Variant report

Variant	nsv521257
Chromosome Location	chr7:78632489-78662425
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	BCL3	chr7:78638128-78638397	GM12878	blood:	n/a	n/a
2	CEBPB	chr7:78660536-78660843	HepG2	liver:	n/a	chr7:78660683-78660694
3	CEBPB	chr7:78660521-78660831	IMR90	lung:	n/a	chr7:78660683-78660694
4	CTCF	chr7:78640280-78640430	GM12866	blood:	n/a	n/a
5	CTCF	chr7:78649972-78650045	GM20000	blood:	n/a	n/a
6	CTCF	chr7:78638180-78638330	HCFaa	heart:	n/a	n/a
7	CTCF	chr7:78648577-78648640	GM13977	blood:	n/a	n/a
8	CTCF	chr7:78648285-78648299	GM13977	blood:	n/a	n/a
9	CTCF	chr7:78637940-78638090	AG09309	skin:	n/a	n/a
10	CTCF	chr7:78654494-78654567	Spleen_OC	spleen:	n/a	n/a
11	EP300	chr7:78636667-78636783	K562	blood:	n/a	n/a
12	GATA3	chr7:78660315-78660632	SH-SY5Y	brain:	n/a	chr7:78660339-78660355 chr7:78660343-78660352
13	GATA3	chr7:78654089-78654141	SH-SY5Y	brain:	n/a	n/a
14	GATA3	chr7:78656376-78656533	SH-SY5Y	brain:	n/a	n/a
15	IKZF1	chr7:78654994-78655028	GM12878	blood:	n/a	n/a
16	MAFF	chr7:78658362-78658606	HepG2	liver:	n/a	n/a
17	MAFK	chr7:78638070-78638351	HepG2	liver:	n/a	chr7:78638238-78638253 chr7:78638196-78638210 chr7:78638197-78638208 chr7:78638193-78638208 chr7:78638198-78638209 chr7:78638193-78638209 chr7:78638198-78638209
18	MAFK	chr7:78638750-78638768	H1-hESC	embryonic stem cell:	n/a	n/a
19	MAFK	chr7:78658382-78658629	HepG2	liver:	n/a	chr7:78658532-78658543 chr7:78658531-78658542 chr7:78658532-78658543 chr7:78658531-78658547 chr7:78658530-78658544 chr7:78658532-78658552 chr7:78658531-78658542
20	MAFK	chr7:78638109-78638280	HepG2	liver:	n/a	chr7:78638238-78638253 chr7:78638196-78638210 chr7:78638197-78638208 chr7:78638193-78638208 chr7:78638198-78638209 chr7:78638193-78638209 chr7:78638198-78638209
21	MAZ	chr7:78657044-78657075	HepG2	liver:	n/a	n/a
22	MYC	chr7:78645920-78646000	MCF-7	breast:	n/a	n/a
23	NFYB	chr7:78661094-78661294	GM12878	blood:	n/a	n/a
24	POLR2A	chr7:78638577-78638775	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr7:78645820-78645986	MCF-7	breast:	n/a	n/a
26	POLR2A	chr7:78644785-78644967	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr7:78645857-78646366	MCF-7	breast:	n/a	n/a
28	POLR2A	chr7:78635394-78635422	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr7:78645817-78645818	MCF-7	breast:	n/a	n/a
30	POLR2A	chr7:78656763-78656852	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr7:78650068-78650192	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr7:78650300-78650421	Gliobla	brain:	n/a	n/a
33	POLR2A	chr7:78645879-78645881	A549	lung:	n/a	n/a
34	POLR2A	chr7:78636108-78636308	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr7:78655921-78655961	ProgFib	skin:	n/a	n/a
36	POLR2A	chr7:78641042-78641600	SK-N-MC	brain:	n/a	n/a
37	RCOR1	chr7:78643028-78643118	K562	blood:	n/a	n/a
38	REST	chr7:78650062-78650249	H1-hESC	embryonic stem cell:	n/a	n/a
39	RFX5	chr7:78635572-78635581	K562	blood:	n/a	n/a
40	TCF7L2	chr7:78636403-78636797	HEK293	kidney:	n/a	chr7:78636637-78636653 chr7:78636638-78636652 chr7:78636637-78636653
41	ZNF384	chr7:78656185-78656277	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr7:78659337-78659387	U87	brain:	n/a
2	chr7:78659337-78659387	HepG2	liver:	n/a
3	chr7:78659337-78659387	SK-N-MC	brain:	n/a
4	chr7:78659337-78659387	H1-hESC	embryonic stem cell:	embryo
5	chr7:78659337-78659387	SK-N-SH_RA	brain:	n/a
6	chr7:78659337-78659387	GM12891	blood:	n/a
7	chr7:78659337-78659387	HCT-116	colon:	n/a
8	chr7:78659337-78659387	SKMC	muscle:	n/a
9	chr7:78659337-78659387	AG09319	gingival:	n/a
10	chr7:78659337-78659387	NB4	blood:	n/a
11	chr7:78659337-78659387	Jurkat	blood:	n/a
12	chr7:78659337-78659387	BE2_C	brain:	n/a
13	chr7:78659337-78659387	AG04449	skin:	fetal
14	chr7:78659337-78659387	RPTEC	kidney:	n/a
15	chr7:78659337-78659387	GM12892	blood:	n/a
16	chr7:78659337-78659387	MCF10A-Er-Src	breast:	n/a
17	chr7:78659337-78659387	AoSMC	blood vessel:	n/a
18	chr7:78659337-78659387	NH-A	brain:	n/a
19	chr7:78659337-78659387	CMK	blood:	n/a
20	chr7:78659337-78659387	HCM	heart:	n/a
21	chr7:78659337-78659387	GM12878	blood:	n/a
22	chr7:78659337-78659387	PrEC	prostate:	n/a
23	chr7:78659337-78659387	HCF	heart:	n/a
24	chr7:78659337-78659387	MCF-7	breast:	n/a
25	chr7:78659337-78659387	ovcar-3	ovarian:	n/a
26	chr7:78659337-78659387	NT2-D1	testis:	n/a
27	chr7:78659337-78659387	HL-60	blood:	n/a
28	chr7:78659337-78659387	HNPCEpiC	eye:	n/a
29	chr7:78659337-78659387	AG10803	skin:	n/a
30	chr7:78659337-78659387	GM19239	blood:	n/a
31	chr7:78659337-78659387	K562	blood:	n/a
32	chr7:78659337-78659387	Caco-2	colon:	n/a
33	chr7:78659337-78659387	SAEC	small airway:	n/a
34	chr7:78659337-78659387	HUVEC	blood vessel:	n/a
35	chr7:78659337-78659387	HRE	kidney:	n/a
36	chr7:78659337-78659387	Hepatocyte	liver:	n/a
37	chr7:78659337-78659387	BJ	skin:	n/a
38	chr7:78659337-78659387	HEK293	kidney:	embryo
39	chr7:78659337-78659387	T-47D	breast:	n/a
40	chr7:78659337-78659387	ECC-1	luminal epithelium:	n/a
41	chr7:78659337-78659387	AG04450	lung:	fetal
42	chr7:78659337-78659387	HEEpiC	esophagus:	n/a
43	chr7:78659337-78659387	Hela-S3	cervix:	n/a
44	chr7:78659337-78659387	HPAEpiC	pulmonary alveolar:	n/a
45	chr7:78659337-78659387	NHDF-neo	bronchial:	n/a
46	chr7:78659337-78659387	HRPEpiC	eye:	n/a
47	chr7:78659337-78659387	IMR90	lung:	fetal
48	chr7:78659337-78659387	HMEC	breast:	n/a
49	chr7:78659337-78659387	HRCEpiC	kidney:	n/a
50	chr7:78659337-78659387	HCPEpiC	choroid plexus:	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:78656805..78659401-chr7:78662080..78664588,2	K562	blood:
2	chr7:78654781..78656773-chr7:78658469..78660779,2	K562	blood:
3	chr7:78656805..78659401-chr7:78662080..78664588,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PHTF2-3	chr7:78640243-78640387	ENSG00000226978.1
2	lnc-PHTF2-3	chr7:78641400-78641593	ENSG00000226978.1
3	lnc-PHTF2-3	chr7:78638304-78638440	ENSG00000226978.1

Variant related genes	Relation type
MAGI2-AS2	TF binding region
RNU6-337P	TF binding region
MAGI2-IT1	TF binding region
MAGI2-AS2	CpG island
RNU6-337P	CpG island
MAGI2-IT1	CpG island
ENSG00000212545	chromatin interactions

Extended variants
information (count: 883 )
Associated
traits (count: 92 )

Variant overlapped rSNPs/rCNVs (count:883 , 50 per page) page: 1 2 3 4 5 6 7 ... 18

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs4730599	chr7:78632489-78632490	ZNF genes & repeats Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs539596107	chr7:78632492-78632493	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs370654946	chr7:78632496-78632497	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs546787351	chr7:78632499-78632500	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs566625395	chr7:78632517-78632518	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs535716761	chr7:78632520-78632521	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs555408842	chr7:78632545-78632546	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs550560568	chr7:78632650-78632651	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs185938299	chr7:78632671-78632672	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs537492608	chr7:78632686-78632687	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs557381559	chr7:78632717-78632718	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs374276222	chr7:78632769-78632770	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs570320200	chr7:78632814-78632815	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs11975533	chr7:78632826-78632827	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs140363144	chr7:78632833-78632834	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs190807833	chr7:78632851-78632852	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs574183335	chr7:78632852-78632853	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs183052860	chr7:78632872-78632873	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs145053397	chr7:78632891-78632892	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs541269764	chr7:78632932-78632933	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs186517444	chr7:78632940-78632941	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs191786543	chr7:78632968-78632969	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs112433620	chr7:78632988-78632989	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs2109713	chr7:78633008-78633009	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
25	rs565342832	chr7:78633021-78633022	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs566369772	chr7:78633109-78633110	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs527807444	chr7:78633143-78633144	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs547602023	chr7:78633161-78633162	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs535266528	chr7:78633209-78633210	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs566643715	chr7:78633219-78633220	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs371703499	chr7:78633220-78633221	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs576535394	chr7:78633223-78633224	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs374888858	chr7:78633228-78633229	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs7777825	chr7:78633252-78633253	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs138868297	chr7:78633279-78633280	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs6466468	chr7:78633309-78633310	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs533866125	chr7:78633320-78633321	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs553622873	chr7:78633326-78633327	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs140425061	chr7:78633355-78633356	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs542900016	chr7:78633381-78633382	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs556849160	chr7:78633485-78633486	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs576820124	chr7:78633495-78633496	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs532715637	chr7:78633502-78633503	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs545392091	chr7:78633504-78633505	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs35975123	chr7:78633522-78633523	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs150407241	chr7:78633538-78633539	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs79778580	chr7:78633563-78633564	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs183140817	chr7:78633590-78633591	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs541505267	chr7:78633593-78633594	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs561269531	chr7:78633690-78633691	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:92)

Disease	PMID	Source
Basal cell lymphoma	17170743	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Thyroid cancer	19087340	CNVD
Seminomas	18059402	CNVD
Testicular cancer	18059402	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Autism	19415332	CNVD
Medulloblastoma	21979893	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
Autism	22495311	CNVD
Wilms tumour	21544195	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Biliary cancer	19435499	CNVD
Multiple myeloma	16461302	CNVD
Glioblastoma multiforme	21750150	CNVD
Cancer	21183584	CNVD
Hepatocellular carcinoma	16750200	CNVD
Non-small cell lung cancer	21829676	CNVD
Gastric cancer	24379144	CNVD
Glioblastoma multiforme	17002787	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Lissencephaly	21572526	CNVD
Breast cancer	17603634	CNVD
Liposarcoma	21253554	CNVD
Breast cancer	16397240	CNVD
Acute myeloid leukemia	16864856	CNVD
Squamous cell cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Astrocytoma	17387387	CNVD
Glioblastoma multiforme	17387387	CNVD
Low-grade fibromyxoid sarcoma	0	CNVD
Oligodendroglial tumors	17285580	CNVD
Endometrial cancer	22040021	CNVD
Burkitt''s lymphoma	18698080	CNVD
Breast cancer	21264507	CNVD
Shwachman-Diamond syndrome	22934832	CNVD
Colorectal cancer	19359472	CNVD
Cutaneous malignant melanoma	17690212	CNVD
Leukemia	17361228	CNVD
Breast cancer	16461572	CNVD
Peripheral t-cell lymphoma	19118030	CNVD
Malignant melanoma	17690212	CNVD
Renal cell carcinoma	18592004	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Multiple myeloma	17550852	CNVD
small cell lung cancer	20016488	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Non-syndromic sensorineural hearing loss	21987784	CNVD
Cancer	20164920	CNVD
Prostate cancer	18632612	CNVD
Neurodevelopmental disorder	22521361	CNVD
Williams Syndrome	20824207	CNVD
Metanephric adenoma	20802469	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
abortions and stillbirths	19751515	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	21364760	CNVD
Acute myeloid leukemia	20729466	CNVD
Lung cancer	18438408	CNVD
Pancreatic cancer	17952125	CNVD
Williams-beuren syndrome	16826523	CNVD
Schizophrenia	20838587	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Melanoma	20877625	CNVD
Breast cancer	22522925	CNVD
Olfactory neuroblastoma	18408657	CNVD
Wilms tumour	19318497	CNVD
Multiple myeloma	16616336	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Schizophrenia	17879154	CNVD
Prostate cancer	16573809	CNVD
Prostate cancer	16461572	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Autism	20858243	CNVD
Glioma	20126413	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78624000-78637600	Weak transcription	Brain Substantia Nigra	brain
2	chr7:78632400-78632600	ZNF genes & repeats	Aorta	Aorta
3	chr7:78632600-78648800	Weak transcription	Aorta	Aorta
4	chr7:78635800-78636000	Enhancers	Brain Cingulate Gyrus	brain
5	chr7:78636000-78638000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr7:78637400-78638000	Enhancers	Pancreatic Islets	Pancreatic Islet
7	chr7:78637600-78639000	Enhancers	Brain Hippocampus Middle	brain
8	chr7:78637600-78639200	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr7:78637600-78639200	Enhancers	Brain Substantia Nigra	brain
10	chr7:78637600-78639400	Enhancers	Brain Angular Gyrus	brain
11	chr7:78637800-78638400	Enhancers	Brain Anterior Caudate	brain
12	chr7:78638000-78638400	Enhancers	Brain Cingulate Gyrus	brain
13	chr7:78645400-78645800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr7:78645400-78645800	Enhancers	Brain Cingulate Gyrus	brain
15	chr7:78645600-78646400	ZNF genes & repeats	Pancreas	Pancrea
16	chr7:78645800-78646000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr7:78645800-78646400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr7:78645800-78646600	Enhancers	Lung	lung
19	chr7:78645800-78646800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr7:78646200-78646600	Enhancers	Brain Angular Gyrus	brain
21	chr7:78646800-78650200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr7:78648800-78649200	ZNF genes & repeats	Aorta	Aorta
23	chr7:78650200-78650600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell

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