Variant report

Variant	nsv1005551
Chromosome Location	chr3:120710530-120803826
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	BACH1	chr3:120782469-120782845	H1-hESC	embryonic stem cell:	n/a	n/a
2	BATF	chr3:120789742-120789992	GM12878	blood:	n/a	n/a
3	BHLHE40	chr3:120784878-120785113	GM12878	blood:	n/a	n/a
4	CEBPB	chr3:120730639-120730757	H1-hESC	embryonic stem cell:	n/a	chr3:120730725-120730736
5	CEBPB	chr3:120730574-120730867	MCF-7	breast:	n/a	chr3:120730725-120730736
6	CEBPB	chr3:120730640-120730877	Hela-S3	cervix:	n/a	chr3:120730725-120730736
7	CEBPB	chr3:120730551-120730896	HepG2	liver:	n/a	chr3:120730725-120730736
8	CEBPB	chr3:120730564-120730863	IMR90	lung:	n/a	chr3:120730725-120730736
9	CEBPB	chr3:120730575-120730885	A549	lung:	n/a	chr3:120730725-120730736
10	CEBPB	chr3:120715480-120715578	A549	lung:	n/a	n/a
11	CHD2	chr3:120782613-120782867	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr3:120793416-120793683	K562	blood:	n/a	n/a
13	CTCF	chr3:120795200-120795350	GM12875	blood:	n/a	n/a
14	CTCF	chr3:120790924-120790943	Kidney_OC	kidney:	n/a	n/a
15	CTCF	chr3:120793479-120793705	K562	blood:	n/a	n/a
16	CTCF	chr3:120719930-120719970	Fibrobl	skin:	n/a	n/a
17	CTCF	chr3:120793604-120793664	K562	blood:	n/a	n/a
18	CTCF	chr3:120786947-120786997	ProgFib	skin:	n/a	n/a
19	CTCF	chr3:120746380-120746530	MCF-7	breast:	n/a	n/a
20	CTCF	chr3:120793504-120793689	HepG2	liver:	n/a	n/a
21	CTCF	chr3:120725424-120725515	Spleen_OC	spleen:	n/a	n/a
22	CTCF	chr3:120783010-120783132	Fibrobl	skin:	n/a	n/a
23	E2F4	chr3:120719405-120719526	MCF10A-Er-Src	breast:	n/a	n/a
24	E2F4	chr3:120730506-120730626	MCF10A-Er-Src	breast:	n/a	n/a
25	EGR1	chr3:120782536-120782726	K562	blood:	n/a	n/a
26	ELF1	chr3:120782952-120783326	MCF-7	breast:	n/a	chr3:120783090-120783103
27	ELF1	chr3:120782914-120783196	K562	blood:	n/a	chr3:120783090-120783103
28	EP300	chr3:120790944-120791338	T-47D	breast:	n/a	n/a
29	EP300	chr3:120790886-120791408	T-47D	breast:	n/a	n/a
30	FAM48A	chr3:120785853-120785959	GM12878	blood:	n/a	n/a
31	FAM48A	chr3:120786341-120786425	GM12878	blood:	n/a	n/a
32	FOS	chr3:120783055-120783468	MCF10A-Er-Src	breast:	n/a	n/a
33	FOS	chr3:120783033-120783469	MCF10A-Er-Src	breast:	n/a	n/a
34	FOS	chr3:120783126-120783364	MCF10A-Er-Src	breast:	n/a	n/a
35	FOS	chr3:120783059-120783508	MCF10A-Er-Src	breast:	n/a	n/a
36	FOSL2	chr3:120782995-120783358	HepG2	liver:	n/a	n/a
37	FOSL2	chr3:120783014-120783485	MCF-7	breast:	n/a	n/a
38	FOXA1	chr3:120791013-120791285	T-47D	breast:	n/a	n/a
39	FOXA1	chr3:120790928-120791261	T-47D	breast:	n/a	n/a
40	FOXA1	chr3:120783208-120783577	HepG2	liver:	n/a	n/a
41	FOXA2	chr3:120726412-120726621	HepG2	liver:	n/a	n/a
42	FOXA2	chr3:120782516-120782749	HepG2	liver:	n/a	n/a
43	GATA2	chr3:120798019-120798349	K562	blood:	n/a	n/a
44	GATA2	chr3:120789017-120789320	K562	blood:	n/a	n/a
45	GATA3	chr3:120798107-120798337	T-47D	breast:	n/a	n/a
46	GATA3	chr3:120790975-120791300	T-47D	breast:	n/a	n/a
47	GATA3	chr3:120789038-120789290	T-47D	breast:	n/a	n/a
48	GATA3	chr3:120736073-120736483	MCF-7	breast:	n/a	n/a
49	HEY1	chr3:120796332-120796463	HepG2	liver:	n/a	n/a
50	HEY1	chr3:120796299-120796610	HepG2	liver:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RABL3-5	chr3:120799296-120799541	predAs_chen_BG200968_1

miRNA name	Chromosome Location	mirBase accession
hsa-miR-5682	chr3:120768531-120768552	MIMAT0022470

Variant related genes	Relation type
MIR5682	TF binding region

Extended variants
information (count: 3165 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:3165 , 50 per page) page: 1 2 3 4 5 6 7 ... 64

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs9811686	chr3:120713605-120713606	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs562771237	chr3:120713611-120713612	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs77163407	chr3:120713621-120713622	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs184708088	chr3:120713635-120713636	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs567262483	chr3:120713642-120713643	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs529647500	chr3:120713650-120713651	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs638343	chr3:120713671-120713672	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs376973447	chr3:120713724-120713725	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs533428175	chr3:120713739-120713740	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs146219535	chr3:120713740-120713741	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs566760780	chr3:120713792-120713793	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs538967857	chr3:120713793-120713794	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs73187407	chr3:120713805-120713806	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs545046914	chr3:120713814-120713815	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs368629347	chr3:120713815-120713816	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs140332305	chr3:120713825-120713826	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs141263238	chr3:120713833-120713834	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs112398749	chr3:120713857-120713858	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs555006808	chr3:120713858-120713859	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs574839254	chr3:120713865-120713866	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs2638584	chr3:120713887-120713888	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs540613369	chr3:120713897-120713898	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs577065868	chr3:120713978-120713979	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs191306014	chr3:120714016-120714017	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs571172253	chr3:120714036-120714037	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs184160548	chr3:120714068-120714069	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs151327001	chr3:120714097-120714098	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs35692450	chr3:120714127-120714128	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs189924587	chr3:120714128-120714129	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs545649624	chr3:120714133-120714134	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs113720811	chr3:120714156-120714157	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs181195705	chr3:120714175-120714176	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs559234799	chr3:120714195-120714196	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs542063185	chr3:120714226-120714227	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs370728007	chr3:120714293-120714294	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs572670913	chr3:120714311-120714312	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs9871852	chr3:120714314-120714315	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs6802170	chr3:120714324-120714325	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs185420640	chr3:120714341-120714342	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs532165597	chr3:120714348-120714349	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs368575500	chr3:120714356-120714357	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs552465482	chr3:120714363-120714364	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs569182739	chr3:120714365-120714366	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs185521683	chr3:120718400-120718401	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs189983317	chr3:120718407-120718408	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs538849726	chr3:120718443-120718444	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs559049697	chr3:120718444-120718445	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs577603582	chr3:120718458-120718459	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs372150137	chr3:120718473-120718474	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs547377804	chr3:120718476-120718477	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:57)

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
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	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
head and neck squamous cell carcinoma	17671120	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
microdeletion syndrome	22180640	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
Breast cancer	16608533	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Developmental delay	22180640	CNVD
Multiple myeloma	17550852	CNVD
Basal cell lymphoma	21115979	CNVD
Ovarian cancer	22174824	CNVD
lymphocytic leukemia	21291569	CNVD
small cell lung cancer	20016488	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Autism	22241247	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120713600-120714400	Weak transcription	Ovary	ovary
2	chr3:120718400-120718800	Weak transcription	Ovary	ovary
3	chr3:120719600-120720600	ZNF genes & repeats	Ovary	ovary
4	chr3:120720600-120737800	Weak transcription	Ovary	ovary
5	chr3:120737800-120738200	ZNF genes & repeats	Ovary	ovary
6	chr3:120737800-120738600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:120737800-120738600	Enhancers	HMEC	breast
8	chr3:120738000-120738400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:120738200-120738600	Weak transcription	Ovary	ovary
10	chr3:120746200-120746800	Enhancers	Brain Substantia Nigra	brain
11	chr3:120762800-120767600	Weak transcription	Ovary	ovary
12	chr3:120763200-120768400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:120764200-120767400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
14	chr3:120766000-120767200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:120766600-120767000	ZNF genes & repeats	Brain Anterior Caudate	brain
16	chr3:120766800-120768200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:120767000-120768000	Weak transcription	Brain Anterior Caudate	brain
18	chr3:120767000-120769000	ZNF genes & repeats	Fetal Brain Female	brain
19	chr3:120767200-120768200	Weak transcription	Gastric	stomach
20	chr3:120767400-120769000	Strong transcription	Pancreatic Islets	Pancreatic Islet
21	chr3:120767600-120768200	Weak transcription	Brain Angular Gyrus	brain
22	chr3:120767600-120769000	Strong transcription	Ovary	ovary
23	chr3:120767600-120770200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr3:120768000-120768400	Strong transcription	Brain Anterior Caudate	brain
25	chr3:120768200-120769000	ZNF genes & repeats	Brain Angular Gyrus	brain
26	chr3:120768200-120769000	ZNF genes & repeats	Brain Germinal Matrix	brain
27	chr3:120768200-120769000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:120768200-120769000	ZNF genes & repeats	Gastric	stomach
29	chr3:120768400-120768800	ZNF genes & repeats	Brain Anterior Caudate	brain
30	chr3:120768400-120768800	Strong transcription	Brain Inferior Temporal Lobe	brain
31	chr3:120768600-120769000	ZNF genes & repeats	Pancreas	Pancrea
32	chr3:120768800-120769000	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
33	chr3:120769000-120769200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr3:120769000-120770600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:120769000-120777000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr3:120769000-120791200	Weak transcription	Ovary	ovary
37	chr3:120777000-120777200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
38	chr3:120781400-120782200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:120781600-120790800	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr3:120782200-120782600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:120782200-120783200	Enhancers	H1 Cell Line	embryonic stem cell
42	chr3:120782200-120783200	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr3:120782400-120783000	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr3:120782400-120783000	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr3:120782400-120783200	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr3:120782600-120782800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:120782600-120782800	Enhancers	A549	lung
48	chr3:120782600-120783000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr3:120782600-120783200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr3:120782600-120783200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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