Variant report

Variant	nsv437886
Chromosome Location	chr3:142610610-142611657
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr3:142611638-142612287	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr3:142611563-142612252	SK-N-SH	brain:	n/a	n/a
3	NFYB	chr3:142611554-142611832	Hela-S3	cervix:	n/a	n/a
4	NFYB	chr3:142611546-142611907	K562	blood:	n/a	n/a
5	PBX3	chr3:142611627-142612074	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr3:142611500-142611640	GM12878	blood:	n/a	n/a
7	POLR2A	chr3:142611650-142611651	GM12878	blood:	n/a	n/a
8	USF1	chr3:142611597-142611891	HCT-116	colon:	n/a	n/a
9	USF1	chr3:142611608-142611853	SK-N-SH_RA	brain:	n/a	n/a
10	USF1	chr3:142611597-142611916	SK-N-SH_RA	brain:	n/a	n/a
11	USF1	chr3:142611654-142611874	H1-hESC	embryonic stem cell:	n/a	n/a
12	USF1	chr3:142611528-142611947	K562	blood:	n/a	n/a
13	USF1	chr3:142611585-142611832	A549	lung:	n/a	n/a
14	USF1	chr3:142611546-142611967	SK-N-SH	brain:	n/a	n/a
15	USF2	chr3:142611638-142611921	Hela-S3	cervix:	n/a	chr3:142611753-142611764

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:142610864-142610914	Hepatocyte	liver:	n/a
2	chr3:142610864-142610914	LNCaP	prostate:	n/a
3	chr3:142610864-142610914	HPAEpiC	pulmonary alveolar:	n/a
4	chr3:142610864-142610914	ovcar-3	ovarian:	n/a
5	chr3:142610864-142610914	HIPEpiC	eye:	n/a
6	chr3:142610864-142610914	HCPEpiC	choroid plexus:	n/a
7	chr3:142610864-142610914	BE2_C	brain:	n/a
8	chr3:142610864-142610914	SKMC	muscle:	n/a
9	chr3:142610864-142610914	K562	blood:	n/a
10	chr3:142610864-142610914	SK-N-SH	brain:	n/a
11	chr3:142610864-142610914	HepG2	liver:	n/a
12	chr3:142610864-142610914	HRCEpiC	kidney:	n/a
13	chr3:142610864-142610914	NH-A	brain:	n/a
14	chr3:142610864-142610914	GM19239	blood:	n/a
15	chr3:142610864-142610914	NT2-D1	testis:	n/a
16	chr3:142610864-142610914	HCT-116	colon:	n/a
17	chr3:142610864-142610914	HRPEpiC	eye:	n/a
18	chr3:142610864-142610914	IMR90	lung:	fetal
19	chr3:142610864-142610914	H1-hESC	embryonic stem cell:	embryo
20	chr3:142610864-142610914	HL-60	blood:	n/a
21	chr3:142610864-142610914	ProgFib	skin:	n/a
22	chr3:142610864-142610914	RPTEC	kidney:	n/a
23	chr3:142610864-142610914	HMEC	breast:	n/a
24	chr3:142610864-142610914	PFSK-1	brain:	n/a
25	chr3:142610864-142610914	HNPCEpiC	eye:	n/a
26	chr3:142610864-142610914	MCF10A-Er-Src	breast:	n/a
27	chr3:142610864-142610914	NHBE	bronchial:	n/a
28	chr3:142610864-142610914	AG04449	skin:	fetal
29	chr3:142610864-142610914	T-47D	breast:	n/a
30	chr3:142610864-142610914	Jurkat	blood:	n/a
31	chr3:142610864-142610914	U87	brain:	n/a
32	chr3:142610864-142610914	Hela-S3	cervix:	n/a
33	chr3:142610864-142610914	HEEpiC	esophagus:	n/a
34	chr3:142610864-142610914	A549	lung:	n/a
35	chr3:142610864-142610914	GM06990	blood:	n/a
36	chr3:142610864-142610914	GM12878	blood:	n/a
37	chr3:142610864-142610914	HUVEC	blood vessel:	n/a
38	chr3:142610864-142610914	SK-N-SH_RA	brain:	n/a
39	chr3:142610864-142610914	AG09309	skin:	n/a
40	chr3:142610864-142610914	HRE	kidney:	n/a
41	chr3:142610864-142610914	Caco-2	colon:	n/a
42	chr3:142610864-142610914	PANC-1	pancreas:	n/a
43	chr3:142610864-142610914	CMK	blood:	n/a
44	chr3:142610864-142610914	ECC-1	luminal epithelium:	n/a
45	chr3:142610864-142610914	AG04450	lung:	fetal
46	chr3:142610864-142610914	HEK293	kidney:	embryo
47	chr3:142610864-142610914	HCM	heart:	n/a
48	chr3:142610864-142610914	NB4	blood:	n/a
49	chr3:142610864-142610914	PrEC	prostate:	n/a
50	chr3:142610864-142610914	AG10803	skin:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:142611367..142612951-chr3:142614638..142616165,2	MCF-7	breast:
2	chr3:142609483..142612071-chr3:142616369..142619084,2	K562	blood:
3	chr3:142606798..142610492-chr3:142610655..142614860,4	K562	blood:
4	chr3:142598080..142600621-chr3:142609257..142610987,2	K562	blood:
5	chr3:142296468..142299283-chr3:142609997..142611852,2	MCF-7	breast:

No data

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

Extended variants
information (count: 53 )
Associated
traits (count: 51 )

Variant overlapped rSNPs/rCNVs (count:53 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs6778966	chr3:142610610-142610611	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs113748740	chr3:142610643-142610644	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs149084292	chr3:142610647-142610648	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs56237202	chr3:142610663-142610664	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs56389497	chr3:142610671-142610672	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs557007014	chr3:142610684-142610685	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs575071355	chr3:142610706-142610707	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs143144756	chr3:142610726-142610727	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs373151539	chr3:142610754-142610755	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs2707974	chr3:142610797-142610798	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs182865641	chr3:142610812-142610813	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs147846969	chr3:142610843-142610844	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs73234726	chr3:142610864-142610865	Weak transcription Enhancers	CpG island Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs187932235	chr3:142610865-142610866	Weak transcription Enhancers	CpG island Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
15	rs191023424	chr3:142610886-142610887	Weak transcription Enhancers	CpG island Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
16	rs551235758	chr3:142610898-142610899	Weak transcription Enhancers	CpG island Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
17	rs73234727	chr3:142610920-142610921	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs530309510	chr3:142610941-142610942	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs116161109	chr3:142610944-142610945	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs141405559	chr3:142610952-142610953	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs534257587	chr3:142611037-142611038	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs182396866	chr3:142611043-142611044	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs570807987	chr3:142611055-142611056	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs558858623	chr3:142611068-142611069	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs117889052	chr3:142611086-142611087	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs147016462	chr3:142611097-142611098	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs575190318	chr3:142611118-142611119	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs536148366	chr3:142611140-142611141	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs554294511	chr3:142611144-142611145	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs111682264	chr3:142611168-142611169	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs572717763	chr3:142611173-142611174	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs540310149	chr3:142611181-142611182	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs577386997	chr3:142611185-142611186	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs564861305	chr3:142611200-142611201	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs576770732	chr3:142611204-142611205	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs543911532	chr3:142611215-142611216	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs562477823	chr3:142611216-142611217	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs11358759	chr3:142611224-142611225	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs75615827	chr3:142611236-142611237	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs63743361	chr3:142611237-142611238	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs72993779	chr3:142611280-142611281	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs548921020	chr3:142611281-142611282	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs75966122	chr3:142611287-142611288	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs527913695	chr3:142611315-142611316	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs192187769	chr3:142611346-142611347	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs544516849	chr3:142611367-142611368	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs570900911	chr3:142611392-142611393	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs55932307	chr3:142611423-142611424	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs549722451	chr3:142611437-142611438	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs533105707	chr3:142611463-142611464	Weak transcription Enhancers	Chromatin interactive region	2 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:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142608400-142615200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:142608600-142615200	Weak transcription	Hela-S3	cervix
3	chr3:142608600-142615400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:142608600-142617800	Weak transcription	Aorta	Aorta
5	chr3:142609600-142613400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:142609600-142616800	Weak transcription	Adipose Nuclei	Adipose
7	chr3:142610000-142615200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:142610600-142611800	Enhancers	K562	blood

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