Variant report

Variant	esv3506087
Chromosome Location	chr3:142609212-142614010
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	CEBPB	chr3:142613503-142613739	K562	blood:	n/a	n/a
2	CEBPB	chr3:142609712-142609819	HepG2	liver:	n/a	chr3:142609726-142609739 chr3:142609726-142609737 chr3:142609726-142609739 chr3:142609726-142609739 chr3:142609728-142609739
3	CEBPB	chr3:142609598-142609811	K562	blood:	n/a	chr3:142609726-142609739 chr3:142609726-142609737 chr3:142609726-142609739 chr3:142609726-142609739 chr3:142609728-142609739
4	EBF1	chr3:142610126-142610469	GM12878	blood:	n/a	n/a
5	EP300	chr3:142611745-142612101	SK-N-SH_RA	brain:	n/a	n/a
6	EP300	chr3:142611828-142612102	SK-N-SH_RA	brain:	n/a	n/a
7	GATA2	chr3:142611753-142612097	SH-SY5Y	brain:	n/a	n/a
8	GATA3	chr3:142611840-142612002	SH-SY5Y	brain:	n/a	n/a
9	GATA3	chr3:142611563-142612252	SK-N-SH	brain:	n/a	n/a
10	GATA3	chr3:142611638-142612287	SK-N-SH	brain:	n/a	n/a
11	GATA3	chr3:142611731-142612124	T-47D	breast:	n/a	n/a
12	MYC	chr3:142612708-142612792	MCF-7	breast:	n/a	n/a
13	NFYA	chr3:142609550-142609709	GM12878	blood:	n/a	n/a
14	NFYB	chr3:142611546-142611907	K562	blood:	n/a	n/a
15	NFYB	chr3:142613405-142613850	K562	blood:	n/a	chr3:142613576-142613590
16	NFYB	chr3:142611554-142611832	Hela-S3	cervix:	n/a	n/a
17	NFYB	chr3:142613511-142613762	GM12878	blood:	n/a	chr3:142613576-142613590
18	PBX3	chr3:142611627-142612074	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr3:142611650-142611651	GM12878	blood:	n/a	n/a
20	POLR2A	chr3:142609360-142609770	SK-N-MC	brain:	n/a	n/a
21	POLR2A	chr3:142611677-142611710	GM12878	blood:	n/a	n/a
22	POLR2A	chr3:142611500-142611640	GM12878	blood:	n/a	n/a
23	POLR2A	chr3:142611797-142611858	ProgFib	skin:	n/a	n/a
24	USF1	chr3:142611597-142611891	HCT-116	colon:	n/a	n/a
25	USF1	chr3:142613365-142613651	A549	lung:	n/a	chr3:142613560-142613571
26	USF1	chr3:142613372-142613786	H1-hESC	embryonic stem cell:	n/a	chr3:142613560-142613571
27	USF1	chr3:142613445-142613772	H1-hESC	embryonic stem cell:	n/a	chr3:142613560-142613571
28	USF1	chr3:142613392-142613713	K562	blood:	n/a	chr3:142613560-142613571
29	USF1	chr3:142613362-142613766	ECC-1	luminal epithelium:	n/a	chr3:142613560-142613571
30	USF1	chr3:142611597-142611916	SK-N-SH_RA	brain:	n/a	n/a
31	USF1	chr3:142611528-142611947	K562	blood:	n/a	n/a
32	USF1	chr3:142611585-142611832	A549	lung:	n/a	n/a
33	USF1	chr3:142613334-142613743	K562	blood:	n/a	chr3:142613560-142613571
34	USF1	chr3:142613433-142613755	ECC-1	luminal epithelium:	n/a	chr3:142613560-142613571
35	USF1	chr3:142613460-142613659	HepG2	liver:	n/a	chr3:142613560-142613571
36	USF1	chr3:142613326-142613844	HCT-116	colon:	n/a	chr3:142613560-142613571
37	USF1	chr3:142611654-142611874	H1-hESC	embryonic stem cell:	n/a	n/a
38	USF1	chr3:142613421-142613667	HepG2	liver:	n/a	chr3:142613560-142613571
39	USF1	chr3:142611608-142611853	SK-N-SH_RA	brain:	n/a	n/a
40	USF1	chr3:142611546-142611967	SK-N-SH	brain:	n/a	n/a
41	USF1	chr3:142613441-142613646	SK-N-SH_RA	brain:	n/a	chr3:142613560-142613571
42	USF1	chr3:142613398-142613687	SK-N-SH_RA	brain:	n/a	chr3:142613560-142613571
43	USF1	chr3:142613398-142613712	A549	lung:	n/a	chr3:142613560-142613571
44	USF2	chr3:142611638-142611921	Hela-S3	cervix:	n/a	chr3:142611753-142611764
45	USF2	chr3:142613451-142613708	HepG2	liver:	n/a	chr3:142613560-142613571
46	USF2	chr3:142613429-142613683	H1-hESC	embryonic stem cell:	n/a	chr3:142613560-142613571
47	USF2	chr3:142613528-142613621	Hela-S3	cervix:	n/a	chr3:142613560-142613571
48	USF2	chr3:142613437-142613666	K562	blood:	n/a	chr3:142613560-142613571

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:142610864-142610914	NT2-D1	testis:	n/a
2	chr3:142610864-142610914	NT2-D1	testis:	n/a
3	chr3:142610864-142610914	ProgFib	skin:	n/a
4	chr3:142610864-142610914	MCF-7	breast:	n/a
5	chr3:142610864-142610914	SKMC	muscle:	n/a
6	chr3:142610864-142610914	GM12891	blood:	n/a
7	chr3:142610864-142610914	GM19239	blood:	n/a
8	chr3:142610864-142610914	HAEpiC	amniotic membrane:	n/a
9	chr3:142610864-142610914	NB4	blood:	n/a
10	chr3:142610864-142610914	IMR90	lung:	fetal
11	chr3:142610864-142610914	HCF	heart:	n/a
12	chr3:142610864-142610914	LNCaP	prostate:	n/a
13	chr3:142610864-142610914	HNPCEpiC	eye:	n/a
14	chr3:142610864-142610914	PFSK-1	brain:	n/a
15	chr3:142610864-142610914	BJ	skin:	n/a
16	chr3:142610864-142610914	HL-60	blood:	n/a
17	chr3:142610864-142610914	T-47D	breast:	n/a
18	chr3:142610864-142610914	AG09319	gingival:	n/a
19	chr3:142610864-142610914	NH-A	brain:	n/a
20	chr3:142610864-142610914	HPAEpiC	pulmonary alveolar:	n/a
21	chr3:142610864-142610914	Caco-2	colon:	n/a
22	chr3:142610864-142610914	NHDF-neo	bronchial:	n/a
23	chr3:142610864-142610914	SK-N-SH_RA	brain:	n/a
24	chr3:142610864-142610914	HRPEpiC	eye:	n/a
25	chr3:142610864-142610914	SK-N-MC	brain:	n/a
26	chr3:142610864-142610914	K562	blood:	n/a
27	chr3:142610864-142610914	SK-N-SH	brain:	n/a
28	chr3:142610864-142610914	NHBE	bronchial:	n/a
29	chr3:142610864-142610914	MCF10A-Er-Src	breast:	n/a
30	chr3:142610864-142610914	Hepatocyte	liver:	n/a
31	chr3:142610864-142610914	AG04449	skin:	fetal
32	chr3:142610864-142610914	A549	lung:	n/a
33	chr3:142610864-142610914	AG09309	skin:	n/a
34	chr3:142610864-142610914	HRCEpiC	kidney:	n/a
35	chr3:142610864-142610914	HCM	heart:	n/a
36	chr3:142610864-142610914	HCPEpiC	choroid plexus:	n/a
37	chr3:142610864-142610914	GM06990	blood:	n/a
38	chr3:142610864-142610914	ECC-1	luminal epithelium:	n/a
39	chr3:142610864-142610914	HEEpiC	esophagus:	n/a
40	chr3:142610864-142610914	GM12892	blood:	n/a
41	chr3:142610864-142610914	HEK293	kidney:	embryo
42	chr3:142610864-142610914	ovcar-3	ovarian:	n/a
43	chr3:142610864-142610914	Hela-S3	cervix:	n/a
44	chr3:142610864-142610914	PANC-1	pancreas:	n/a
45	chr3:142610864-142610914	RPTEC	kidney:	n/a
46	chr3:142610864-142610914	GM12878	blood:	n/a
47	chr3:142610864-142610914	HMEC	breast:	n/a
48	chr3:142610864-142610914	PrEC	prostate:	n/a
49	chr3:142610864-142610914	AG10803	skin:	n/a
50	chr3:142610864-142610914	AoSMC	blood vessel:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:142598080..142600621-chr3:142609257..142610987,2	K562	blood:
2	chr3:142609483..142612071-chr3:142616369..142619084,2	K562	blood:
3	chr3:142606684..142610842-chr3:142612134..142615334,5	MCF-7	breast:
4	chr3:142606798..142610492-chr3:142610655..142614860,4	K562	blood:
5	chr3:142611367..142612951-chr3:142614638..142616165,2	MCF-7	breast:
6	chr3:142613521..142615754-chr3:142620913..142622791,2	K562	blood:
7	chr3:142612125..142613700-chr3:142616630..142618763,2	K562	blood:
8	chr3:142296468..142299283-chr3:142609997..142611852,2	MCF-7	breast:

Variant related genes	Relation type
PCOLCE2	TF binding region
PCOLCE2	CpG island
ENSG00000163710	chromatin interactions
ENSG00000175054	chromatin interactions

Extended variants
information (count: 176 )
Associated
traits (count: 51 )

Variant overlapped rSNPs/rCNVs (count:176 , 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	rs541318202	chr3:142609232-142609233	Weak transcription Flanking Active TSS Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
2	rs35876180	chr3:142609236-142609237	Weak transcription Flanking Active TSS Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
3	rs199734060	chr3:142609295-142609296	Weak transcription Flanking Active TSS Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
4	rs530395582	chr3:142609296-142609297	Weak transcription Flanking Active TSS Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
5	rs559628823	chr3:142609299-142609300	Weak transcription Flanking Active TSS Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
6	rs397991276	chr3:142609311-142609312	Weak transcription Flanking Active TSS Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
7	rs78223972	chr3:142609318-142609319	Weak transcription Flanking Active TSS Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs189157373	chr3:142609329-142609330	Weak transcription Flanking Active TSS Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs181008129	chr3:142609347-142609348	Weak transcription Flanking Active TSS Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
10	rs538284861	chr3:142609385-142609386	Weak transcription Flanking Active TSS Enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs556129826	chr3:142609389-142609390	Weak transcription Flanking Active TSS Enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs11721314	chr3:142609411-142609412	Weak transcription Flanking Active TSS Enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs186080925	chr3:142609470-142609471	Weak transcription Flanking Active TSS Enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs559775597	chr3:142609487-142609488	Weak transcription Flanking Active TSS Enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs191305063	chr3:142609499-142609500	Weak transcription Flanking Active TSS Enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs566887865	chr3:142609522-142609523	Weak transcription Flanking Active TSS Enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs2707973	chr3:142609536-142609537	Weak transcription Flanking Active TSS Enhancers Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs546866035	chr3:142609543-142609544	Weak transcription Flanking Active TSS Enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs181244836	chr3:142609624-142609625	Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs538846653	chr3:142609655-142609656	Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs373857651	chr3:142609668-142609669	Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs73864499	chr3:142609729-142609730	Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs575774260	chr3:142609731-142609732	Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs139777863	chr3:142609753-142609754	Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs555136725	chr3:142609759-142609760	Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs3755734	chr3:142609767-142609768	Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs186220175	chr3:142609807-142609808	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs144524042	chr3:142609837-142609838	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs552982864	chr3:142609858-142609859	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs4683434	chr3:142609913-142609914	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs369020205	chr3:142610044-142610045	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs571439630	chr3:142610085-142610086	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs528238307	chr3:142610118-142610119	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs546183182	chr3:142610126-142610127	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs544977054	chr3:142610157-142610158	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs563469896	chr3:142610208-142610209	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs114723150	chr3:142610239-142610240	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs190724503	chr3:142610290-142610291	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs558474481	chr3:142610293-142610294	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs532271340	chr3:142610316-142610317	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs146656542	chr3:142610356-142610357	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs528071402	chr3:142610358-142610359	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs139096746	chr3:142610361-142610362	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs149893665	chr3:142610409-142610410	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs532816392	chr3:142610412-142610413	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs551008265	chr3:142610419-142610420	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs569420486	chr3:142610423-142610424	Weak transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs112345129	chr3:142610487-142610488	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs555099576	chr3:142610522-142610523	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs567011673	chr3:142610528-142610529	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:51)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
microdeletion syndrome	22180640	CNVD
Basal cell lymphoma	21115979	CNVD
Ovarian cancer	22174824	CNVD
Colorectal cancer	18645599	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Hepatocellular carcinoma	16750200	CNVD
Lung cancer	16740712	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Blepharophimosis-ptosis-epicanthus inversus syndrome	22067867	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
abnormal development	18461090	CNVD
Cancer	21129771	CNVD
Ovarian cancer	23621864	CNVD
Breast cancer	21364760	CNVD
Congenital anomalies of the kidney and urinary tract	20605837	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142607600-142609600	Active TSS	Osteobl	bone
2	chr3:142608200-142610600	Weak transcription	K562	blood
3	chr3:142608400-142615200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:142608600-142615200	Weak transcription	Hela-S3	cervix
5	chr3:142608600-142615400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:142608600-142617800	Weak transcription	Aorta	Aorta
7	chr3:142608800-142609600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:142609000-142609600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:142609200-142609600	Active TSS	Adipose Nuclei	Adipose
10	chr3:142609200-142609800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:142609600-142613400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:142609600-142616800	Weak transcription	Adipose Nuclei	Adipose
13	chr3:142609800-142610000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:142610000-142610200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:142610000-142615200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:142610400-142610600	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr3:142610600-142611800	Enhancers	K562	blood
18	chr3:142611800-142613400	Weak transcription	K562	blood
19	chr3:142613400-142613600	Enhancers	K562	blood
20	chr3:142613400-142613800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:142613800-142615200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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