Variant report

Variant	nsv979809
Chromosome Location	chr3:20052873-20056586
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:60)
CpG islands
(count:123)
Chromatin interactive
region (count:4)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:60 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr3:20056175-20056432	K562	blood:	n/a	n/a
2	ATF3	chr3:20052769-20053055	K562	blood:	n/a	n/a
3	BHLHE40	chr3:20056080-20056539	K562	blood:	n/a	n/a
4	CBX3	chr3:20054860-20055250	K562	blood:	n/a	chr3:20054863-20054874
5	CBX3	chr3:20056025-20056546	K562	blood:	n/a	n/a
6	CCNT2	chr3:20056065-20056482	K562	blood:	n/a	n/a
7	CEBPB	chr3:20053764-20053964	K562	blood:	n/a	chr3:20053812-20053823
8	CEBPB	chr3:20052779-20053038	K562	blood:	n/a	chr3:20052961-20052972 chr3:20052958-20052975
9	CEBPB	chr3:20052808-20053114	IMR90	lung:	n/a	chr3:20052961-20052972 chr3:20052958-20052975
10	CEBPB	chr3:20056170-20056429	K562	blood:	n/a	n/a
11	CEBPB	chr3:20052792-20053013	HepG2	liver:	n/a	chr3:20052961-20052972 chr3:20052958-20052975
12	CEBPB	chr3:20052810-20053020	A549	lung:	n/a	chr3:20052961-20052972 chr3:20052958-20052975
13	CEBPB	chr3:20053662-20053918	HepG2	liver:	n/a	chr3:20053812-20053823
14	CEBPB	chr3:20052848-20053007	K562	blood:	n/a	chr3:20052961-20052972 chr3:20052958-20052975
15	CEBPB	chr3:20052789-20053140	K562	blood:	n/a	chr3:20052961-20052972 chr3:20052958-20052975
16	CEBPD	chr3:20056001-20056502	K562	blood:	n/a	n/a
17	CEBPD	chr3:20056020-20056625	K562	blood:	n/a	n/a
18	EGR1	chr3:20056126-20056394	K562	blood:	n/a	n/a
19	EGR1	chr3:20056130-20056396	K562	blood:	n/a	n/a
20	EP300	chr3:20056053-20056494	K562	blood:	n/a	n/a
21	EP300	chr3:20056173-20056404	K562	blood:	n/a	n/a
22	GABPA	chr3:20056095-20056430	K562	blood:	n/a	n/a
23	GATA1	chr3:20054692-20056656	PBDE	blood:	n/a	n/a
24	GATA1	chr3:20055922-20056780	K562	blood:	n/a	n/a
25	GATA2	chr3:20056033-20056467	K562	blood:	n/a	n/a
26	GATA2	chr3:20056025-20056454	K562	blood:	n/a	n/a
27	GATA2	chr3:20056077-20056514	K562	blood:	n/a	n/a
28	GTF3C2	chr3:20055846-20056504	K562	blood:	n/a	n/a
29	HDAC2	chr3:20056117-20056504	K562	blood:	n/a	n/a
30	HDAC2	chr3:20056179-20056482	K562	blood:	n/a	n/a
31	IRF1	chr3:20052759-20052886	K562	blood:	n/a	n/a
32	JUND	chr3:20056070-20056452	K562	blood:	n/a	n/a
33	MAX	chr3:20056106-20056481	K562	blood:	n/a	n/a
34	MAX	chr3:20056204-20056313	K562	blood:	n/a	n/a
35	MAZ	chr3:20056109-20056509	K562	blood:	n/a	n/a
36	MYC	chr3:20056051-20056510	K562	blood:	n/a	n/a
37	MYC	chr3:20056161-20056449	K562	blood:	n/a	n/a
38	MYC	chr3:20056288-20056318	K562	blood:	n/a	n/a
39	MYC	chr3:20056279-20056280	K562	blood:	n/a	n/a
40	NR2F2	chr3:20055976-20056600	K562	blood:	n/a	n/a
41	PML	chr3:20056117-20056489	K562	blood:	n/a	n/a
42	POLR2A	chr3:20056147-20056443	K562	blood:	n/a	n/a
43	POLR2A	chr3:20056393-20056419	K562	blood:	n/a	n/a
44	POLR2A	chr3:20056425-20056447	K562	blood:	n/a	n/a
45	POLR2A	chr3:20056206-20056229	K562	blood:	n/a	n/a
46	POLR2A	chr3:20056253-20056392	K562	blood:	n/a	n/a
47	RCOR1	chr3:20056021-20056579	K562	blood:	n/a	n/a
48	RCOR1	chr3:20056069-20056528	K562	blood:	n/a	n/a
49	STAT5A	chr3:20056033-20056529	K562	blood:	n/a	n/a
50	TAL1	chr3:20054861-20055286	K562	blood:	n/a	n/a

(count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:20053940-20053990	AG04450	lung:	fetal
2	chr3:20053940-20053990	AG04450	lung:	fetal
3	chr3:20053708-20053758	HEK293	kidney:	embryo
4	chr3:20053940-20053990	HNPCEpiC	eye:	n/a
5	chr3:20053708-20053758	GM12878	blood:	n/a
6	chr3:20053708-20053758	AG09309	skin:	n/a
7	chr3:20053708-20053758	HPAEpiC	pulmonary alveolar:	n/a
8	chr3:20053940-20053990	HAEpiC	amniotic membrane:	n/a
9	chr3:20053940-20053990	LNCaP	prostate:	n/a
10	chr3:20053940-20053990	PFSK-1	brain:	n/a
11	chr3:20053708-20053758	NHBE	bronchial:	n/a
12	chr3:20053708-20053758	T-47D	breast:	n/a
13	chr3:20053940-20053990	SK-N-SH_RA	brain:	n/a
14	chr3:20053940-20053990	ECC-1	luminal epithelium:	n/a
15	chr3:20053708-20053758	GM19239	blood:	n/a
16	chr3:20053708-20053758	K562	blood:	n/a
17	chr3:20053940-20053990	GM06990	blood:	n/a
18	chr3:20053940-20053990	GM12878	blood:	n/a
19	chr3:20053940-20053990	K562	blood:	n/a
20	chr3:20053940-20053990	HUVEC	blood vessel:	n/a
21	chr3:20053940-20053990	HRCEpiC	kidney:	n/a
22	chr3:20053708-20053758	ProgFib	skin:	n/a
23	chr3:20053708-20053758	HNPCEpiC	eye:	n/a
24	chr3:20053708-20053758	SK-N-SH_RA	brain:	n/a
25	chr3:20053708-20053758	HCT-116	colon:	n/a
26	chr3:20053940-20053990	HEEpiC	esophagus:	n/a
27	chr3:20053940-20053990	T-47D	breast:	n/a
28	chr3:20053708-20053758	CMK	blood:	n/a
29	chr3:20053708-20053758	NT2-D1	testis:	n/a
30	chr3:20053708-20053758	SAEC	small airway:	n/a
31	chr3:20053940-20053990	NHDF-neo	bronchial:	n/a
32	chr3:20053708-20053758	HRCEpiC	kidney:	n/a
33	chr3:20053940-20053990	CMK	blood:	n/a
34	chr3:20053940-20053990	Hela-S3	cervix:	n/a
35	chr3:20053708-20053758	HEEpiC	esophagus:	n/a
36	chr3:20053940-20053990	PrEC	prostate:	n/a
37	chr3:20053708-20053758	HIPEpiC	eye:	n/a
38	chr3:20053708-20053758	AG10803	skin:	n/a
39	chr3:20053940-20053990	HCF	heart:	n/a
40	chr3:20053708-20053758	AG04450	lung:	fetal
41	chr3:20053940-20053990	SK-N-MC	brain:	n/a
42	chr3:20053940-20053990	IMR90	lung:	fetal
43	chr3:20053940-20053990	NH-A	brain:	n/a
44	chr3:20053940-20053990	HRE	kidney:	n/a
45	chr3:20053708-20053758	AG04449	skin:	fetal
46	chr3:20053708-20053758	PrEC	prostate:	n/a
47	chr3:20053940-20053990	SAEC	small airway:	n/a
48	chr3:20053708-20053758	MCF-7	breast:	n/a
49	chr3:20053940-20053990	ovcar-3	ovarian:	n/a
50	chr3:20053708-20053758	AoSMC	blood vessel:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:19991110..19993492-chr3:20053410..20056377,2	K562	blood:
2	chr3:20053872..20056558-chr3:20225792..20227888,2	K562	blood:
3	chr3:20046912..20049769-chr3:20052524..20055370,2	K562	blood:
4	chr3:19987096..19989154-chr3:20054828..20057448,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EFHB-4	chr3:20053542-20053749	NONHSAT088608
2	lnc-EFHB-4	chr3:20053542-20053765	NR_027694

No data

Variant related genes	Relation type
ENSG00000229468	TF binding region
ENSG00000230697	TF binding region
PP2D1	TF binding region
ENSG00000229468	CpG island
ENSG00000230697	CpG island
PP2D1	CpG island
ENSG00000144566	chromatin interactions
ENSG00000163576	chromatin interactions
ENSG00000230697	chromatin interactions
ENSG00000129810	chromatin interactions

Extended variants
information (count: 184 )
Associated
traits (count: 75 )

Variant overlapped rSNPs/rCNVs (count:184 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs540930358	chr3:20052884-20052885	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs180986073	chr3:20052909-20052910	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs34872212	chr3:20052928-20052929	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
4	rs115502592	chr3:20052943-20052944	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs563785925	chr3:20052992-20052993	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs142081131	chr3:20053012-20053013	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs62241335	chr3:20053014-20053015	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs570861131	chr3:20053015-20053016	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs528752943	chr3:20053061-20053062	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs547329640	chr3:20053062-20053063	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs568530621	chr3:20053068-20053069	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs6784536	chr3:20053072-20053073	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
13	rs557309195	chr3:20053102-20053103	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs569724721	chr3:20053104-20053105	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs201472169	chr3:20053117-20053118	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs536801164	chr3:20053129-20053130	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs202007107	chr3:20053138-20053139	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs576441024	chr3:20053143-20053144	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs540893382	chr3:20053147-20053148	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs553255616	chr3:20053148-20053149	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs574673436	chr3:20053149-20053150	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs541996942	chr3:20053162-20053163	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs563382864	chr3:20053164-20053165	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs6799824	chr3:20053172-20053173	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs546329286	chr3:20053182-20053183	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs138683950	chr3:20053183-20053184	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs528515149	chr3:20053184-20053185	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs141121870	chr3:20053216-20053217	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs568722707	chr3:20053239-20053240	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs529602256	chr3:20053248-20053249	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs551154640	chr3:20053277-20053278	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs201099657	chr3:20053292-20053293	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs569356349	chr3:20053304-20053305	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs10607560	chr3:20053316-20053317	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs72035028	chr3:20053327-20053328	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs62241336	chr3:20053396-20053397	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs536708787	chr3:20053401-20053402	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs146920364	chr3:20053419-20053420	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs570087801	chr3:20053506-20053507	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs188842668	chr3:20053509-20053510	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs574672069	chr3:20053533-20053534	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs2686326	chr3:20053581-20053582	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs148377652	chr3:20053602-20053603	Weak transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
44	rs575522478	chr3:20053603-20053604	Weak transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
45	rs547099249	chr3:20053620-20053621	Weak transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
46	rs546288724	chr3:20053649-20053650	Weak transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
47	rs6802632	chr3:20053676-20053677	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
48	rs181594108	chr3:20053708-20053709	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
49	rs375400486	chr3:20053709-20053710	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
50	rs540623333	chr3:20053713-20053714	Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:75)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	17327916	CNVD
Glioblastoma multiforme	21080181	CNVD
Neuroblastoma	18923191	CNVD
Colorectal cancer	21297112	CNVD
Lynch syndrome	18415027	CNVD
Renal cell carcinoma	18592004	CNVD
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
lymphocytic leukemia	21291569	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Esophageal cancer	20955586	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Myelofibrosis	22110671	CNVD
Gastric adenocarcinoma	19115996	CNVD
Squamous cell cancer	20885788	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Breast cancer	17133270	CNVD
Developmental delay	21147756	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Autism	20531469	CNVD
Prostate cancer	19363497	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20050800-20053600	Weak transcription	K562	blood
2	chr3:20052000-20056400	Weak transcription	Right Atrium	heart
3	chr3:20053600-20058000	Enhancers	K562	blood
4	chr3:20054800-20055600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:20054800-20055800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:20055000-20055400	Enhancers	NHEK	skin
7	chr3:20056200-20056600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr3:20056400-20056600	Enhancers	Right Atrium	heart

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