Variant report

Variant	nsv536728
Chromosome Location	chr3:138854490-138988546
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:102)
LncRNA
region (count:11)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:102 , 50 per page) page: 1 2 3

No.	Distal block	Cell Line	Cell type
1	chr3:138917144..138919365-chr3:138920471..138923779,4	K562	blood:
2	chr3:138660094..138660757-chr3:138920977..138921829,3	MCF-7	breast:
3	chr3:138917144..138919365-chr3:138920471..138923779,4	K562	blood:
4	chr3:138928837..138931530-chr3:138940057..138942404,2	K562	blood:
5	chr3:138847994..138851900-chr3:138852497..138855700,4	K562	blood:
6	chr3:138962108..138964016-chr3:138967080..138968620,2	K562	blood:
7	chr3:138655102..138656710-chr3:138945646..138947395,2	K562	blood:
8	chr3:138963876..138966393-chr3:138976343..138978891,2	MCF-7	breast:
9	chr3:138987122..138989037-chr3:138990550..138993523,2	K562	blood:
10	chr3:138853618..138855657-chr3:138955881..138958627,2	K562	blood:
11	chr3:138956360..138959090-chr3:138963409..138965265,3	K562	blood:
12	chr3:138921447..138922242-chr3:139047879..139048473,2	K562	blood:
13	chr3:138962108..138964016-chr3:138967080..138968620,2	K562	blood:
14	chr3:138954298..138956086-chr3:138966985..138968712,2	K562	blood:
15	chr3:138850568..138852847-chr3:138857740..138859655,2	K562	blood:
16	chr3:138846515..138849332-chr3:138852696..138854714,2	K562	blood:
17	chr3:138878195..138880764-chr3:138882286..138885028,2	K562	blood:
18	chr3:138919443..138921426-chr3:139032883..139034956,2	K562	blood:
19	chr3:138893718..138895445-chr3:138902754..138905101,2	K562	blood:
20	chr3:138972220..138975029-chr3:138977276..138980675,3	MCF-7	breast:
21	chr3:138956947..138959449-chr3:138965975..138968805,2	K562	blood:
22	chr3:138852662..138855349-chr3:139061361..139063361,3	K562	blood:
23	chr3:138847852..138850374-chr3:138879997..138881522,2	K562	blood:
24	chr3:138941568..138947245-chr3:138948597..138953877,8	K562	blood:
25	chr3:138878195..138880764-chr3:138882286..138885028,2	K562	blood:
26	chr3:138853618..138855657-chr3:138955881..138958627,2	K562	blood:
27	chr3:138852662..138855349-chr3:139061361..139062870,2	K562	blood:
28	chr3:138892076..138893039-chr3:139048050..139048806,2	MCF-7	breast:
29	chr3:138956947..138959449-chr3:138965975..138968805,2	K562	blood:
30	chr3:138979371..138982300-chr3:138984390..138987330,2	MCF-7	breast:
31	chr3:138937350..138939627-chr3:138942237..138943921,2	MCF-7	breast:
32	chr3:138966028..138968084-chr3:138972408..138975261,2	K562	blood:
33	chr3:138663277..138665291-chr3:138920079..138922965,2	K562	blood:
34	chr3:138968454..138970679-chr3:138975620..138978024,2	K562	blood:
35	chr3:138893718..138895445-chr3:138902754..138905101,2	K562	blood:
36	chr3:138920879..138921958-chr3:139047535..139048488,5	MCF-7	breast:
37	chr3:138935193..138937011-chr3:138939160..138941395,2	K562	blood:
38	chr3:138978048..138980422-chr3:138985255..138986781,2	K562	blood:
39	chr3:138920304..138922321-chr3:138962433..138964751,2	K562	blood:
40	chr3:138957472..138959168-chr3:139040158..139041899,2	K562	blood:
41	chr3:138943440..138945169-chr3:138946867..138949658,2	MCF-7	breast:
42	chr3:138944830..138948093-chr3:138950393..138952787,3	K562	blood:
43	chr3:138928837..138931530-chr3:138940057..138942404,2	K562	blood:
44	chr3:138975901..138977496-chr3:138977709..138980522,2	K562	blood:
45	chr3:138972220..138975029-chr3:138977276..138980675,3	MCF-7	breast:
46	chr3:138941747..138943879-chr3:138954779..138956623,2	K562	blood:
47	chr3:138961086..138963608-chr3:138965773..138968580,2	K562	blood:
48	chr3:138899218..138902119-chr3:138905837..138907445,2	K562	blood:
49	chr3:138939169..138941125-chr3:138976594..138979201,2	MCF-7	breast:
50	chr3:138830591..138831327-chr3:138920891..138921850,5	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C3orf72-7	chr3:138981594-138982407	ucscGeneNc_uc003ern_2
2	lnc-COPB2-2	chr3:138951834-138952364	NONHSAT092350
3	lnc-C3orf72-7	chr3:138977814-138977936	ucscGeneNc_uc003ern_2
4	lnc-C3orf72-7	chr3:138979325-138979671	l_2483_chr3:138972836-138979311_testes
5	lnc-C3orf72-7	chr3:138972837-138973666	l_2483_chr3:138972836-138979311_testes
6	lnc-C3orf72-7	chr3:138976619-138976882	l_2483_chr3:138972836-138979311_testes
7	lnc-C3orf72-7	chr3:138977814-138977975	l_2483_chr3:138972836-138979311_testes
8	lnc-C3orf72-7	chr3:138976056-138976146	l_2483_chr3:138972836-138979311_testes
9	lnc-C3orf72-7	chr3:138976060-138976146	ucscGeneNc_uc003ern_2
10	lnc-C3orf72-7	chr3:138976808-138976882	ucscGeneNc_uc003ern_2
11	lnc-C3orf72-7	chr3:138978965-138979322	l_2483_chr3:138972836-138979311_testes

No data

Variant related genes	Relation type
ENSG00000175110	chromatin interactions

Extended variants
information (count: 3224 )
Associated
traits (count: 54 )

Variant overlapped rSNPs/rCNVs (count:3224 , 50 per page) page: 1 2 3 4 5 6 7 ... 65

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs566203524	chr3:138854552-138854553	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs57272617	chr3:138854579-138854580	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs112550523	chr3:138854614-138854615	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs185254312	chr3:138854703-138854704	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs7626912	chr3:138854718-138854719	Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs149195069	chr3:138854805-138854806	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs567996707	chr3:138854815-138854816	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs73864950	chr3:138854820-138854821	Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs79275425	chr3:138854821-138854822	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs190349004	chr3:138854833-138854834	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs113911562	chr3:138854875-138854876	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs7627087	chr3:138854883-138854884	Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs182021856	chr3:138854888-138854889	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs13083364	chr3:138854890-138854891	Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs567844621	chr3:138854909-138854910	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs547047958	chr3:138855041-138855042	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs536486961	chr3:138855076-138855077	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs4383549	chr3:138855143-138855144	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs556603335	chr3:138855147-138855148	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs12632107	chr3:138855190-138855191	Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
21	rs12632125	chr3:138855289-138855290	Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs370646426	chr3:138855315-138855316	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs185064726	chr3:138855329-138855330	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs571965944	chr3:138855330-138855331	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs77672943	chr3:138855345-138855346	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs554610758	chr3:138855380-138855381	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs4894384	chr3:138859846-138859847	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs374801565	chr3:138859877-138859878	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs575894839	chr3:138859950-138859951	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs6762801	chr3:138860006-138860007	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs115734145	chr3:138860007-138860008	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs139294180	chr3:138860032-138860033	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs76471269	chr3:138860126-138860127	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs370053206	chr3:138860150-138860151	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs574269664	chr3:138860172-138860173	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs373538820	chr3:138860189-138860190	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs553679482	chr3:138871854-138871855	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs573474454	chr3:138871867-138871868	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs13068617	chr3:138871888-138871889	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs562565810	chr3:138871907-138871908	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs576061407	chr3:138871918-138871919	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs562517227	chr3:138871924-138871925	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs184562579	chr3:138871945-138871946	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs527316507	chr3:138871960-138871961	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs529668122	chr3:138871989-138871990	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs149292197	chr3:138872018-138872019	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs531427595	chr3:138872037-138872038	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs189280409	chr3:138872039-138872040	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs569287985	chr3:138872046-138872047	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs531708349	chr3:138872047-138872048	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:54)

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
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:481 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138849400-138854600	Weak transcription	Pancreas	Pancrea
2	chr3:138853000-138854800	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr3:138853200-138855400	Enhancers	K562	blood
4	chr3:138854600-138855400	Enhancers	Pancreas	Pancrea
5	chr3:138859800-138860000	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr3:138860000-138860200	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr3:138871800-138872200	Enhancers	Brain Hippocampus Middle	brain
8	chr3:138872200-138875600	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:138873400-138876000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:138875400-138876200	Enhancers	K562	blood
11	chr3:138875600-138876000	Enhancers	Left Ventricle	heart
12	chr3:138875600-138876200	Enhancers	Brain Cingulate Gyrus	brain
13	chr3:138875600-138876200	Enhancers	Brain Hippocampus Middle	brain
14	chr3:138875600-138876400	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr3:138875600-138876600	Enhancers	H1 Cell Line	embryonic stem cell
16	chr3:138875800-138876200	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr3:138875800-138876800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:138876000-138876600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:138876000-138876600	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr3:138876200-138876600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:138876200-138876600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:138876400-138876600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:138877800-138878000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:138882200-138882600	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr3:138883800-138884000	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr3:138892000-138892200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:138892000-138892200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:138892000-138892200	Enhancers	Brain Angular Gyrus	brain
29	chr3:138892000-138892200	Enhancers	Brain Anterior Caudate	brain
30	chr3:138892000-138892200	Enhancers	Hela-S3	cervix
31	chr3:138892000-138892400	Enhancers	Brain Hippocampus Middle	brain
32	chr3:138892000-138892400	Enhancers	Ovary	ovary
33	chr3:138892200-138892400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:138892200-138892400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:138892200-138892400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:138892200-138892400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:138892200-138892400	Enhancers	Muscle Satellite Cultured Cells	--
38	chr3:138892200-138892400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:138892200-138892400	Enhancers	Adipose Nuclei	Adipose
40	chr3:138892200-138892400	Flanking Active TSS	Brain Angular Gyrus	brain
41	chr3:138892200-138892400	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr3:138892200-138892400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:138892200-138892400	Enhancers	Fetal Muscle Leg	muscle
44	chr3:138892200-138892400	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr3:138892200-138892400	Enhancers	HSMMtube	muscle
46	chr3:138892200-138892400	Enhancers	NHDF-Ad	bronchial
47	chr3:138892200-138892600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:138892200-138892600	Enhancers	Brain Germinal Matrix	brain
49	chr3:138892200-138892600	Enhancers	Fetal Muscle Trunk	muscle
50	chr3:138892200-138892600	Enhancers	Rectal Smooth Muscle	rectum

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