Variant report

Variant	nsv528558
Chromosome Location	chr3:21106656-21251319
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	chr3:21174936-21175053	K562	blood:	n/a	n/a
2	BACH1	chr3:21190793-21191040	H1-hESC	embryonic stem cell:	n/a	n/a
3	BATF	chr3:21194098-21194329	GM12878	blood:	n/a	n/a
4	BATF	chr3:21201055-21201284	GM12878	blood:	n/a	chr3:21201159-21201170
5	BATF	chr3:21194072-21194305	GM12878	blood:	n/a	n/a
6	BHLHE40	chr3:21159378-21159417	K562	blood:	n/a	n/a
7	CCNT2	chr3:21119156-21119258	K562	blood:	n/a	n/a
8	CEBPB	chr3:21183980-21184119	A549	lung:	n/a	chr3:21184052-21184063 chr3:21184051-21184064
9	CEBPB	chr3:21238993-21239167	K562	blood:	n/a	chr3:21239061-21239072
10	CEBPB	chr3:21238940-21239196	IMR90	lung:	n/a	chr3:21239061-21239072
11	CEBPB	chr3:21226911-21227207	K562	blood:	n/a	n/a
12	CEBPB	chr3:21226940-21227188	A549	lung:	n/a	n/a
13	CEBPB	chr3:21183926-21184131	K562	blood:	n/a	chr3:21184052-21184063 chr3:21184051-21184064
14	CEBPB	chr3:21183929-21184180	HepG2	liver:	n/a	chr3:21184052-21184063 chr3:21184051-21184064
15	CEBPB	chr3:21226907-21227191	IMR90	lung:	n/a	n/a
16	CEBPB	chr3:21218651-21218851	HepG2	liver:	n/a	chr3:21218750-21218761
17	CEBPB	chr3:21164426-21164631	HepG2	liver:	n/a	chr3:21164567-21164578 chr3:21164606-21164617
18	CEBPB	chr3:21126029-21126290	K562	blood:	n/a	chr3:21126144-21126155
19	CEBPB	chr3:21183910-21184219	K562	blood:	n/a	chr3:21184052-21184063 chr3:21184051-21184064
20	CEBPB	chr3:21164447-21164713	A549	lung:	n/a	chr3:21164567-21164578 chr3:21164606-21164617
21	CEBPB	chr3:21108530-21108777	A549	lung:	n/a	n/a
22	CEBPB	chr3:21183893-21184180	IMR90	lung:	n/a	chr3:21184052-21184063 chr3:21184051-21184064
23	CEBPB	chr3:21226898-21227212	HepG2	liver:	n/a	n/a
24	CEBPB	chr3:21126025-21126248	A549	lung:	n/a	chr3:21126144-21126155
25	CEBPB	chr3:21125984-21126294	HepG2	liver:	n/a	chr3:21126144-21126155
26	CEBPB	chr3:21125988-21126321	IMR90	lung:	n/a	chr3:21126144-21126155
27	CEBPB	chr3:21238940-21239212	HepG2	liver:	n/a	chr3:21239061-21239072
28	CEBPB	chr3:21243291-21243434	A549	lung:	n/a	n/a
29	CHD1	chr3:21187707-21187761	H1-hESC	embryonic stem cell:	n/a	n/a
30	CHD1	chr3:21244067-21244119	H1-hESC	embryonic stem cell:	n/a	n/a
31	CHD2	chr3:21194221-21194308	GM12878	blood:	n/a	n/a
32	CTCF	chr3:21212580-21212730	RPTEC	kidney:	n/a	n/a
33	CTCF	chr3:21212600-21212750	HAc	cerebellar:	n/a	n/a
34	CTCF	chr3:21212620-21212770	MCF-7	breast:	n/a	n/a
35	CTCF	chr3:21212600-21212750	HVMF	connective:	n/a	n/a
36	CTCF	chr3:21212543-21212763	Hela-S3	cervix:	n/a	n/a
37	CTCF	chr3:21212480-21212630	HFF-Myc	foreskin:	n/a	n/a
38	CTCF	chr3:21212550-21212762	HUVEC	blood vessel:	n/a	n/a
39	CTCF	chr3:21212520-21212670	HVMF	connective:	n/a	n/a
40	CTCF	chr3:21212680-21212830	HA-sp	spinal cord:	n/a	n/a
41	CTCF	chr3:21212620-21212770	GM12872	blood:	n/a	n/a
42	CTCF	chr3:21212527-21212783	MCF-7	breast:	n/a	n/a
43	CTCF	chr3:21212590-21212737	GM10248	blood:	n/a	n/a
44	CTCF	chr3:21212545-21212750	ProgFib	skin:	n/a	n/a
45	CTCF	chr3:21212553-21212764	GM13977	blood:	n/a	n/a
46	CTCF	chr3:21212600-21212750	GM12872	blood:	n/a	n/a
47	CTCF	chr3:21212580-21212730	GM12801	blood:	n/a	n/a
48	CTCF	chr3:21212580-21212730	AG09319	gingival:	n/a	n/a
49	CTCF	chr3:21212620-21212770	NHLF	lung:	n/a	n/a
50	CTCF	chr3:21212620-21212770	HFF	foreskin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:21207903..21212103-chr3:21235234..21238537,4	K562	blood:
2	chr3:21175037..21177371-chr3:21182384..21184259,2	K562	blood:
3	chr3:21100031..21101592-chr3:21111513..21113234,2	K562	blood:
4	chr3:21049220..21051443-chr3:21113228..21114946,2	K562	blood:
5	chr3:21194222..21197075-chr3:21200094..21202897,2	K562	blood:
6	chr3:21207950..21210850-chr3:21212178..21213928,2	K562	blood:
7	chr3:21188799..21190342-chr3:21193601..21195363,2	K562	blood:
8	chr3:21207950..21210850-chr3:21212178..21213928,2	K562	blood:
9	chr3:21188799..21190342-chr3:21193601..21195363,2	K562	blood:
10	chr3:21205402..21208322-chr3:21209638..21211827,2	K562	blood:
11	chr3:21205402..21208322-chr3:21209638..21211827,2	K562	blood:
12	chr3:21132848..21134885-chr3:21136213..21138179,2	K562	blood:
13	chr3:21207903..21212103-chr3:21235234..21238537,4	K562	blood:
14	chr3:21175037..21177371-chr3:21182384..21184259,2	K562	blood:
15	chr3:21194222..21197075-chr3:21200094..21202897,2	K562	blood:
16	chr3:21132848..21134885-chr3:21136213..21138179,2	K562	blood:

Variant related genes	Relation type
ENSG00000221659	TF binding region

Extended variants
information (count: 2062 )
Associated
traits (count: 78 )

Variant overlapped rSNPs/rCNVs (count:2062 , 50 per page) page: 1 2 3 4 5 6 7 ... 42

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs4858289	chr3:21106656-21106657	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs547024306	chr3:21106672-21106673	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs567953552	chr3:21106706-21106707	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs535837561	chr3:21106709-21106710	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs4857976	chr3:21106756-21106757	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs569318728	chr3:21106794-21106795	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs145735954	chr3:21106803-21106804	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs558301919	chr3:21106814-21106815	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs146599622	chr3:21106826-21106827	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs537181160	chr3:21106866-21106867	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs552938782	chr3:21106890-21106891	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs574398594	chr3:21106904-21106905	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs143374924	chr3:21106952-21106953	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs563276618	chr3:21106956-21106957	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs575268884	chr3:21106960-21106961	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs148381653	chr3:21106991-21106992	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs191012134	chr3:21106993-21106994	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs528796105	chr3:21107003-21107004	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs547362364	chr3:21107015-21107016	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs73038928	chr3:21107076-21107077	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs182164818	chr3:21107101-21107102	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs187764001	chr3:21107162-21107163	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs141604456	chr3:21107178-21107179	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs192716641	chr3:21107206-21107207	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs9850499	chr3:21107235-21107236	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs546679795	chr3:21107250-21107251	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs35098892	chr3:21107267-21107268	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs372042817	chr3:21107270-21107271	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs536029300	chr3:21107277-21107278	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs553035620	chr3:21107284-21107285	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs184616043	chr3:21107285-21107286	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs535135993	chr3:21107291-21107292	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs568421076	chr3:21107292-21107293	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs556879002	chr3:21107295-21107296	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs552817894	chr3:21107297-21107298	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs369246137	chr3:21107301-21107302	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs201543189	chr3:21107303-21107304	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs564193004	chr3:21107304-21107305	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs62234875	chr3:21107305-21107306	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs140673797	chr3:21107307-21107308	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs146226190	chr3:21107309-21107310	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs376529619	chr3:21107311-21107312	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs57444192	chr3:21107330-21107331	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs71935600	chr3:21107331-21107332	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs9850797	chr3:21107332-21107333	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs34759402	chr3:21107368-21107369	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs372759860	chr3:21107370-21107371	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs188352968	chr3:21107386-21107387	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs4019490	chr3:21107493-21107494	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs114126640	chr3:21107527-21107528	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:78)

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
Cancer	20164919	CNVD
Melanoma	20688739	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Breast cancer	22522925	CNVD
early-passage human iPS cells	21368824	CNVD

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:21086800-21108800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:21101400-21106800	Weak transcription	Aorta	Aorta
3	chr3:21104600-21108600	Weak transcription	Fetal Lung	lung
4	chr3:21106800-21107000	Enhancers	Fetal Muscle Leg	muscle
5	chr3:21108600-21109000	Enhancers	Fetal Kidney	kidney
6	chr3:21108600-21109200	Enhancers	Fetal Lung	lung
7	chr3:21126800-21128600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:21128600-21131000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:21132600-21132800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:21132800-21139600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr3:21145200-21146200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr3:21147400-21148000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:21147400-21148000	Enhancers	Gastric	stomach
14	chr3:21150200-21151000	Enhancers	Brain Germinal Matrix	brain
15	chr3:21159000-21159200	ZNF genes & repeats	Lung	lung
16	chr3:21159200-21159400	Enhancers	Lung	lung
17	chr3:21171400-21171800	ZNF genes & repeats	Psoas Muscle	Psoas
18	chr3:21180000-21184600	Weak transcription	Pancreas	Pancrea
19	chr3:21181600-21182800	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr3:21181800-21182800	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr3:21181800-21182800	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr3:21182200-21182400	Enhancers	Aorta	Aorta
23	chr3:21182200-21182600	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr3:21182200-21182600	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr3:21182200-21182600	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr3:21182200-21182800	Enhancers	H9 Cell Line	embryonic stem cell
27	chr3:21182200-21182800	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr3:21182400-21182800	Enhancers	H1 Cell Line	embryonic stem cell
29	chr3:21182400-21184600	Weak transcription	Aorta	Aorta
30	chr3:21184600-21184800	Enhancers	Aorta	Aorta
31	chr3:21184600-21184800	Enhancers	Pancreas	Pancrea
32	chr3:21184800-21185200	Weak transcription	Pancreas	Pancrea
33	chr3:21184800-21186600	Weak transcription	Aorta	Aorta
34	chr3:21187000-21187200	ZNF genes & repeats	Aorta	Aorta
35	chr3:21196200-21197000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:21197000-21198800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:21198800-21199400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:21198800-21199600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr3:21199600-21201400	Enhancers	Fetal Stomach	stomach
40	chr3:21199800-21201600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:21200000-21200400	Enhancers	NHDF-Ad	bronchial
42	chr3:21200000-21201400	Enhancers	Colon Smooth Muscle	Colon
43	chr3:21200000-21201600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:21200400-21200800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:21200400-21200800	Flanking Active TSS	NHDF-Ad	bronchial
46	chr3:21200400-21201000	Enhancers	NH-A	brain
47	chr3:21200400-21201200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr3:21200400-21201200	Enhancers	Rectal Smooth Muscle	rectum
49	chr3:21200400-21201400	Enhancers	Muscle Satellite Cultured Cells	--
50	chr3:21200400-21201400	Enhancers	NHLF	lung

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