Variant report

Variant	nsv1045040
Chromosome Location	chr12:39038114-39084094
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	ATF1	chr12:39071567-39071659	K562	blood:	n/a	n/a
2	CBX3	chr12:39063333-39063714	K562	blood:	n/a	n/a
3	CCNT2	chr12:39063401-39063641	K562	blood:	n/a	n/a
4	CEBPB	chr12:39057555-39057649	HepG2	liver:	n/a	chr12:39057586-39057597
5	CEBPB	chr12:39058615-39058676	A549	lung:	n/a	n/a
6	CEBPB	chr12:39071847-39072062	HepG2	liver:	n/a	chr12:39071883-39071894 chr12:39071971-39071980
7	CEBPB	chr12:39063350-39063709	K562	blood:	n/a	n/a
8	CEBPB	chr12:39063418-39063594	K562	blood:	n/a	n/a
9	CEBPB	chr12:39063374-39063663	K562	blood:	n/a	n/a
10	CTCF	chr12:39058580-39058730	GM06990	blood:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672
11	CTCF	chr12:39058466-39058832	K562	blood:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672
12	CTCF	chr12:39058940-39059090	HUVEC	blood vessel:	n/a	n/a
13	CTCF	chr12:39058616-39058703	GM19240	blood:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672
14	CTCF	chr12:39058500-39058781	A549	lung:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672
15	CTCF	chr12:39058323-39059168	A549	lung:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672 chr12:39058821-39058842
16	CTCF	chr12:39058600-39058750	BJ	skin:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672
17	CTCF	chr12:39058580-39058730	NHEK	skin:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672
18	CTCF	chr12:39058500-39058650	HFF-Myc	foreskin:	n/a	n/a
19	CTCF	chr12:39058530-39058731	HepG2	liver:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672
20	CTCF	chr12:39059320-39059590	BE2_C	brain:	n/a	n/a
21	CTCF	chr12:39058580-39058730	HepG2	liver:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672
22	CTCF	chr12:39058580-39058730	AG09309	skin:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672
23	CTCF	chr12:39058580-39058730	WERI-Rb-1	eye:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672
24	CTCF	chr12:39058460-39058610	HAc	cerebellar:	n/a	n/a
25	CTCF	chr12:39058600-39058750	SAEC	small airway:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672
26	CTCF	chr12:39058560-39058710	GM12869	blood:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672
27	CTCF	chr12:39058546-39058809	A549	lung:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672
28	CTCF	chr12:39058541-39058785	GM12878	blood:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672
29	CTCF	chr12:39058480-39058750	GM12867	blood:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672
30	CTCF	chr12:39058580-39058730	HVMF	connective:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672
31	CTCF	chr12:39058580-39058730	HFF	foreskin:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672
32	CTCF	chr12:39058562-39058770	MCF-7	breast:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672
33	CTCF	chr12:39058580-39058730	GM12864	blood:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672
34	CTCF	chr12:39058540-39058690	HBMEC	blood vessel:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672
35	CTCF	chr12:39058640-39058790	Hela-S3	cervix:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672
36	CTCF	chr12:39058500-39058650	HL-60	blood:	n/a	n/a
37	CTCF	chr12:39058600-39058750	BE2_C	brain:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672
38	CTCF	chr12:39058560-39058710	MCF-7	breast:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672
39	CTCF	chr12:39058640-39058790	HFF-Myc	foreskin:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672
40	CTCF	chr12:39058600-39058750	NB4	blood:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672
41	CTCF	chr12:39058620-39058770	HEK293	kidney:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672
42	CTCF	chr12:39058503-39058816	MCF-7	breast:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672
43	CTCF	chr12:39058567-39058734	GM20000	blood:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672
44	CTCF	chr12:39058511-39058757	HepG2	liver:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672
45	CTCF	chr12:39058592-39058728	Fibrobl	skin:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672
46	CTCF	chr12:39058520-39058670	GM12868	blood:	n/a	n/a
47	CTCF	chr12:39058581-39058702	GM13976	blood:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672
48	CTCF	chr12:39058580-39058730	HMEC	breast:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672
49	CTCF	chr12:39058680-39058830	HMEC	breast:	n/a	n/a
50	CTCF	chr12:39058580-39058730	SAEC	small airway:	n/a	chr12:39058655-39058671 chr12:39058656-39058677 chr12:39058654-39058672

No.	Distal block	Cell Line	Cell type
1	chr12:39078731..39079461-chr2:68493058..68493608,2	MCF-7	breast:
2	chr12:39058213..39059596-chr12:39300191..39301086,4	MCF-7	breast:
3	chr12:39058333..39059128-chr12:39497120..39498000,2	MCF-7	breast:

No.	miRNA target gene	miRNA name	Chromosome Location
1	CPNE8	hsa-miR-124-3p	chr12:39046441-39046460
2	CPNE8	hsa-miR-30a-5p	chr12:39047301-39047322
3	CPNE8	hsa-miR-30a-5p	chr12:39047307-39047300

Variant related genes	Relation type
CPNE8	TF binding region
ENSG00000257718	chromatin interactions

Extended variants
information (count: 1681 )
Associated
traits (count: 59 )

Variant overlapped rSNPs/rCNVs (count:1681 , 50 per page) page: 1 2 3 4 5 6 7 ... 34

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs533188919	chr12:39038805-39038806	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs2653761	chr12:39038834-39038835	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs566204185	chr12:39038836-39038837	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs535192588	chr12:39038851-39038852	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs554904897	chr12:39038876-39038877	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs568518636	chr12:39038882-39038883	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs1472657	chr12:39038917-39038918	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs556927876	chr12:39038939-39038940	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs17125500	chr12:39039018-39039019	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs17125503	chr12:39039026-39039027	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs546475540	chr12:39039047-39039048	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs1472658	chr12:39039076-39039077	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs76608113	chr12:39039111-39039112	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs542255953	chr12:39039149-39039150	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs2653762	chr12:39039258-39039259	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs111756355	chr12:39039281-39039282	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs367762759	chr12:39039373-39039374	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs115004186	chr12:39039424-39039425	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs143843825	chr12:39039436-39039437	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs76087879	chr12:39039440-39039441	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs550657821	chr12:39039451-39039452	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs546357325	chr12:39039469-39039470	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs559927180	chr12:39039487-39039488	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs190907299	chr12:39039517-39039518	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs562901797	chr12:39039526-39039527	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs146832453	chr12:39039528-39039529	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs568748845	chr12:39039538-39039539	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs71461463	chr12:39039543-39039544	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs76956407	chr12:39039551-39039552	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs183106043	chr12:39039560-39039561	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs367741748	chr12:39039584-39039585	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs142579371	chr12:39039606-39039607	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs571096019	chr12:39039610-39039611	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs371701475	chr12:39039635-39039636	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs539758533	chr12:39039694-39039695	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs188382404	chr12:39039716-39039717	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs140613756	chr12:39039718-39039719	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs12366684	chr12:39039735-39039736	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs570688875	chr12:39039740-39039741	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs71449466	chr12:39039779-39039780	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs10450771	chr12:39039794-39039795	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs112453922	chr12:39039795-39039796	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs575501950	chr12:39039796-39039797	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs4002266	chr12:39039797-39039798	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs200403306	chr12:39039803-39039804	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs555932490	chr12:39039824-39039825	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs12310904	chr12:39039871-39039872	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs4627123	chr12:39039880-39039881	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs147916918	chr12:39039890-39039891	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs564341018	chr12:39039903-39039904	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:59)

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
Breast cancer	21509527	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
Breast cancer	21364760	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
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:311 , 50 per page) page: 1 2 3 4 5 6 7

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39038800-39041400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr12:39039200-39039400	Enhancers	Left Ventricle	heart
3	chr12:39039400-39053000	Weak transcription	Left Ventricle	heart
4	chr12:39039600-39039800	Enhancers	Hela-S3	cervix
5	chr12:39039800-39055800	Weak transcription	Hela-S3	cervix
6	chr12:39041000-39041200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr12:39041200-39041800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:39041400-39049400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr12:39041800-39043000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr12:39042400-39043200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr12:39042600-39043200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr12:39043000-39043400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr12:39043200-39044000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:39043200-39049800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:39043400-39045200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr12:39043600-39043800	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr12:39043800-39050600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr12:39044000-39045200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:39044200-39055400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr12:39044600-39046400	Weak transcription	Liver	Liver
21	chr12:39044600-39046400	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr12:39044800-39046400	Weak transcription	GM12878-XiMat	blood
23	chr12:39045000-39046800	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr12:39045200-39045800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr12:39045200-39045800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr12:39045200-39055400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr12:39045400-39068000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:39045800-39047400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr12:39045800-39050200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:39046000-39085400	Weak transcription	Aorta	Aorta
31	chr12:39046200-39051400	Weak transcription	Lung	lung
32	chr12:39046200-39055400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr12:39046200-39055600	Weak transcription	Adipose Nuclei	Adipose
34	chr12:39046400-39047800	Strong transcription	Liver	Liver
35	chr12:39046400-39047800	Strong transcription	GM12878-XiMat	blood
36	chr12:39046400-39048000	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr12:39046800-39048000	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr12:39046800-39080400	Weak transcription	Spleen	Spleen
39	chr12:39047200-39055800	Weak transcription	Ovary	ovary
40	chr12:39047400-39048000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr12:39047600-39047800	Enhancers	Brain Anterior Caudate	brain
42	chr12:39047600-39047800	ZNF genes & repeats	Gastric	stomach
43	chr12:39047600-39051200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr12:39047800-39055400	Weak transcription	Liver	Liver
45	chr12:39047800-39055400	Weak transcription	GM12878-XiMat	blood
46	chr12:39048000-39055400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr12:39048000-39055400	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr12:39048000-39056400	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr12:39050200-39051800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:39050600-39051600	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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