Variant report

Variant	nsv1009573
Chromosome Location	chr3:142896048-142959777
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:72)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:72 , 50 per page) page: 1 2

No.	Distal block	Cell Line	Cell type
1	chr3:142938475..142939430-chr3:142950578..142951319,2	MCF-7	breast:
2	chr3:142951962..142955904-chr3:142971401..142974768,3	K562	blood:
3	chr3:142954351..142956458-chr3:142960764..142964653,3	K562	blood:
4	chr3:142910443..142912503-chr3:142926393..142928620,2	K562	blood:
5	chr3:142949903..142951935-chr3:143002034..143003795,2	K562	blood:
6	chr3:142956744..142958765-chr3:142965944..142967632,2	K562	blood:
7	chr3:142895472..142897996-chr3:143019191..143020977,2	K562	blood:
8	chr3:142947986..142949747-chr3:143028626..143030178,2	K562	blood:
9	chr3:142938667..142941480-chr3:142941937..142946054,4	K562	blood:
10	chr3:142907021..142910266-chr3:142911152..142913564,3	K562	blood:
11	chr3:142940072..142941625-chr3:142954271..142955900,2	K562	blood:
12	chr3:142930578..142932212-chr3:142932647..142934719,2	K562	blood:
13	chr3:142901683..142905677-chr3:142909688..142913196,5	K562	blood:
14	chr3:142883459..142885076-chr3:142902502..142904668,2	K562	blood:
15	chr3:142948047..142951312-chr3:142952653..142957193,4	K562	blood:
16	chr3:142935120..142937637-chr3:142937877..142939570,2	MCF-7	breast:
17	chr3:142945884..142947891-chr3:142949125..142952561,4	K562	blood:
18	chr3:142933374..142937118-chr3:142939813..142945037,5	K562	blood:
19	chr3:142917101..142918800-chr3:142923414..142925582,2	K562	blood:
20	chr3:142929008..142930843-chr3:142953006..142954925,2	K562	blood:
21	chr3:142922192..142925185-chr3:142931380..142934358,2	K562	blood:
22	chr3:142837194..142839590-chr3:142902275..142903779,2	K562	blood:
23	chr3:142899439..142901462-chr3:142905793..142908005,2	K562	blood:
24	chr3:142907861..142909717-chr3:142911559..142913814,2	K562	blood:
25	chr3:142842312..142844525-chr3:142920222..142922927,2	K562	blood:
26	chr3:142900165..142901896-chr3:142950119..142953076,2	K562	blood:
27	chr3:142917669..142921522-chr3:142924910..142927664,3	K562	blood:
28	chr3:142901683..142905677-chr3:142909688..142913196,5	K562	blood:
29	chr3:142918300..142920057-chr3:142921412..142923080,2	K562	blood:
30	chr3:142933374..142937118-chr3:142939813..142945037,5	K562	blood:
31	chr3:142945884..142947891-chr3:142949125..142952561,4	K562	blood:
32	chr3:142922192..142925185-chr3:142931380..142934358,2	K562	blood:
33	chr3:142899439..142901462-chr3:142905793..142908005,2	K562	blood:
34	chr3:142929546..142932145-chr3:142933219..142936261,3	K562	blood:
35	chr3:142918300..142920442-chr3:142921412..142923086,3	K562	blood:
36	chr3:142875650..142878540-chr3:142902217..142903747,2	K562	blood:
37	chr3:142955679..142958275-chr3:142964132..142966713,2	K562	blood:
38	chr3:142889235..142895118-chr3:142897231..142901814,7	K562	blood:
39	chr3:142917101..142918800-chr3:142923414..142925582,2	K562	blood:
40	chr3:142904057..142907019-chr3:142910125..142912001,3	K562	blood:
41	chr3:142925537..142928123-chr3:142932131..142934327,2	K562	blood:
42	chr3:142908825..142914026-chr3:142914356..142919906,7	K562	blood:
43	chr3:142935120..142937637-chr3:142937877..142939570,2	MCF-7	breast:
44	chr3:142938667..142941480-chr3:142941937..142946054,4	K562	blood:
45	chr3:142914308..142916627-chr3:142918947..142921480,2	K562	blood:
46	chr3:142900165..142901896-chr3:142950119..142953076,2	K562	blood:
47	chr3:142904057..142907019-chr3:142910125..142912001,3	K562	blood:
48	chr3:142746681..142748663-chr3:142941428..142944295,2	K562	blood:
49	chr3:142929008..142930843-chr3:142953006..142954925,2	K562	blood:
50	chr3:142921678..142924452-chr3:142925121..142926893,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHST2-10	chr3:142951419-142951544	l_2486_chr3:142951418-142976230_ovary
2	lnc-CHST2-10	chr3:142951611-142951872	l_2486_chr3:142951418-142976230_ovary

No data

Variant related genes	Relation type
ENSG00000211483	chromatin interactions
ENSG00000175040	chromatin interactions

Extended variants
information (count: 2445 )
Associated
traits (count: 55 )

Variant overlapped rSNPs/rCNVs (count:2445 , 50 per page) page: 1 2 3 4 5 6 7 ... 49

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs2352731	chr3:142896048-142896049	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs550866148	chr3:142896057-142896058	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs569157737	chr3:142896068-142896069	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs188478389	chr3:142896084-142896085	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs61733670	chr3:142896107-142896108	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs1661133	chr3:142896131-142896132	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs566563977	chr3:142896151-142896152	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs180856786	chr3:142896177-142896178	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs533273073	chr3:142896187-142896188	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs558144061	chr3:142896255-142896256	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs570083817	chr3:142896271-142896272	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs7614004	chr3:142896275-142896276	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs556476787	chr3:142896285-142896286	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs7646486	chr3:142896286-142896287	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs542457714	chr3:142896319-142896320	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs537537284	chr3:142896347-142896348	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs554027761	chr3:142896397-142896398	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs185929959	chr3:142896404-142896405	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs546286427	chr3:142896444-142896445	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs564494862	chr3:142896504-142896505	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs201573222	chr3:142896506-142896507	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs531774480	chr3:142896570-142896571	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs371708752	chr3:142896581-142896582	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs543829030	chr3:142896623-142896624	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs562846751	chr3:142896648-142896649	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs549239116	chr3:142896650-142896651	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs7626853	chr3:142896688-142896689	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs374843999	chr3:142896702-142896703	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs7649151	chr3:142896703-142896704	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs367824844	chr3:142896704-142896705	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs7616505	chr3:142896705-142896706	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs551877953	chr3:142896732-142896733	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs570200278	chr3:142896754-142896755	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs537490846	chr3:142896755-142896756	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs555739832	chr3:142896757-142896758	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs73866412	chr3:142896758-142896759	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs13079070	chr3:142896784-142896785	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs143016823	chr3:142896804-142896805	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs554360559	chr3:142896835-142896836	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs572519910	chr3:142896863-142896864	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs56235419	chr3:142896865-142896866	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs558323814	chr3:142896939-142896940	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs372337390	chr3:142896960-142896961	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs576608097	chr3:142896998-142896999	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs141928280	chr3:142897016-142897017	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs539008383	chr3:142897037-142897038	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs561892459	chr3:142897041-142897042	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs574690419	chr3:142897042-142897043	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs191207198	chr3:142897067-142897068	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs541447224	chr3:142897134-142897135	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:55)

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
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
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	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
microdeletion syndrome	22180640	CNVD
Basal cell lymphoma	21115979	CNVD
Ovarian cancer	22174824	CNVD
Colorectal cancer	18645599	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Hepatocellular carcinoma	16750200	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Blepharophimosis-ptosis-epicanthus inversus syndrome	22067867	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
abnormal development	18461090	CNVD
Cancer	21129771	CNVD
Ovarian cancer	23621864	CNVD
Breast cancer	21364760	CNVD
Mental retardation	17847001	CNVD
Basal cell lymphoma	17170743	CNVD
Congenital anomalies of the kidney and urinary tract	20605837	CNVD
Cancer	20164919	CNVD
Gastric cancer	22014070	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:610 , 50 per page) page: 1 2 3 4 5 6 7 ... 13

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142891600-142897000	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr3:142892000-142898400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr3:142893200-142909200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr3:142894200-142900200	Weak transcription	GM12878-XiMat	blood
5	chr3:142894400-142897800	Weak transcription	Fetal Lung	lung
6	chr3:142894400-142898400	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr3:142894400-142898400	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr3:142894400-142898400	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr3:142894400-142899600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:142894400-142900800	Weak transcription	K562	blood
11	chr3:142894800-142896200	Weak transcription	Dnd41	blood
12	chr3:142894800-142898200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr3:142894800-142898400	Weak transcription	Primary T cells from cord blood	blood
14	chr3:142896200-142896800	Enhancers	Dnd41	blood
15	chr3:142896800-142898200	Weak transcription	Dnd41	blood
16	chr3:142896800-142898800	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr3:142897000-142898800	Enhancers	Monocytes-CD14+_RO01746	blood
18	chr3:142897800-142898800	Enhancers	Fetal Lung	lung
19	chr3:142898200-142898800	Enhancers	Dnd41	blood
20	chr3:142898200-142899000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr3:142898400-142898600	Enhancers	Primary T cells from cord blood	blood
22	chr3:142898400-142898600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr3:142898400-142898600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:142898400-142898800	Enhancers	Primary T cells fromperipheralblood	blood
25	chr3:142898400-142898800	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr3:142898400-142898800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:142898400-142899000	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr3:142898400-142899000	Enhancers	Fetal Thymus	thymus
29	chr3:142898600-142901600	Weak transcription	Primary T cells from cord blood	blood
30	chr3:142898800-142900000	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr3:142898800-142900600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:142898800-142901200	Weak transcription	Dnd41	blood
33	chr3:142898800-142901800	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr3:142898800-142902200	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr3:142899000-142901600	Weak transcription	Fetal Thymus	thymus
36	chr3:142899000-142902200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr3:142899000-142902400	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr3:142899400-142902000	Enhancers	Primary B cells from peripheral blood	blood
39	chr3:142899600-142900000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr3:142900000-142901600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:142900000-142902000	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr3:142900200-142901000	ZNF genes & repeats	GM12878-XiMat	blood
43	chr3:142900200-142903400	Enhancers	Primary hematopoietic stem cells	blood
44	chr3:142900400-142901800	Enhancers	Primary B cells from cord blood	blood
45	chr3:142900400-142902200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr3:142900600-142901800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:142900800-142902000	Enhancers	K562	blood
48	chr3:142900800-142903000	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr3:142901000-142901600	Weak transcription	GM12878-XiMat	blood
50	chr3:142901200-142902600	Enhancers	Dnd41	blood

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