Variant report

Variant	nsv591856
Chromosome Location	chr3:139000844-139037832
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:64)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:64 , 50 per page) page: 1 2

No.	Distal block	Cell Line	Cell type
1	chr3:138946432..138948702-chr3:139036353..139038366,2	K562	blood:
2	chr3:139006378..139009772-chr3:139015328..139017740,4	K562	blood:
3	chr3:138843769..138846337-chr3:139006537..139008534,2	K562	blood:
4	chr3:138988508..138990235-chr3:139005528..139008514,2	K562	blood:
5	chr3:139033989..139036963-chr3:139038914..139041363,3	K562	blood:
6	chr3:139020760..139022826-chr3:139025503..139028478,3	K562	blood:
7	chr17:59486810..59488861-chr3:139024743..139026838,2	MCF-7	breast:
8	chr3:138661847..138664673-chr3:139014563..139016797,2	K562	blood:
9	chr3:139006585..139008816-chr3:139010719..139013496,3	K562	blood:
10	chr3:139020760..139022826-chr3:139025503..139028478,3	K562	blood:
11	chr3:139025903..139027748-chr3:139030207..139032306,2	MCF-7	breast:
12	chr3:139010032..139013156-chr3:139014475..139018273,5	K562	blood:
13	chr3:139012834..139014774-chr3:139021817..139024693,2	K562	blood:
14	chr3:139021730..139024477-chr3:139029081..139032333,3	K562	blood:
15	chr3:139035215..139036963-chr3:139038914..139040454,2	K562	blood:
16	chr3:139024562..139026768-chr3:139028600..139030441,3	K562	blood:
17	chr3:139007076..139010029-chr3:139046748..139049075,2	K562	blood:
18	chr3:139030696..139032773-chr3:139036962..139038733,2	MCF-7	breast:
19	chr3:138999143..139001318-chr3:139037402..139040316,2	K562	blood:
20	chr3:139029076..139033479-chr3:139037377..139040244,5	K562	blood:
21	chr3:139002749..139004310-chr3:139044203..139046434,2	K562	blood:
22	chr3:139035203..139037991-chr3:139045251..139047764,2	K562	blood:
23	chr3:139017341..139017858-chr3:139048005..139048507,2	MCF-7	breast:
24	chr3:139030696..139032773-chr3:139036962..139038733,2	MCF-7	breast:
25	chr1:17231226..17231822-chr3:139018131..139018817,2	HCT-116	colon:
26	chr3:139030742..139033115-chr3:139035613..139037316,2	K562	blood:
27	chr3:139015934..139019030-chr3:139020317..139024087,4	K562	blood:
28	chr3:139015801..139019925-chr3:139024525..139029594,6	K562	blood:
29	chr3:138993561..138997338-chr3:139000852..139004803,5	K562	blood:
30	chr3:139020846..139021771-chr3:139048220..139048728,2	MCF-7	breast:
31	chr3:139037501..139040197-chr3:139041266..139044238,3	K562	blood:
32	chr3:138999898..139002887-chr3:139003436..139005432,3	K562	blood:
33	chr3:139005012..139006687-chr3:139008062..139010094,3	K562	blood:
34	chr3:139005012..139006687-chr3:139008062..139010094,3	K562	blood:
35	chr3:139021730..139024477-chr3:139029081..139032333,3	K562	blood:
36	chr3:138919443..138921426-chr3:139032883..139034956,2	K562	blood:
37	chr3:139007080..139008631-chr3:139011861..139014744,2	K562	blood:
38	chr3:138991451..138994299-chr3:139017114..139019582,2	MCF-7	breast:
39	chr3:138667185..138669200-chr3:139015942..139017731,2	K562	blood:
40	chr3:138985392..138988178-chr3:139036045..139038689,2	MCF-7	breast:
41	chr3:139018241..139020069-chr3:139035996..139037498,2	K562	blood:
42	chr3:139015758..139018462-chr3:139108556..139110094,2	K562	blood:
43	chr3:139025903..139027748-chr3:139030207..139032306,2	MCF-7	breast:
44	chr3:139036581..139037328-chr8:118743673..118744182,2	MCF-7	breast:
45	chr3:139005216..139007477-chr3:139015482..139017611,2	K562	blood:
46	chr3:139018241..139020069-chr3:139035996..139037498,2	K562	blood:
47	chr3:139030742..139033115-chr3:139035613..139037316,2	K562	blood:
48	chr3:139007080..139008631-chr3:139011861..139014744,2	K562	blood:
49	chr3:139018398..139020047-chr3:139060000..139061761,2	K562	blood:
50	chr3:139006378..139009772-chr3:139015328..139017740,4	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C3orf72-8	chr3:139001373-139001738	NONHSAT092352

No data

Variant related genes	Relation type
ENSG00000184432	chromatin interactions
ENSG00000248932	chromatin interactions
ENSG00000244578	chromatin interactions
ENSG00000272426	chromatin interactions
ENSG00000175110	chromatin interactions

Extended variants
information (count: 1383 )
Associated
traits (count: 53 )

Variant overlapped rSNPs/rCNVs (count:1383 , 50 per page) page: 1 2 3 4 5 6 7 ... 28

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs4894342	chr3:139000844-139000845	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs564332916	chr3:139000851-139000852	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	n/a	n/a	Overlapped CNVs	n/a
3	rs577467585	chr3:139000854-139000855	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	n/a	n/a	Overlapped CNVs	n/a
4	rs189263708	chr3:139000870-139000871	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	n/a	n/a	Overlapped CNVs	n/a
5	rs147411609	chr3:139000884-139000885	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	n/a	n/a	Overlapped CNVs	n/a
6	rs73868564	chr3:139000939-139000940	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs115549075	chr3:139000942-139000943	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs548934844	chr3:139000995-139000996	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs139657574	chr3:139001034-139001035	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
10	rs552497098	chr3:139001035-139001036	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
11	rs570114792	chr3:139001051-139001052	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
12	rs551319276	chr3:139001103-139001104	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
13	rs571268228	chr3:139001135-139001136	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
14	rs538830504	chr3:139001143-139001144	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
15	rs142584321	chr3:139001156-139001157	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
16	rs182005750	chr3:139001169-139001170	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
17	rs113942352	chr3:139001176-139001177	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
18	rs150524818	chr3:139001189-139001190	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
19	rs569292521	chr3:139001190-139001191	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
20	rs537956646	chr3:139001248-139001249	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs557702120	chr3:139001262-139001263	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs528692685	chr3:139001287-139001288	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs577632625	chr3:139001304-139001305	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs534139789	chr3:139001311-139001312	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs189177958	chr3:139001314-139001315	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	n/a	n/a	Overlapped CNVs	n/a
26	rs115983816	chr3:139001325-139001326	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	n/a	n/a	Overlapped CNVs	n/a
27	rs80092729	chr3:139001326-139001327	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	n/a	n/a	Overlapped CNVs	n/a
28	rs548359139	chr3:139001342-139001343	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	n/a	n/a	Overlapped CNVs	n/a
29	rs542801295	chr3:139001377-139001378	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
30	rs562553415	chr3:139001381-139001382	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
31	rs531391129	chr3:139001383-139001384	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
32	rs371917527	chr3:139001396-139001397	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
33	rs565004715	chr3:139001397-139001398	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
34	rs376887080	chr3:139001412-139001413	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
35	rs527254538	chr3:139001421-139001422	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
36	rs547459944	chr3:139001464-139001465	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
37	rs369060836	chr3:139001472-139001473	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
38	rs181116796	chr3:139001482-139001483	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
39	rs115720970	chr3:139001486-139001487	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
40	rs529569980	chr3:139001509-139001510	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
41	rs139475257	chr3:139001547-139001548	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
42	rs73866039	chr3:139001575-139001576	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs76178758	chr3:139001576-139001577	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
44	rs557816515	chr3:139001591-139001592	Weak transcription Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
45	rs79119603	chr3:139001608-139001609	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
46	rs533930003	chr3:139001641-139001642	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
47	rs553790308	chr3:139001677-139001678	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
48	rs186395352	chr3:139001684-139001685	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
49	rs542564692	chr3:139001692-139001693	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
50	rs556298335	chr3:139001734-139001735	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:53)

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	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
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
T-cell prolymphocytic leukemia	17713554	CNVD
Multiple myeloma	17550852	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
Lung cancer	16740712	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
Developmental delay	21147756	CNVD
lymphocytic leukemia	21291569	CNVD
Myelofibrosis	22110671	CNVD
abnormal development	18461090	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:568 , 50 per page) page: 1 2 3 4 5 6 7 ... 12

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138999000-139006800	Weak transcription	Pancreas	Pancrea
2	chr3:138999200-139001800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:138999400-139001000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:138999800-139001000	Enhancers	Osteobl	bone
5	chr3:138999800-139001200	Flanking Active TSS	Brain Cingulate Gyrus	brain
6	chr3:139000000-139001200	Flanking Active TSS	Brain Hippocampus Middle	brain
7	chr3:139000000-139001600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:139000000-139001800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:139000200-139001000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
10	chr3:139000200-139001000	Active TSS	Brain Angular Gyrus	brain
11	chr3:139000400-139001000	Flanking Active TSS	Brain Anterior Caudate	brain
12	chr3:139000400-139001200	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr3:139000400-139001200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:139000400-139001400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr3:139000400-139001400	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr3:139000600-139001000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:139000600-139001000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:139000600-139001000	Bivalent Enhancer	Placenta	Placenta
19	chr3:139000600-139001200	Enhancers	Right Ventricle	heart
20	chr3:139000600-139001200	Flanking Active TSS	HSMM	muscle
21	chr3:139000600-139001400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
22	chr3:139000600-139001600	Enhancers	Left Ventricle	heart
23	chr3:139000600-139003000	Flanking Active TSS	NHDF-Ad	bronchial
24	chr3:139000800-139001000	Active TSS	Brain Substantia Nigra	brain
25	chr3:139000800-139001000	Enhancers	HSMMtube	muscle
26	chr3:139000800-139001200	Enhancers	Ovary	ovary
27	chr3:139000800-139001400	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr3:139000800-139002600	Enhancers	K562	blood
29	chr3:139000800-139004400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:139000800-139011200	Weak transcription	NHLF	lung
31	chr3:139001000-139001200	Enhancers	Muscle Satellite Cultured Cells	--
32	chr3:139001000-139001200	Enhancers	Brain Anterior Caudate	brain
33	chr3:139001000-139001200	Flanking Active TSS	Brain Substantia Nigra	brain
34	chr3:139001000-139001400	Flanking Active TSS	Brain Angular Gyrus	brain
35	chr3:139001000-139001600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:139001200-139001400	Active TSS	HSMM	muscle
37	chr3:139001200-139001800	Enhancers	Brain Substantia Nigra	brain
38	chr3:139001200-139002800	Weak transcription	Ovary	ovary
39	chr3:139001200-139003200	Enhancers	Brain Cingulate Gyrus	brain
40	chr3:139001200-139003200	Enhancers	Brain Hippocampus Middle	brain
41	chr3:139001200-139004600	Weak transcription	Right Ventricle	heart
42	chr3:139001400-139001600	Flanking Active TSS	HSMM	muscle
43	chr3:139001400-139001800	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr3:139001400-139003200	Enhancers	Brain Angular Gyrus	brain
45	chr3:139001600-139002000	Active TSS	HSMM	muscle
46	chr3:139001600-139002800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr3:139001600-139003600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:139001600-139005000	Weak transcription	Left Ventricle	heart
49	chr3:139001800-139002200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:139001800-139002200	Weak transcription	Brain Inferior Temporal Lobe	brain

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