Muscle Trunk	muscle

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