Variant report

Variant	esv3419208
Chromosome Location	chr10:56351995-56372121
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	CTCF	chr10:56354640-56354790	HepG2	liver:	n/a	n/a
2	CTCF	chr10:56365480-56365630	GM12864	blood:	n/a	n/a
3	CTCF	chr10:56358460-56358493	GM10248	blood:	n/a	n/a
4	EBF1	chr10:56367734-56368066	GM12878	blood:	n/a	chr10:56367900-56367913 chr10:56367901-56367912 chr10:56367902-56367911
5	FAM48A	chr10:56365261-56365409	GM12878	blood:	n/a	n/a
6	GATA2	chr10:56365914-56366691	HUVEC	blood vessel:	n/a	n/a
7	GATA3	chr10:56365251-56365446	SH-SY5Y	brain:	n/a	n/a
8	GATA3	chr10:56363804-56364057	SH-SY5Y	brain:	n/a	n/a
9	GATA3	chr10:56366654-56366782	SH-SY5Y	brain:	n/a	n/a
10	GTF2F1	chr10:56367699-56367761	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAFK	chr10:56363067-56363187	HepG2	liver:	n/a	n/a
12	MAX	chr10:56354815-56354919	NB4	blood:	n/a	chr10:56354847-56354857 chr10:56354870-56354880
13	MAZ	chr10:56354795-56354858	HepG2	liver:	n/a	n/a
14	NANOG	chr10:56367842-56368152	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr10:56354733-56354765	A549	lung:	n/a	n/a
16	POLR2A	chr10:56354460-56354517	A549	lung:	n/a	n/a
17	POLR2A	chr10:56354506-56354532	Gliobla	brain:	n/a	n/a
18	POLR2A	chr10:56358300-56358308	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr10:56356096-56356296	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr10:56367505-56367732	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr10:56354418-56354446	Gliobla	brain:	n/a	n/a
22	POLR2A	chr10:56354335-56354349	Gliobla	brain:	n/a	n/a
23	RFX5	chr10:56371239-56371247	K562	blood:	n/a	n/a
24	SETDB1	chr10:56356123-56356795	U2OS	brain:	n/a	n/a
25	SPI1	chr10:56359573-56359874	HL-60	blood:	n/a	n/a
26	STAT3	chr10:56370195-56370470	MCF10A-Er-Src	breast:	n/a	n/a
27	TAF7	chr10:56367422-56367828	H1-hESC	embryonic stem cell:	n/a	n/a
28	TBP	chr10:56367598-56367937	H1-hESC	embryonic stem cell:	n/a	n/a
29	TCF12	chr10:56367788-56368093	H1-hESC	embryonic stem cell:	n/a	n/a
30	TCF12	chr10:56367798-56368054	H1-hESC	embryonic stem cell:	n/a	n/a
31	TCF7L2	chr10:56369218-56369675	HEK293	kidney:	n/a	chr10:56369332-56369342
32	WRNIP1	chr10:56365458-56365710	GM12878	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MTRNR2L5-4	chr10:56365452-56366745	NONHSAT013457
2	lnc-MTRNR2L5-4	chr10:56365452-56366745	ENSG00000234173.1

miRNA name	Chromosome Location	mirBase accession
hsa-miR-548f-5p	chr10:56367686-56367707	MIMAT0026739
hsa-miR-548f-3p	chr10:56367649-56367667	MIMAT0005895

Variant related genes	Relation type
NEFMP1	TF binding region
MIR548F1	TF binding region

Extended variants
information (count: 341 )
Associated
traits (count: 72 )

Variant overlapped rSNPs/rCNVs (count:341 , 50 per page) page: 1 2 3 4 5 6 7

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs367736023	chr10:56354230-56354231	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs150783802	chr10:56354236-56354237	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs139139371	chr10:56354253-56354254	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs547282482	chr10:56354264-56354265	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs540044850	chr10:56354266-56354267	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs558416373	chr10:56354291-56354292	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs538801119	chr10:56354301-56354302	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs112964866	chr10:56354313-56354314	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs575740626	chr10:56354332-56354333	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs529429602	chr10:56354342-56354343	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs538223913	chr10:56354360-56354361	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs554977191	chr10:56354364-56354365	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs1937407	chr10:56354383-56354384	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs115615872	chr10:56354384-56354385	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs560524945	chr10:56354403-56354404	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs145116417	chr10:56354404-56354405	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs545620781	chr10:56354424-56354425	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs117146140	chr10:56354461-56354462	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs142225164	chr10:56354487-56354488	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs182133037	chr10:56354488-56354489	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs372276735	chr10:56354498-56354499	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs144213925	chr10:56354502-56354503	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs185928032	chr10:56354527-56354528	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs541496427	chr10:56354528-56354529	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs559825090	chr10:56354534-56354535	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs547664358	chr10:56354535-56354536	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs116110741	chr10:56354539-56354540	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs539600824	chr10:56354555-56354556	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs552729882	chr10:56354583-56354584	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs532877578	chr10:56354725-56354726	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs569398668	chr10:56354743-56354744	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs190846275	chr10:56354747-56354748	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs555013985	chr10:56354764-56354765	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs11492307	chr10:56354771-56354772	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs12244151	chr10:56354806-56354807	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs147769450	chr10:56354810-56354811	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs35655891	chr10:56354837-56354838	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs12265998	chr10:56354890-56354891	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs570709002	chr10:56356134-56356135	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs539789208	chr10:56356165-56356166	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs556428816	chr10:56356234-56356235	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs2154267	chr10:56356273-56356274	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs535628165	chr10:56356276-56356277	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs183937124	chr10:56356324-56356325	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs140557666	chr10:56356325-56356326	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs150447980	chr10:56356337-56356338	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs187751701	chr10:56356350-56356351	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs557739638	chr10:56356393-56356394	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs12246636	chr10:56356437-56356438	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs192422504	chr10:56356454-56356455	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:72)

Disease	PMID	Source
Pancreatic endocrine tumor	17639061	CNVD
Gastric cancer	17908304	CNVD
Chordoma	21602918	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Medulloblastoma	21979893	CNVD
Melanoma	18172304	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Ewing''s sarcoma	17952124	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Acute lymphoblastic leukemia	20724749	CNVD
Autism	22495311	CNVD
Esophageal cancer	21851588	CNVD
Prostate cancer	18632612	CNVD
Autism	18414403	CNVD
Cockayne syndrome	18421352	CNVD
Glioblastoma	16823260	CNVD
Medulloblastoma	16968546	CNVD
Neuroblastoma	17533364	CNVD
T-cell lymphomas	19863542	CNVD
Testicular germ cell tumor	18059402	CNVD
Squamous cell cancer	21044232	CNVD
Glioma	21971842	CNVD
Cancer	21637783	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Colorectal cancer	20709793	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oligodendroglial tumors	17285580	CNVD
Obesity	21956041	CNVD
Developmental delay	21948486	CNVD
Intellectual disability	21948486	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Lung cancer	18438408	CNVD
Breast cancer	21364760	CNVD
small cell lung cancer	20016488	CNVD
Colorectal cancer	16272173	CNVD
Metanephric adenoma	20802469	CNVD
Autism	20841430	CNVD
Mental retardation	17124404	CNVD
Epilepsy	20923578	CNVD
Prostate cancer	16573809	CNVD
Schizophrenia	19329560	CNVD
Heart failure	18772530	CNVD
Heart failure	18854381	CNVD
Hyperglycemia	19060297	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myelofibrosis	22110671	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Glioblastoma multiforme	22286061	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Usher syndrome	20538994	CNVD
Glioblastoma multiforme	17002787	CNVD
Colorectal cancer	16774939	CNVD
Autism	20858243	CNVD
Breast cancer	22522925	CNVD
Usher type I cohort	17277737	CNVD
Usher type I cohort	21436283	CNVD
Leukemia	21357790	CNVD
Medulloblastoma	22832581	CNVD
Melanoma	17363583	CNVD
Bipolar disorder	19114987	CNVD
Cancer	20164919	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:56354200-56354600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr10:56364600-56367600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr10:56365600-56366800	Enhancers	HUVEC	blood vessel
4	chr10:56366800-56371200	Weak transcription	HUVEC	blood vessel
5	chr10:56367000-56367800	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr10:56367200-56368400	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr10:56367600-56368000	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr10:56367600-56368200	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr10:56367600-56369200	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr10:56368600-56368800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr10:56371200-56372800	Enhancers	HUVEC	blood vessel

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