Variant report

Variant	nsv1007347
Chromosome Location	chr2:56904928-57100439
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	chr2:57013062-57013304	K562	blood:	n/a	n/a
2	ATF1	chr2:56994176-56994258	K562	blood:	n/a	n/a
3	ATF2	chr2:56997583-56998016	GM12878	blood:	n/a	n/a
4	ATF3	chr2:56968584-56969210	A549	lung:	n/a	n/a
5	ATF3	chr2:56968638-56969377	A549	lung:	n/a	n/a
6	BATF	chr2:56997704-56997941	GM12878	blood:	n/a	chr2:56997831-56997842
7	BATF	chr2:56980310-56980554	GM12878	blood:	n/a	n/a
8	BATF	chr2:56997653-56997934	GM12878	blood:	n/a	chr2:56997831-56997842
9	BCL11A	chr2:56997668-56997942	GM12878	blood:	n/a	n/a
10	BCL3	chr2:56968619-56969314	A549	lung:	n/a	n/a
11	BCL3	chr2:56968527-56969366	A549	lung:	n/a	n/a
12	BRCA1	chr2:56968715-56969165	Hela-S3	cervix:	n/a	n/a
13	BRCA1	chr2:56958792-56958802	Hela-S3	cervix:	n/a	n/a
14	CBX3	chr2:56968576-56969072	HCT-116	colon:	n/a	n/a
15	CBX3	chr2:57067124-57067469	HCT-116	colon:	n/a	n/a
16	CBX3	chr2:56926175-56926458	HCT-116	colon:	n/a	n/a
17	CCNT2	chr2:56997165-56997365	K562	blood:	n/a	n/a
18	CCNT2	chr2:57041614-57041799	K562	blood:	n/a	n/a
19	CEBPB	chr2:57034021-57034373	MCF-7	breast:	n/a	n/a
20	CEBPB	chr2:56908106-56908673	Hela-S3	cervix:	n/a	chr2:56908635-56908648 chr2:56908634-56908651
21	CEBPB	chr2:56968732-56969245	IMR90	lung:	n/a	chr2:56968916-56968929
22	CEBPB	chr2:57010416-57010803	HepG2	liver:	n/a	chr2:57010540-57010551 chr2:57010503-57010514
23	CEBPB	chr2:57098748-57099073	IMR90	lung:	n/a	n/a
24	CEBPB	chr2:57039646-57040011	MCF-7	breast:	n/a	n/a
25	CEBPB	chr2:57020847-57021162	HepG2	liver:	n/a	chr2:57020979-57020990
26	CEBPB	chr2:57098783-57099024	H1-hESC	embryonic stem cell:	n/a	n/a
27	CEBPB	chr2:56915907-56916098	Hela-S3	cervix:	n/a	n/a
28	CEBPB	chr2:56922336-56922436	H1-hESC	embryonic stem cell:	n/a	n/a
29	CEBPB	chr2:57037725-57038047	Hela-S3	cervix:	n/a	chr2:57037916-57037927 chr2:57037758-57037775 chr2:57037918-57037929
30	CEBPB	chr2:56990938-56991146	A549	lung:	n/a	n/a
31	CEBPB	chr2:57092289-57092556	HepG2	liver:	n/a	chr2:57092419-57092430
32	CEBPB	chr2:56908127-56908508	A549	lung:	n/a	n/a
33	CEBPB	chr2:57033949-57034555	A549	lung:	n/a	n/a
34	CEBPB	chr2:57037746-57038047	HepG2	liver:	n/a	chr2:57037916-57037927 chr2:57037758-57037775 chr2:57037918-57037929
35	CEBPB	chr2:57034031-57034462	Hela-S3	cervix:	n/a	n/a
36	CEBPB	chr2:56945055-56945211	IMR90	lung:	n/a	chr2:56945065-56945078 chr2:56945066-56945077
37	CEBPB	chr2:57007014-57007204	K562	blood:	n/a	chr2:57007078-57007089
38	CEBPB	chr2:57088139-57088500	HepG2	liver:	n/a	n/a
39	CEBPB	chr2:57034077-57034391	A549	lung:	n/a	n/a
40	CEBPB	chr2:57006911-57007265	HepG2	liver:	n/a	chr2:57007078-57007089
41	CEBPB	chr2:56908093-56908547	A549	lung:	n/a	n/a
42	CEBPB	chr2:56968483-56969408	A549	lung:	n/a	chr2:56968916-56968929
43	CEBPB	chr2:57006992-57007246	IMR90	lung:	n/a	chr2:57007078-57007089
44	CEBPB	chr2:56985119-56985377	HepG2	liver:	n/a	chr2:56985235-56985248 chr2:56985235-56985246 chr2:56985236-56985247
45	CEBPB	chr2:57010410-57010654	A549	lung:	n/a	chr2:57010540-57010551 chr2:57010503-57010514
46	CEBPB	chr2:57098783-57099028	A549	lung:	n/a	n/a
47	CEBPB	chr2:56944997-56945240	HepG2	liver:	n/a	chr2:56945065-56945078 chr2:56945066-56945077
48	CEBPB	chr2:57098758-57099052	HepG2	liver:	n/a	n/a
49	CEBPB	chr2:56971118-56971236	HepG2	liver:	n/a	chr2:56971168-56971179
50	CEBPB	chr2:57072133-57072333	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:56418873..56419603-chr2:56975911..56976760,2	MCF-7	breast:
2	chr2:56963796..56964597-chr4:36669358..36670047,2	MCF-7	breast:
3	chr2:56919330..56921444-chr2:57050867..57052484,2	MCF-7	breast:
4	chr2:57048488..57050051-chr2:57058805..57060828,2	MCF-7	breast:
5	chr2:57037052..57037562-chr2:57367504..57368073,2	MCF-7	breast:
6	chr2:57035108..57036803-chr2:57124744..57126282,2	K562	blood:
7	chr2:56940349..56941971-chr2:56943071..56945568,2	MCF-7	breast:
8	chr2:56410374..56411316-chr2:56976212..56976966,3	MCF-7	breast:
9	chr2:56997703..56999296-chr2:57011926..57014412,2	K562	blood:
10	chr2:56919330..56921444-chr2:57050867..57052484,2	MCF-7	breast:
11	chr2:56962863..56964748-chr2:56970862..56973633,2	MCF-7	breast:
12	chr2:57078712..57081570-chr2:57085174..57087217,2	MCF-7	breast:
13	chr2:57011309..57011934-chr2:57604188..57604743,2	MCF-7	breast:
14	chr2:56438471..56441225-chr2:57051813..57054565,2	MCF-7	breast:
15	chr2:57078712..57081570-chr2:57085174..57087217,2	MCF-7	breast:
16	chr2:56997703..56999296-chr2:57011926..57014412,2	K562	blood:
17	chr2:56940349..56941971-chr2:56943071..56945568,2	MCF-7	breast:
18	chr2:56962863..56964748-chr2:56970862..56973633,2	MCF-7	breast:
19	chr2:56410661..56411329-chr2:56976031..56976883,5	MCF-7	breast:
20	chr2:57069877..57070526-chr8:126036477..126036977,2	MCF-7	breast:
21	chr2:57048488..57050051-chr2:57058805..57060828,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC85A-3	chr2:56977435-56977698	NONHSAT070829

Variant related genes	Relation type
ENSG00000231570	TF binding region
ENSG00000055813	chromatin interactions

Extended variants
information (count: 4012 )
Associated
traits (count: 82 )

Variant overlapped rSNPs/rCNVs (count:4012 , 50 per page) page: 1 2 3 4 5 6 7 ... 81

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs17048312	chr2:56906810-56906811	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs550727215	chr2:56906869-56906870	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs570692601	chr2:56906873-56906874	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs568820204	chr2:56906931-56906932	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs56990723	chr2:56906948-56906949	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs533253540	chr2:56907055-56907056	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs375885638	chr2:56907057-56907058	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs546962603	chr2:56907064-56907065	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs566775082	chr2:56907079-56907080	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs559452350	chr2:56907085-56907086	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs535395671	chr2:56907102-56907103	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs555090631	chr2:56907113-56907114	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs568913686	chr2:56907158-56907159	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs34414383	chr2:56907161-56907162	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs185309857	chr2:56907163-56907164	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs557523883	chr2:56907171-56907172	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs577070923	chr2:56907184-56907185	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs138792756	chr2:56907191-56907192	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs528682244	chr2:56907228-56907229	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs75591055	chr2:56907248-56907249	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs367863165	chr2:56907251-56907252	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs7574093	chr2:56907253-56907254	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs542176420	chr2:56907296-56907297	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs377066965	chr2:56907435-56907436	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs142289379	chr2:56907453-56907454	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs544418364	chr2:56907479-56907480	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs150904039	chr2:56907535-56907536	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs190551636	chr2:56907554-56907555	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs531221008	chr2:56907561-56907562	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs182327353	chr2:56907614-56907615	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs550608016	chr2:56907616-56907617	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs139373429	chr2:56907638-56907639	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs373853785	chr2:56907646-56907647	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs12472267	chr2:56907655-56907656	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs186058036	chr2:56907686-56907687	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs150032059	chr2:56907710-56907711	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs549484236	chr2:56907718-56907719	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs568802318	chr2:56907725-56907726	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs188333115	chr2:56907832-56907833	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs551018687	chr2:56907843-56907844	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs533115464	chr2:56907857-56907858	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs546690707	chr2:56907921-56907922	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs17048313	chr2:56907929-56907930	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs181098619	chr2:56907953-56907954	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs10190939	chr2:56907976-56907977	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs573459051	chr2:56908031-56908032	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
47	rs185793880	chr2:56908061-56908062	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs144322428	chr2:56908085-56908086	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs575594666	chr2:56908104-56908105	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs544597238	chr2:56908157-56908158	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:82)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17387387	CNVD
Neuroblastoma	17533364	CNVD
Neuroblastoma	18923191	CNVD
Endometrial cancer	22040021	CNVD
Adrenal tumor	17535989	CNVD
Breast cancer	21264507	CNVD
Basal cell lymphoma	17053054	CNVD
Medulloblastoma	17522785	CNVD
Cancer	23418310	CNVD
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Breast cancer	21785460	CNVD
Lung cancer	18438408	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21508638	CNVD
Neurodevelopmental disorder	22521361	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Williams Syndrome	20824207	CNVD
Breast cancer	16272173	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Ovarian cancer	21720365	CNVD
abnormal development	18461090	CNVD
Retinoblastoma	22278416	CNVD
Cancer	21183584	CNVD
Breast cancer	16397240	CNVD
Chronic lymphocytic leukemia	17053054	CNVD
Hereditary non-polyposis colorectal cancer	19566914	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
small cell lung cancer	20016488	CNVD
Developmental delay	21147756	CNVD
Mental retardation	19951919	CNVD
Myelofibrosis	22110671	CNVD
Microcephaly	20799320	CNVD
camptodactyly	20799320	CNVD
cognitive delay	20799320	CNVD
prenatal and postnatal growth deficiency	20799320	CNVD
ptosis of eyelids	20799320	CNVD
Maculopathy	20981449	CNVD
2p16.1 microdeletion syndrome	22283845	CNVD
Autism	22579565	CNVD
Autism	16963482	CNVD
Autism	21750575	CNVD
idiopathic intellectual disability	16963482	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Multiple myeloma	16616336	CNVD
Follicular lymphoma	17699855	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Seminomas	18059402	CNVD
Testicular germ cell tumor	18059402	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:239 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:56906800-56909800	Enhancers	Muscle Satellite Cultured Cells	--
2	chr2:56907000-56908000	Enhancers	HUVEC	blood vessel
3	chr2:56907000-56909800	Enhancers	HSMM	muscle
4	chr2:56907200-56909200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr2:56907200-56909400	Enhancers	NHEK	skin
6	chr2:56907200-56909600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:56907200-56909800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:56907400-56907800	Enhancers	Placenta Amnion	Placenta Amnion
9	chr2:56907400-56907800	Enhancers	HSMMtube	muscle
10	chr2:56907400-56909600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:56907600-56908000	Enhancers	Osteobl	bone
12	chr2:56907600-56909200	Enhancers	NHDF-Ad	bronchial
13	chr2:56907800-56909200	Weak transcription	HSMMtube	muscle
14	chr2:56907800-56909400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:56907800-56914200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr2:56908000-56908400	Flanking Active TSS	HUVEC	blood vessel
17	chr2:56908000-56909000	Weak transcription	Osteobl	bone
18	chr2:56908200-56909800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:56908400-56909800	Enhancers	HUVEC	blood vessel
20	chr2:56909200-56909400	Enhancers	HSMMtube	muscle
21	chr2:56909200-56909400	Enhancers	Osteobl	bone
22	chr2:56909200-56914000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:56909400-56914200	Weak transcription	NHEK	skin
24	chr2:56909600-56914200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr2:56909800-56913200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr2:56909800-56913600	Weak transcription	HUVEC	blood vessel
27	chr2:56909800-56914200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:56911400-56913200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:56911600-56911800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:56913200-56916000	Enhancers	Muscle Satellite Cultured Cells	--
31	chr2:56913600-56914600	Enhancers	HUVEC	blood vessel
32	chr2:56914000-56915200	Enhancers	HSMM	muscle
33	chr2:56914000-56916200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr2:56914200-56914400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:56914200-56914600	Enhancers	Placenta Amnion	Placenta Amnion
36	chr2:56914200-56916000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:56914200-56916000	Enhancers	NHEK	skin
38	chr2:56914400-56914600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr2:56914600-56928600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr2:56928600-56929000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr2:56932000-56932200	Enhancers	Psoas Muscle	Psoas
42	chr2:56932200-56943000	Weak transcription	Psoas Muscle	Psoas
43	chr2:56932600-56933800	Enhancers	NHEK	skin
44	chr2:56933000-56933800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr2:56933000-56935000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:56933800-56934800	Weak transcription	NHEK	skin
47	chr2:56933800-56935000	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr2:56933800-56940400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr2:56934600-56935000	Enhancers	H1 Cell Line	embryonic stem cell
50	chr2:56934600-56935000	Enhancers	HUES6 Cell Line	embryonic stem cell

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