Variant report

Variant	esv3429579
Chromosome Location	chr3:42898402-42907671
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:122)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:42901423-42901471	GM10266	blood:	n/a	n/a
2	FOXA1	chr3:42899274-42899576	HepG2	liver:	n/a	n/a
3	FOXA2	chr3:42899257-42899567	A549	lung:	n/a	n/a
4	YY1	chr3:42905840-42906121	K562	blood:	n/a	n/a
5	YY1	chr3:42905801-42906251	H1-hESC	embryonic stem cell:	n/a	n/a
6	YY1	chr3:42905908-42906130	GM12892	blood:	n/a	n/a
7	YY1	chr3:42905835-42906125	K562	blood:	n/a	n/a
8	YY1	chr3:42905917-42906092	K562	blood:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:42906014-42906064	AG09309	skin:	n/a
2	chr3:42906014-42906064	SK-N-MC	brain:	n/a
3	chr3:42906014-42906064	GM12891	blood:	n/a
4	chr3:42905968-42906018	SK-N-SH_RA	brain:	n/a
5	chr3:42906014-42906064	RPTEC	kidney:	n/a
6	chr3:42906014-42906064	NH-A	brain:	n/a
7	chr3:42905968-42906018	GM19239	blood:	n/a
8	chr3:42906014-42906064	H1-hESC	embryonic stem cell:	embryo
9	chr3:42905968-42906018	NH-A	brain:	n/a
10	chr3:42905968-42906018	AG04449	skin:	fetal
11	chr3:42905968-42906018	AoSMC	blood vessel:	n/a
12	chr3:42905968-42906018	HUVEC	blood vessel:	n/a
13	chr3:42906014-42906064	K562	blood:	n/a
14	chr3:42906014-42906064	HCM	heart:	n/a
15	chr3:42906014-42906064	SKMC	muscle:	n/a
16	chr3:42906014-42906064	HRCEpiC	kidney:	n/a
17	chr3:42905968-42906018	Caco-2	colon:	n/a
18	chr3:42906014-42906064	BJ	skin:	n/a
19	chr3:42906014-42906064	Jurkat	blood:	n/a
20	chr3:42905968-42906018	ProgFib	skin:	n/a
21	chr3:42905968-42906018	H1-hESC	embryonic stem cell:	embryo
22	chr3:42906014-42906064	A549	lung:	n/a
23	chr3:42906014-42906064	AoSMC	blood vessel:	n/a
24	chr3:42906014-42906064	U87	brain:	n/a
25	chr3:42905968-42906018	HCF	heart:	n/a
26	chr3:42906014-42906064	AG10803	skin:	n/a
27	chr3:42906014-42906064	PFSK-1	brain:	n/a
28	chr3:42905968-42906018	HL-60	blood:	n/a
29	chr3:42905968-42906018	MCF10A-Er-Src	breast:	n/a
30	chr3:42906014-42906064	MCF-7	breast:	n/a
31	chr3:42905968-42906018	SKMC	muscle:	n/a
32	chr3:42906014-42906064	CMK	blood:	n/a
33	chr3:42906014-42906064	HAEpiC	amniotic membrane:	n/a
34	chr3:42906014-42906064	HEK293	kidney:	embryo
35	chr3:42905968-42906018	HCM	heart:	n/a
36	chr3:42906014-42906064	BE2_C	brain:	n/a
37	chr3:42906014-42906064	NHBE	bronchial:	n/a
38	chr3:42905968-42906018	ovcar-3	ovarian:	n/a
39	chr3:42905968-42906018	LNCaP	prostate:	n/a
40	chr3:42905968-42906018	AG04450	lung:	fetal
41	chr3:42906014-42906064	NT2-D1	testis:	n/a
42	chr3:42905968-42906018	BE2_C	brain:	n/a
43	chr3:42905968-42906018	U87	brain:	n/a
44	chr3:42906014-42906064	Hepatocyte	liver:	n/a
45	chr3:42905968-42906018	Hela-S3	cervix:	n/a
46	chr3:42905968-42906018	ECC-1	luminal epithelium:	n/a
47	chr3:42905968-42906018	NT2-D1	testis:	n/a
48	chr3:42905968-42906018	NB4	blood:	n/a
49	chr3:42906014-42906064	HepG2	liver:	n/a
50	chr3:42906014-42906064	GM06990	blood:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42904072..42907303-chr3:42909890..42911615,3	K562	blood:
2	chr3:42907660..42910304-chr3:42911917..42914590,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KRBOX1-1	chr3:42905958-42906026	NONHSAT089268

No data

Variant related genes	Relation type
ENSG00000235288	TF binding region
ENSG00000235288	CpG island

Extended variants
information (count: 362 )
Associated
traits (count: 89 )

Variant overlapped rSNPs/rCNVs (count:362 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs373272586	chr3:42898407-42898408	Weak transcription Enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs373849718	chr3:42898421-42898422	Weak transcription Enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs536529436	chr3:42898442-42898443	Weak transcription Enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs201037635	chr3:42898488-42898489	Weak transcription Enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs547002368	chr3:42898529-42898530	Weak transcription Enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs566826477	chr3:42898530-42898531	Weak transcription Enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs189755983	chr3:42898567-42898568	Weak transcription Enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs556039385	chr3:42898590-42898591	Weak transcription Enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs574585811	chr3:42898597-42898598	Weak transcription Enhancers Flanking Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs182820258	chr3:42898602-42898603	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs575647463	chr3:42898603-42898604	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs114152462	chr3:42898615-42898616	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs17239701	chr3:42898649-42898650	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs141159546	chr3:42898712-42898713	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs367834869	chr3:42898753-42898754	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs4683347	chr3:42898788-42898789	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs576723910	chr3:42898866-42898867	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs554264140	chr3:42898922-42898923	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs545477916	chr3:42898942-42898943	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs144870731	chr3:42898997-42898998	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs531288012	chr3:42898998-42898999	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs369702549	chr3:42899017-42899018	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs547912265	chr3:42899086-42899087	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs116177715	chr3:42899119-42899120	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs1346416	chr3:42899143-42899144	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs547233493	chr3:42899175-42899176	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs567057100	chr3:42899262-42899263	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs539367449	chr3:42899286-42899287	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs552279705	chr3:42899303-42899304	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs569309017	chr3:42899314-42899315	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs538313976	chr3:42899349-42899350	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs149126424	chr3:42899394-42899395	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs138322731	chr3:42899439-42899440	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs574644325	chr3:42899440-42899441	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs533748893	chr3:42899477-42899478	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs553977813	chr3:42899480-42899481	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs193157931	chr3:42899537-42899538	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs546110312	chr3:42899538-42899539	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs555861657	chr3:42899563-42899564	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs575656354	chr3:42899584-42899585	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs572091998	chr3:42899604-42899605	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs13083715	chr3:42899638-42899639	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs531328465	chr3:42899645-42899646	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs561458148	chr3:42899708-42899709	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs530186956	chr3:42899799-42899800	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs540467890	chr3:42899856-42899857	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs201989860	chr3:42899860-42899861	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs200315355	chr3:42899901-42899902	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs201390925	chr3:42899906-42899907	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs143302141	chr3:42899922-42899923	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:89)

Disease	PMID	Source
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
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	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
Breast cancer	17603634	CNVD
Esophageal cancer	20955586	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Melanoma	20688739	CNVD
Acute myeloid leukemia	21251322	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Wilms tumour	17204608	CNVD
Biliary cancer	19435499	CNVD
Non-small cell lung cancer	20864512	CNVD
Non-small cell lung cancer	21829676	CNVD
Kartagener syndrome	16639409	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Breast cancer	21509527	CNVD
Melanoma	21693616	CNVD
Myelofibrosis	22110671	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Breast cancer	20409316	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Breast cancer	21364760	CNVD
abnormal development	18461090	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Prostate cancer	18632612	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42893400-42906000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:42894800-42912800	Weak transcription	Right Atrium	heart
3	chr3:42897000-42898600	Enhancers	Primary B cells from peripheral blood	blood
4	chr3:42897400-42898600	Enhancers	Primary B cells from cord blood	blood
5	chr3:42897800-42905800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:42897800-42913400	Weak transcription	Pancreas	Pancrea
7	chr3:42898000-42898600	Strong transcription	Placenta	Placenta
8	chr3:42898000-42899000	Enhancers	HepG2	liver
9	chr3:42898400-42899000	Flanking Active TSS	Liver	Liver
10	chr3:42898600-42905600	Weak transcription	Placenta	Placenta
11	chr3:42899000-42899200	Enhancers	Liver	Liver
12	chr3:42904600-42905600	Weak transcription	K562	blood
13	chr3:42905600-42912800	Strong transcription	Placenta	Placenta
14	chr3:42905800-42906000	Flanking Active TSS	K562	blood
15	chr3:42905800-42907000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:42906000-42906200	Flanking Bivalent TSS/Enh	K562	blood
17	chr3:42906000-42906800	Strong transcription	Placenta Amnion	Placenta Amnion
18	chr3:42906000-42907800	Weak transcription	Liver	Liver
19	chr3:42906200-42906400	Bivalent Enhancer	K562	blood
20	chr3:42906200-42907000	Active TSS	Brain Substantia Nigra	brain
21	chr3:42906800-42907000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:42906800-42908400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr3:42907000-42907400	Weak transcription	Brain Substantia Nigra	brain
24	chr3:42907000-42909000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:42907000-42915800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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