Variant report

Variant	nsv1009097
Chromosome Location	chr3:19539647-19787978
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:12)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:2)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:19679630..19681949-chr3:19683459..19685004,2	K562	blood:
2	chr3:16317176..16319617-chr3:19576040..19578450,2	MCF-7	breast:
3	chr3:19390113..19391205-chr3:19584358..19585952,11	MCF-7	breast:
4	chr1:62901559..62902065-chr3:19594424..19594924,2	Hela-S3	cervix:
5	chr3:19745768..19748356-chr3:19750935..19754447,3	K562	blood:
6	chr3:19106420..19107155-chr3:19584445..19585029,2	MCF-7	breast:
7	chr3:19679630..19681949-chr3:19683459..19685004,2	K562	blood:
8	chr3:19747542..19750159-chr3:19752091..19755330,3	MCF-7	breast:
9	chr3:19745768..19748356-chr3:19750935..19754447,3	K562	blood:
10	chr3:19525585..19527422-chr3:19576707..19579689,2	MCF-7	breast:
11	chr3:19390558..19391094-chr3:19584541..19585367,2	MCF-7	breast:
12	chr3:19747542..19750159-chr3:19752091..19755330,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EFHB-1	chr3:19729726-19729972	XLOC_003064
2	lnc-EFHB-1	chr3:19717560-19717598	XLOC_003064

No data

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

No.	miRNA target gene	miRNA name	Chromosome Location	mirBase accession
1	KCNH8	hsa-miR-143-3p	chr3:19576066-19576072
2	KCNH8	hsa-miR-143-3p	chr3:19576050-19576073

Variant related genes	Relation type
ENSG00000162607	chromatin interactions
ENSG00000270739	chromatin interactions
ESYT1	miRNA target sites

Extended variants
information (count: 4550 )
Associated
traits (count: 75 )

Variant overlapped rSNPs/rCNVs (count:4550 , 50 per page) page: 1 2 3 4 5 6 7 ... 91

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs182761976	chr3:19539666-19539667	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
2	rs556912738	chr3:19539673-19539674	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
3	rs141821213	chr3:19539682-19539683	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
4	rs546141433	chr3:19539685-19539686	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
5	rs75248961	chr3:19539704-19539705	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
6	rs543127367	chr3:19539705-19539706	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
7	rs528508130	chr3:19539714-19539715	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
8	rs540310928	chr3:19539715-19539716	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
9	rs570044343	chr3:19539717-19539718	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
10	rs531570082	chr3:19539720-19539721	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
11	rs529394054	chr3:19539737-19539738	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
12	rs551036300	chr3:19539749-19539750	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
13	rs569120699	chr3:19539755-19539756	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
14	rs533321026	chr3:19539760-19539761	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
15	rs188228893	chr3:19539773-19539774	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
16	rs550131377	chr3:19539775-19539776	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
17	rs566782515	chr3:19539786-19539787	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
18	rs557051364	chr3:19539798-19539799	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
19	rs534497059	chr3:19539824-19539825	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
20	rs576423002	chr3:19539861-19539862	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
21	rs77315845	chr3:19539862-19539863	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
22	rs538979122	chr3:19539864-19539865	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
23	rs545442454	chr3:19539865-19539866	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
24	rs375876756	chr3:19539877-19539878	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
25	rs80146706	chr3:19539881-19539882	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
26	rs191719379	chr3:19539898-19539899	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
27	rs528330691	chr3:19539916-19539917	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
28	rs145470222	chr3:19539917-19539918	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
29	rs575516691	chr3:19539930-19539931	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
30	rs539606256	chr3:19539939-19539940	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
31	rs570028675	chr3:19539952-19539953	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
32	rs138013610	chr3:19539953-19539954	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
33	rs9860607	chr3:19539956-19539957	ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs561972729	chr3:19540005-19540006	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
35	rs184187705	chr3:19540023-19540024	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
36	rs544398083	chr3:19540028-19540029	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
37	rs562595347	chr3:19540045-19540046	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
38	rs149495824	chr3:19540048-19540049	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
39	rs535160885	chr3:19540076-19540077	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
40	rs551265577	chr3:19540087-19540088	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
41	rs560309917	chr3:19540091-19540092	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
42	rs528011134	chr3:19540123-19540124	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
43	rs549619796	chr3:19540137-19540138	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
44	rs143946198	chr3:19540140-19540141	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
45	rs570971026	chr3:19540152-19540153	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
46	rs550707190	chr3:19540187-19540188	ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
47	rs148620562	chr3:19540238-19540239	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs539538205	chr3:19540244-19540245	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs202224122	chr3:19540257-19540258	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs187461454	chr3:19540262-19540263	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:75)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	17327916	CNVD
Glioblastoma multiforme	21080181	CNVD
Neuroblastoma	18923191	CNVD
Colorectal cancer	21297112	CNVD
Lynch syndrome	18415027	CNVD
Renal cell carcinoma	18592004	CNVD
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
lymphocytic leukemia	21291569	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Esophageal cancer	20955586	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Myelofibrosis	22110671	CNVD
Gastric adenocarcinoma	19115996	CNVD
Squamous cell cancer	20885788	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Breast cancer	17133270	CNVD
Developmental delay	21147756	CNVD
Uveal melanoma	20484589	CNVD
Autism	20531469	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:308 , 50 per page) page: 1 2 3 4 5 6 7

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19538800-19540000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:19539000-19540200	ZNF genes & repeats	Primary B cells from cord blood	blood
3	chr3:19540200-19557200	Weak transcription	Primary B cells from cord blood	blood
4	chr3:19542200-19552800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:19547600-19548600	Enhancers	Primary B cells from peripheral blood	blood
6	chr3:19547600-19548600	Enhancers	GM12878-XiMat	blood
7	chr3:19548000-19549200	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr3:19548200-19549200	Enhancers	Brain Hippocampus Middle	brain
9	chr3:19548200-19549400	Enhancers	Brain Substantia Nigra	brain
10	chr3:19548400-19549200	Enhancers	Brain Cingulate Gyrus	brain
11	chr3:19548600-19550800	Weak transcription	Fetal Brain Male	brain
12	chr3:19548600-19551200	Weak transcription	Primary B cells from peripheral blood	blood
13	chr3:19549200-19555800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:19549400-19552000	Weak transcription	Brain Substantia Nigra	brain
15	chr3:19550000-19557600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr3:19550200-19550400	Enhancers	Brain Germinal Matrix	brain
17	chr3:19550400-19566200	Weak transcription	Brain Germinal Matrix	brain
18	chr3:19551000-19551200	Enhancers	Fetal Brain Male	brain
19	chr3:19551200-19551800	Enhancers	Primary B cells from peripheral blood	blood
20	chr3:19551600-19551800	Enhancers	Gastric	stomach
21	chr3:19551800-19559200	Weak transcription	Primary B cells from peripheral blood	blood
22	chr3:19552000-19552600	Enhancers	Brain Substantia Nigra	brain
23	chr3:19552800-19564200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:19553200-19565200	Weak transcription	Pancreas	Pancrea
25	chr3:19553600-19567400	Weak transcription	Fetal Brain Female	brain
26	chr3:19554400-19555200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:19555200-19557600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:19557200-19557600	Strong transcription	Primary B cells from cord blood	blood
29	chr3:19557600-19558800	Weak transcription	Primary B cells from cord blood	blood
30	chr3:19557600-19561200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:19557600-19561200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:19558800-19559000	Enhancers	Primary B cells from cord blood	blood
33	chr3:19559000-19559400	Weak transcription	Primary B cells from cord blood	blood
34	chr3:19559200-19561200	Enhancers	Primary B cells from peripheral blood	blood
35	chr3:19559400-19561400	Enhancers	Primary B cells from cord blood	blood
36	chr3:19560400-19560800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:19560400-19560800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr3:19561200-19561800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:19561200-19564000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr3:19561200-19572600	Weak transcription	Primary B cells from peripheral blood	blood
41	chr3:19561400-19571000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr3:19561400-19572800	Weak transcription	Primary B cells from cord blood	blood
43	chr3:19561800-19562800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr3:19562800-19563800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:19563800-19564000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:19564000-19564200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
47	chr3:19564000-19566200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:19564200-19567400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr3:19564200-19569200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:19566200-19566600	Enhancers	Brain Germinal Matrix	brain

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