Variant report

Variant	esv3409286
Chromosome Location	chr7:39054027-39056825
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:29)
CpG islands
(count:62)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:29 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr7:39056169-39056356	HepG2	liver:	n/a	n/a
2	BHLHE40	chr7:39056365-39056469	K562	blood:	n/a	n/a
3	ELF1	chr7:39056288-39056625	MCF-7	breast:	n/a	n/a
4	FOXA1	chr7:39056185-39056695	T-47D	breast:	n/a	n/a
5	FOXA1	chr7:39056090-39057036	T-47D	breast:	n/a	n/a
6	GATA3	chr7:39056100-39056669	T-47D	breast:	n/a	n/a
7	GATA3	chr7:39056167-39056494	MCF-7	breast:	n/a	n/a
8	GATA3	chr7:39055990-39056769	MCF-7	breast:	n/a	n/a
9	GATA3	chr7:39056017-39056736	MCF-7	breast:	n/a	n/a
10	GATA3	chr7:39056201-39056431	MCF-7	breast:	n/a	n/a
11	GATA3	chr7:39056139-39056658	T-47D	breast:	n/a	n/a
12	HDAC2	chr7:39056201-39056736	MCF-7	breast:	n/a	n/a
13	IRF1	chr7:39054447-39054570	K562	blood:	n/a	chr7:39054483-39054495 chr7:39054469-39054482 chr7:39054468-39054482 chr7:39054483-39054500 chr7:39054483-39054495
14	JUND	chr7:39056264-39056332	K562	blood:	n/a	n/a
15	MAX	chr7:39056138-39056671	MCF-7	breast:	n/a	n/a
16	MYC	chr7:39056343-39056450	MCF-7	breast:	n/a	n/a
17	MYC	chr7:39056264-39056537	MCF-7	breast:	n/a	n/a
18	MYC	chr7:39056284-39056541	MCF-7	breast:	n/a	n/a
19	NR2F2	chr7:39056124-39056658	MCF-7	breast:	n/a	n/a
20	POLR2A	chr7:39056430-39056435	Gliobla	brain:	n/a	n/a
21	POLR2A	chr7:39056397-39056424	A549	lung:	n/a	n/a
22	POLR2A	chr7:39056180-39056393	ProgFib	skin:	n/a	n/a
23	STAT3	chr7:39054373-39054406	MCF10A-Er-Src	breast:	n/a	n/a
24	TCF7L2	chr7:39056149-39056824	MCF-7	breast:	n/a	n/a
25	TEAD4	chr7:39056221-39056674	ECC-1	luminal epithelium:	n/a	n/a
26	TEAD4	chr7:39056205-39056628	ECC-1	luminal epithelium:	n/a	n/a
27	YY1	chr7:39056379-39056551	HCT-116	colon:	n/a	n/a
28	ZNF217	chr7:39056223-39056574	MCF-7	breast:	n/a	n/a
29	ZNF274	chr7:39054907-39056022	K562	blood:	n/a	n/a

(count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:39056400-39056450	HEEpiC	esophagus:	n/a
2	chr7:39056400-39056450	HEEpiC	esophagus:	n/a
3	chr7:39056400-39056450	BJ	skin:	n/a
4	chr7:39056400-39056450	AoSMC	blood vessel:	n/a
5	chr7:39056400-39056450	SK-N-SH_RA	brain:	n/a
6	chr7:39056400-39056450	AG04449	skin:	fetal
7	chr7:39056400-39056450	GM12878	blood:	n/a
8	chr7:39056400-39056450	HCF	heart:	n/a
9	chr7:39056400-39056450	RPTEC	kidney:	n/a
10	chr7:39056400-39056450	BE2_C	brain:	n/a
11	chr7:39056400-39056450	HL-60	blood:	n/a
12	chr7:39056400-39056450	GM12891	blood:	n/a
13	chr7:39056400-39056450	ECC-1	luminal epithelium:	n/a
14	chr7:39056400-39056450	HepG2	liver:	n/a
15	chr7:39056400-39056450	Hepatocyte	liver:	n/a
16	chr7:39056400-39056450	NT2-D1	testis:	n/a
17	chr7:39056400-39056450	Caco-2	colon:	n/a
18	chr7:39056400-39056450	Jurkat	blood:	n/a
19	chr7:39056400-39056450	NB4	blood:	n/a
20	chr7:39056400-39056450	HCT-116	colon:	n/a
21	chr7:39056400-39056450	NHBE	bronchial:	n/a
22	chr7:39056400-39056450	A549	lung:	n/a
23	chr7:39056400-39056450	T-47D	breast:	n/a
24	chr7:39056400-39056450	GM12892	blood:	n/a
25	chr7:39056400-39056450	HCM	heart:	n/a
26	chr7:39056400-39056450	SK-N-SH	brain:	n/a
27	chr7:39056400-39056450	HRE	kidney:	n/a
28	chr7:39056400-39056450	NH-A	brain:	n/a
29	chr7:39056400-39056450	HPAEpiC	pulmonary alveolar:	n/a
30	chr7:39056400-39056450	MCF-7	breast:	n/a
31	chr7:39056400-39056450	HMEC	breast:	n/a
32	chr7:39056400-39056450	K562	blood:	n/a
33	chr7:39056400-39056450	HCPEpiC	choroid plexus:	n/a
34	chr7:39056400-39056450	PFSK-1	brain:	n/a
35	chr7:39056400-39056450	PrEC	prostate:	n/a
36	chr7:39056400-39056450	HUVEC	blood vessel:	n/a
37	chr7:39056400-39056450	MCF10A-Er-Src	breast:	n/a
38	chr7:39056400-39056450	HEK293	kidney:	embryo
39	chr7:39056400-39056450	ProgFib	skin:	n/a
40	chr7:39056400-39056450	NHDF-neo	bronchial:	n/a
41	chr7:39056400-39056450	AG09319	gingival:	n/a
42	chr7:39056400-39056450	HRPEpiC	eye:	n/a
43	chr7:39056400-39056450	AG09309	skin:	n/a
44	chr7:39056400-39056450	GM19239	blood:	n/a
45	chr7:39056400-39056450	CMK	blood:	n/a
46	chr7:39056400-39056450	SK-N-MC	brain:	n/a
47	chr7:39056400-39056450	LNCaP	prostate:	n/a
48	chr7:39056400-39056450	HRCEpiC	kidney:	n/a
49	chr7:39056400-39056450	HNPCEpiC	eye:	n/a
50	chr7:39056400-39056450	IMR90	lung:	fetal

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

No.	Distal block	Cell Line	Cell type
1	chr7:39052158..39055296-chr7:39055387..39058245,4	K562	blood:
2	chr7:39053567..39055132-chr7:39055413..39056943,2	K562	blood:
3	chr7:39053567..39055132-chr7:39055413..39056943,2	K562	blood:
4	chr7:39056516..39058385-chr7:39059051..39061295,2	K562	blood:

No data

Variant related genes	Relation type
POU6F2-AS2	TF binding region
POU6F2-AS2	CpG island
ENSG00000233854	chromatin interactions
ENSG00000106536	chromatin interactions

Extended variants
information (count: 142 )
Associated
traits (count: 82 )

Variant overlapped rSNPs/rCNVs (count:142 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs560445491	chr7:39054090-39054091	Active TSS Enhancers ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs550983681	chr7:39054092-39054093	Active TSS Enhancers ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs181488387	chr7:39054105-39054106	Active TSS Enhancers ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs539426040	chr7:39054155-39054156	Active TSS Enhancers ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs145975840	chr7:39054200-39054201	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
6	rs138504591	chr7:39054202-39054203	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
7	rs548356647	chr7:39054221-39054222	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs200150526	chr7:39054222-39054223	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs189438746	chr7:39054236-39054237	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
10	rs181351326	chr7:39054301-39054302	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
11	rs572967342	chr7:39054316-39054317	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
12	rs1229058	chr7:39054360-39054361	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
13	rs570751894	chr7:39054379-39054380	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs116648223	chr7:39054388-39054389	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs556167327	chr7:39054397-39054398	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs576017379	chr7:39054474-39054475	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs141540275	chr7:39054494-39054495	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs554717323	chr7:39054496-39054497	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs144606730	chr7:39054500-39054501	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs1229057	chr7:39054538-39054539	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
21	rs558810169	chr7:39054598-39054599	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs200273770	chr7:39054677-39054678	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs73381669	chr7:39054693-39054694	Weak transcription Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs73381671	chr7:39054704-39054705	Weak transcription Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs545837503	chr7:39054735-39054736	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
26	rs562903744	chr7:39054759-39054760	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
27	rs10435033	chr7:39054837-39054838	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs548715293	chr7:39054898-39054899	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs201723529	chr7:39054902-39054903	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs199939535	chr7:39054947-39054948	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs202210635	chr7:39054950-39054951	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs71536622	chr7:39054951-39054952	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs200390604	chr7:39054954-39054955	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs111348917	chr7:39054982-39054983	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs527462632	chr7:39054988-39054989	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs77081298	chr7:39055001-39055002	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs570646496	chr7:39055012-39055013	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs72351476	chr7:39055015-39055016	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs539732738	chr7:39055049-39055050	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs555843022	chr7:39055067-39055068	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs10544661	chr7:39055115-39055116	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs200701411	chr7:39055117-39055118	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs12701688	chr7:39055118-39055119	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs569657472	chr7:39055149-39055150	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs367804264	chr7:39055172-39055173	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs375741201	chr7:39055173-39055174	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs12701689	chr7:39055186-39055187	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs181065109	chr7:39055204-39055205	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs28971956	chr7:39055248-39055249	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs372019889	chr7:39055249-39055250	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:82)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Biliary cancer	19435499	CNVD
Cancer	16751803	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Wilms tumour	21544195	CNVD
Glioblastoma multiforme	17387387	CNVD
Astrocytoma	17387387	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	18923191	CNVD
Glioma	21971842	CNVD
Glioblastoma multiforme	21080181	CNVD
Liposarcoma	21253554	CNVD
Oligodendroglial tumors	17285580	CNVD
Oral cancer	21386901	CNVD
colon cancer	17210682	CNVD
Lung adenocarcinoma	21810691	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Colorectal cancer	19359472	CNVD
Hypothalamic hamartomas	18252217	CNVD
Human rectal carcinomas	16397240	CNVD
Peripheral t-cell lymphoma	19118030	CNVD
Medulloblastoma	18056178	CNVD
Basal cell lymphoma	17170743	CNVD
Ewing''s sarcoma	21437220	CNVD
Thyroid cancer	19087340	CNVD
Seminomas	18059402	CNVD
Testicular cancer	18059402	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Autism	19415332	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
T-cell lymphomas	19863542	CNVD
Malaria	21533027	CNVD
Melanoma	18172304	CNVD
Renal cell carcinoma	19461508	CNVD
head and neck squamous cell carcinoma	19289630	CNVD
Stenocardia	21860640	CNVD
Vasospasm	21860640	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Ewing''s sarcoma	17952124	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Lung cancer	18438408	CNVD
lymphocytic leukemia	21291569	CNVD
Autism	22495311	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Cancer	21637783	CNVD
Squamous cell cancer	20885788	CNVD
Breast cancer	16397240	CNVD
Non-small cell lung cancer	21829676	CNVD
Glioblastoma multiforme	17002787	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Glioblastoma multiforme	18628472	CNVD
Cancer	21183584	CNVD
Breast cancer	21785460	CNVD
Follicular lymphoma	20505157	CNVD
Williams-beuren syndrome	22470819	CNVD
Renal cell carcinoma	18765545	CNVD
Breast cancer	21364760	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute myeloid leukemia	21251322	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Multiple myeloma	16461302	CNVD
Glioblastoma multiforme	21750150	CNVD
Hepatocellular carcinoma	16750200	CNVD
Prostate cancer	18632612	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Acute myeloid leukemia	17237825	CNVD
Breast cancer	17899364	CNVD
Breast cancer	20409316	CNVD
Acute monocytic leukemia	16498392	CNVD
Myelofibrosis	22110671	CNVD
Colorectal cancer	21645411	CNVD
Colorectal cancer	19455253	CNVD
Glioblastoma multiforme	22286061	CNVD
T-cell acute lymphoblastic leukemia	19406988	CNVD
Sezary syndrome	18413736	CNVD
Gastric cancer	24379144	CNVD
small cell lung cancer	20016488	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39052600-39054200	Active TSS	H1 Cell Line	embryonic stem cell
2	chr7:39052600-39054400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr7:39052600-39054400	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr7:39052800-39054200	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr7:39052800-39054200	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr7:39052800-39054200	Active TSS	K562	blood
7	chr7:39053000-39054200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr7:39053000-39054200	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr7:39053200-39054600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr7:39053200-39056200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr7:39053400-39056200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr7:39053600-39056400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr7:39053600-39056400	Weak transcription	Placenta	Placenta
14	chr7:39053800-39054200	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr7:39054000-39054600	Enhancers	H9 Cell Line	embryonic stem cell
16	chr7:39054200-39054600	Enhancers	H1 Cell Line	embryonic stem cell
17	chr7:39054200-39054600	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr7:39054200-39054600	Flanking Active TSS	K562	blood
19	chr7:39054200-39056200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr7:39054200-39057000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr7:39054200-39062000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr7:39054400-39056400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr7:39054600-39054800	Active TSS	K562	blood
24	chr7:39054600-39056200	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr7:39054600-39056400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr7:39054600-39056400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr7:39056000-39056200	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr7:39056200-39056400	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr7:39056200-39056600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr7:39056200-39056600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr7:39056200-39056600	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr7:39056200-39056600	Enhancers	Gastric	stomach
33	chr7:39056200-39056800	Enhancers	Fetal Kidney	kidney
34	chr7:39056200-39057000	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr7:39056200-39058000	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr7:39056400-39056600	Enhancers	H9 Cell Line	embryonic stem cell
37	chr7:39056400-39056600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr7:39056400-39056800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr7:39056400-39057200	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr7:39056400-39057400	Enhancers	Placenta	Placenta
41	chr7:39056400-39058000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr7:39056600-39057200	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr7:39056600-39057200	Enhancers	Placenta Amnion	Placenta Amnion
44	chr7:39056800-39057200	Enhancers	iPS-18 Cell Line	embryonic stem cell

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