Variant report

Variant	nsv554222
Chromosome Location	chr11:48504596-48616694
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	ARID3A	chr11:48600198-48600306	K562	blood:	n/a	n/a
2	CTCF	chr11:48555681-48555969	MCF-7	breast:	n/a	n/a
3	CTCF	chr11:48555456-48555509	MCF-7	breast:	n/a	n/a
4	CTCF	chr11:48531743-48531775	MCF-7	breast:	n/a	n/a
5	CTCF	chr11:48555880-48556030	MCF-7	breast:	n/a	n/a
6	CTCF	chr11:48559950-48559991	LNCaP	prostate:	n/a	n/a
7	CTCF	chr11:48592671-48592738	GM13976	blood:	n/a	n/a
8	CTCF	chr11:48588680-48588719	LNCaP	prostate:	n/a	n/a
9	CTCF	chr11:48582661-48582724	GM10248	blood:	n/a	n/a
10	CTCF	chr11:48541822-48541922	GM20000	blood:	n/a	n/a
11	CTCF	chr11:48527334-48527432	Lung_OC	lung:	n/a	n/a
12	CTCF	chr11:48517944-48518015	Lung_OC	lung:	n/a	n/a
13	CTCF	chr11:48555740-48555890	MCF-7	breast:	n/a	n/a
14	CTCF	chr11:48541201-48541226	Kidney_OC	kidney:	n/a	n/a
15	CTCF	chr11:48521160-48521251	Fibrobl	skin:	n/a	n/a
16	CTCF	chr11:48569780-48569930	MCF-7	breast:	n/a	n/a
17	CTCF	chr11:48518266-48518294	Fibrobl	skin:	n/a	n/a
18	CTCF	chr11:48518807-48518840	Lung_OC	lung:	n/a	n/a
19	CTCF	chr11:48555446-48555538	MCF-7	breast:	n/a	n/a
20	CTCF	chr11:48555785-48555888	MCF-7	breast:	n/a	n/a
21	CTCF	chr11:48523124-48523262	Pancreas_OC	pancreas:	n/a	n/a
22	E2F4	chr11:48614004-48614186	MCF10A-Er-Src	breast:	n/a	n/a
23	FOS	chr11:48560636-48560920	MCF10A-Er-Src	breast:	n/a	chr11:48560713-48560724 chr11:48560802-48560810
24	FOS	chr11:48558396-48558412	MCF10A-Er-Src	breast:	n/a	n/a
25	FOS	chr11:48591550-48591741	MCF10A-Er-Src	breast:	n/a	chr11:48591633-48591642 chr11:48591632-48591643 chr11:48591634-48591645 chr11:48591633-48591640
26	FOS	chr11:48560582-48561077	MCF10A-Er-Src	breast:	n/a	chr11:48560713-48560724 chr11:48560802-48560810
27	FOS	chr11:48546291-48546631	MCF10A-Er-Src	breast:	n/a	chr11:48546576-48546584 chr11:48546614-48546626 chr11:48546576-48546583
28	FOS	chr11:48591482-48591782	MCF10A-Er-Src	breast:	n/a	chr11:48591633-48591642 chr11:48591632-48591643 chr11:48591634-48591645 chr11:48591633-48591640
29	FOS	chr11:48560655-48560969	MCF10A-Er-Src	breast:	n/a	chr11:48560713-48560724 chr11:48560802-48560810
30	FOS	chr11:48560560-48561029	MCF10A-Er-Src	breast:	n/a	chr11:48560713-48560724 chr11:48560802-48560810
31	FOXA2	chr11:48554965-48555317	A549	lung:	n/a	n/a
32	FOXA2	chr11:48576502-48576828	A549	lung:	n/a	n/a
33	FOXA2	chr11:48568892-48569278	A549	lung:	n/a	n/a
34	JUND	chr11:48591502-48591801	HepG2	liver:	n/a	chr11:48591633-48591642 chr11:48591632-48591643 chr11:48591634-48591645 chr11:48591633-48591640 chr11:48591631-48591642
35	MAFF	chr11:48595050-48595172	HepG2	liver:	n/a	n/a
36	MAFK	chr11:48608635-48608825	IMR90	lung:	n/a	chr11:48608719-48608730
37	MAFK	chr11:48608572-48608830	HepG2	liver:	n/a	chr11:48608719-48608730
38	MAFK	chr11:48595018-48595214	HepG2	liver:	n/a	n/a
39	MAZ	chr11:48611732-48611913	HepG2	liver:	n/a	n/a
40	MYC	chr11:48576765-48576847	GM12878	blood:	n/a	n/a
41	MYC	chr11:48512160-48512276	MCF-7	breast:	n/a	n/a
42	POLR2A	chr11:48606369-48606520	MCF10A-Er-Src	breast:	n/a	n/a
43	POLR2A	chr11:48562712-48562800	MCF10A-Er-Src	breast:	n/a	n/a
44	POLR2A	chr11:48616256-48616323	MCF10A-Er-Src	breast:	n/a	n/a
45	POLR2A	chr11:48512036-48512150	A549	lung:	n/a	n/a
46	POLR2A	chr11:48566175-48566301	MCF10A-Er-Src	breast:	n/a	n/a
47	POLR2A	chr11:48512156-48512296	A549	lung:	n/a	n/a
48	POLR2A	chr11:48559061-48559104	MCF10A-Er-Src	breast:	n/a	n/a
49	POLR2A	chr11:48521179-48521241	A549	lung:	n/a	n/a
50	POLR2A	chr11:48543004-48543009	MCF10A-Er-Src	breast:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:48510647-48510697	HPAEpiC	pulmonary alveolar:	n/a
2	chr11:48509778-48509828	GM19239	blood:	n/a
3	chr11:48509488-48509538	ProgFib	skin:	n/a
4	chr11:48509488-48509538	SK-N-SH	brain:	n/a
5	chr11:48509488-48509538	LNCaP	prostate:	n/a
6	chr11:48509778-48509828	GM12891	blood:	n/a
7	chr11:48509778-48509828	SKMC	muscle:	n/a
8	chr11:48509778-48509828	H1-hESC	embryonic stem cell:	embryo
9	chr11:48510647-48510697	SK-N-SH	brain:	n/a
10	chr11:48510647-48510697	SKMC	muscle:	n/a
11	chr11:48510647-48510697	GM12891	blood:	n/a
12	chr11:48509488-48509538	AoSMC	blood vessel:	n/a
13	chr11:48509778-48509828	SAEC	small airway:	n/a
14	chr11:48509488-48509538	SK-N-SH_RA	brain:	n/a
15	chr11:48510647-48510697	MCF10A-Er-Src	breast:	n/a
16	chr11:48509778-48509828	AG04450	lung:	fetal
17	chr11:48509778-48509828	ECC-1	luminal epithelium:	n/a
18	chr11:48510647-48510697	ECC-1	luminal epithelium:	n/a
19	chr11:48509488-48509538	HCT-116	colon:	n/a
20	chr11:48510647-48510697	BJ	skin:	n/a
21	chr11:48509778-48509828	MCF10A-Er-Src	breast:	n/a
22	chr11:48509488-48509538	AG09309	skin:	n/a
23	chr11:48510647-48510697	IMR90	lung:	fetal
24	chr11:48509778-48509828	AG10803	skin:	n/a
25	chr11:48509488-48509538	CMK	blood:	n/a
26	chr11:48509488-48509538	GM06990	blood:	n/a
27	chr11:48509488-48509538	PFSK-1	brain:	n/a
28	chr11:48509488-48509538	HUVEC	blood vessel:	n/a
29	chr11:48510647-48510697	HRCEpiC	kidney:	n/a
30	chr11:48510647-48510697	SAEC	small airway:	n/a
31	chr11:48509488-48509538	Hepatocyte	liver:	n/a
32	chr11:48510647-48510697	ProgFib	skin:	n/a
33	chr11:48509778-48509828	HCM	heart:	n/a
34	chr11:48510647-48510697	NT2-D1	testis:	n/a
35	chr11:48509488-48509538	IMR90	lung:	fetal
36	chr11:48509488-48509538	HEK293	kidney:	embryo
37	chr11:48510647-48510697	CMK	blood:	n/a
38	chr11:48509488-48509538	AG04449	skin:	fetal
39	chr11:48509778-48509828	K562	blood:	n/a
40	chr11:48509778-48509828	NHBE	bronchial:	n/a
41	chr11:48509778-48509828	IMR90	lung:	fetal
42	chr11:48509778-48509828	GM12878	blood:	n/a
43	chr11:48509778-48509828	GM06990	blood:	n/a
44	chr11:48510647-48510697	HL-60	blood:	n/a
45	chr11:48509778-48509828	HepG2	liver:	n/a
46	chr11:48510647-48510697	HCM	heart:	n/a
47	chr11:48509778-48509828	CMK	blood:	n/a
48	chr11:48509488-48509538	BJ	skin:	n/a
49	chr11:48509488-48509538	HRCEpiC	kidney:	n/a
50	chr11:48510647-48510697	AoSMC	blood vessel:	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OR4C5-1	chr11:48507915-48508377	NONHSAT021297

Variant related genes	Relation type
OR4A47	TF binding region
OR4A41P	TF binding region
OR4A46P	TF binding region
OR4A45P	TF binding region
OR4R1P	TF binding region
OR4A43P	TF binding region
OR4A40P	TF binding region
OR4A48P	TF binding region
OR4A47	CpG island
OR4A41P	CpG island
OR4A46P	CpG island
OR4A45P	CpG island
OR4R1P	CpG island
OR4A43P	CpG island
OR4A40P	CpG island
OR4A48P	CpG island

Extended variants
information (count: 248 )
Associated
traits (count: 64 )

Variant overlapped rSNPs/rCNVs (count:248 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs573165138	chr11:48507969-48507970	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
2	rs538884728	chr11:48507981-48507982	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
3	rs532028336	chr11:48507982-48507983	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
4	rs182597874	chr11:48507995-48507996	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
5	rs187106158	chr11:48508046-48508047	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
6	rs150949989	chr11:48508073-48508074	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
7	rs543988692	chr11:48508088-48508089	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
8	rs192022201	chr11:48508116-48508117	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
9	rs368896113	chr11:48508122-48508123	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
10	rs542289416	chr11:48508143-48508144	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
11	rs546450913	chr11:48508166-48508167	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
12	rs539841979	chr11:48508217-48508218	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
13	rs560455772	chr11:48508240-48508241	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
14	rs532677683	chr11:48508250-48508251	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
15	rs185446737	chr11:48508251-48508252	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
16	rs562954422	chr11:48508264-48508265	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
17	rs531916637	chr11:48508271-48508272	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
18	rs190370956	chr11:48508286-48508287	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
19	rs56236821	chr11:48508287-48508288	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
20	rs563179325	chr11:48508329-48508330	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
21	rs193256459	chr11:48508334-48508335	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
22	rs534226319	chr11:48508346-48508347	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
23	rs146662264	chr11:48508358-48508359	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
24	rs570812374	chr11:48508372-48508373	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
25	rs114739604	chr11:48508373-48508374	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
26	rs370581488	chr11:48509488-48509489	Inactive region	CpG island	3 gene(s)	Overlapped CNVs	n/a
27	rs550139976	chr11:48509489-48509490	Inactive region	CpG island	3 gene(s)	Overlapped CNVs	n/a
28	rs189621104	chr11:48509492-48509493	Inactive region	CpG island	3 gene(s)	Overlapped CNVs	n/a
29	rs12574451	chr11:48509516-48509517	Inactive region	CpG island	3 gene(s)	Overlapped CNVs	n/a
30	rs117721030	chr11:48509778-48509779	Inactive region	CpG island	3 gene(s)	Overlapped CNVs	mRNA abundance
31	rs116165539	chr11:48509779-48509780	Inactive region	CpG island	3 gene(s)	Overlapped CNVs	n/a
32	rs572707661	chr11:48509808-48509809	Inactive region	CpG island	3 gene(s)	Overlapped CNVs	n/a
33	rs201991606	chr11:48510647-48510648	Inactive region	CpG island	2 gene(s)	Overlapped CNVs	n/a
34	rs200185395	chr11:48510648-48510649	Inactive region	CpG island	2 gene(s)	Overlapped CNVs	n/a
35	rs7103557	chr11:48510654-48510655	Inactive region	CpG island	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs369032935	chr11:48510659-48510660	Inactive region	CpG island	2 gene(s)	Overlapped CNVs	n/a
37	rs144972231	chr11:48510663-48510664	Inactive region	CpG island	2 gene(s)	Overlapped CNVs	n/a
38	rs535364101	chr11:48510693-48510694	Inactive region	CpG island	2 gene(s)	Overlapped CNVs	n/a
39	rs532040098	chr11:48510696-48510697	Inactive region	CpG island	2 gene(s)	Overlapped CNVs	n/a
40	rs181848663	chr11:48512057-48512058	Inactive region	TF binding region	2 gene(s)	Overlapped CNVs	n/a
41	rs370397302	chr11:48512118-48512119	Inactive region	TF binding region	2 gene(s)	Overlapped CNVs	n/a
42	rs7108553	chr11:48512125-48512126	Inactive region	TF binding region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs368280719	chr11:48512147-48512148	Inactive region	TF binding region	2 gene(s)	Overlapped CNVs	n/a
44	rs561241986	chr11:48512168-48512169	Inactive region	TF binding region	2 gene(s)	Overlapped CNVs	n/a
45	rs372024458	chr11:48512171-48512172	Inactive region	TF binding region	2 gene(s)	Overlapped CNVs	n/a
46	rs186202997	chr11:48512192-48512193	Inactive region	TF binding region	2 gene(s)	Overlapped CNVs	n/a
47	rs7124853	chr11:48512208-48512209	Inactive region	TF binding region	2 gene(s)	Overlapped CNVs	n/a
48	rs144680071	chr11:48512235-48512236	Inactive region	TF binding region	2 gene(s)	Overlapped CNVs	n/a
49	rs538778609	chr11:48512251-48512252	Inactive region	TF binding region	2 gene(s)	Overlapped CNVs	n/a
50	rs539589777	chr11:48512258-48512259	Inactive region	TF binding region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:64)

Disease	PMID	Source
Parathyroid adenoma	22454399	CNVD
Medulloblastoma	21979893	CNVD
Chordoma	21602918	CNVD
Breast cancer	21949216	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	19222835	CNVD
T-cell acute lymphoblastic leukemia	20065082	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Endometrial cancer	22040021	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Beckwith-Wiedemann syndrome	21518781	CNVD
Wilms tumour	21518781	CNVD
Hepatoblastoma	21518781	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Gastrointestinal stromal cancer	17535989	CNVD
Paraganglioma	17535989	CNVD
Pulmonary chondroma	17535989	CNVD
Wilms tumour	21544195	CNVD
Gastric cancer	17908304	CNVD
Multiple myeloma	20724749	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Autism	22495311	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Non-small cell lung cancer	21385341	CNVD
Intellectual disability	22102821	CNVD
Renal cell carcinoma	18194544	CNVD
Breast cancer	17603634	CNVD
Chordoma	18071362	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Potocki-Shaffer syndrome	19222835	CNVD
WAGR syndrome	19222835	CNVD
Lung cancer	18438408	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Myelofibrosis	22110671	CNVD
Melanoma	18172304	CNVD
Intracranial ependymoma	16609018	CNVD
Myxofibrosarcoma	16751306	CNVD
Potocki-Shaffer syndrome	22470819	CNVD
Neurodevelopmental disorder	22521361	CNVD
Breast cancer	16608533	CNVD
Hirschsprung''s Disease	21712996	CNVD
Follicular lymphoma	20505157	CNVD
Colorectal cancer	21128281	CNVD
Breast cancer	20409316	CNVD
Neurocytoma	17123091	CNVD
Central neurocytomas	17123091	CNVD
Multiple myeloma	16616336	CNVD
Cancer	17160897	CNVD
Mantle cell lymphoma	19029149	CNVD
Glioblastoma multiforme	21138945	CNVD
Breast cancer	21364760	CNVD
Prostate cancer	18632612	CNVD
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	22581003	CNVD
Breast cancer	21990379	CNVD
Acute myeloid leukemia	20729466	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Schizophrenia	20967226	CNVD
small cell lung cancer	20016488	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Glioma	20126413	CNVD
Breast cancer	22522925	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:48515600-48516600	Enhancers	Pancreatic Islets	Pancreatic Islet
2	chr11:48569000-48569600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
3	chr11:48569200-48569600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
4	chr11:48576800-48577000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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