Variant report

Variant	esv1829505
Chromosome Location	chr3:19554497-19754793
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	chr3:19106420..19107155-chr3:19584445..19585029,2	MCF-7	breast:
2	chr3:19745768..19748356-chr3:19750935..19754447,3	K562	blood:
3	chr3:19747542..19750159-chr3:19752091..19755330,3	MCF-7	breast:
4	chr3:19679630..19681949-chr3:19683459..19685004,2	K562	blood:
5	chr3:19679630..19681949-chr3:19683459..19685004,2	K562	blood:
6	chr3:19747542..19750159-chr3:19752091..19755330,3	MCF-7	breast:
7	chr3:16317176..16319617-chr3:19576040..19578450,2	MCF-7	breast:
8	chr3:19745768..19748356-chr3:19750935..19754447,3	K562	blood:
9	chr3:19390558..19391094-chr3:19584541..19585367,2	MCF-7	breast:
10	chr1:62901559..62902065-chr3:19594424..19594924,2	Hela-S3	cervix:
11	chr3:19390113..19391205-chr3:19584358..19585952,11	MCF-7	breast:
12	chr3:19525585..19527422-chr3:19576707..19579689,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EFHB-1	chr3:19717560-19717598	XLOC_003064
2	lnc-EFHB-1	chr3:19729726-19729972	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: 3360 )
Associated
traits (count: 73 )

Variant overlapped rSNPs/rCNVs (count:3360 , 50 per page) page: 1 2 3 4 5 6 7 ... 68

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs138374380	chr3:19554508-19554509	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs200207926	chr3:19554510-19554511	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs373577840	chr3:19554519-19554520	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs377578191	chr3:19554547-19554548	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs536734321	chr3:19554574-19554575	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs558659525	chr3:19554585-19554586	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs141540785	chr3:19554587-19554588	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs115216381	chr3:19554593-19554594	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs138619397	chr3:19554594-19554595	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs147438113	chr3:19554656-19554657	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs141916436	chr3:19554662-19554663	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs368682045	chr3:19554677-19554678	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs150550466	chr3:19554685-19554686	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs116701468	chr3:19554686-19554687	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs373240665	chr3:19554688-19554689	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs542257136	chr3:19554695-19554696	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs376325121	chr3:19554783-19554784	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs143570675	chr3:19554790-19554791	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs371843151	chr3:19554827-19554828	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs575707377	chr3:19554828-19554829	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs572710637	chr3:19554847-19554848	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs114214436	chr3:19554848-19554849	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs574462335	chr3:19554862-19554863	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs534739192	chr3:19554863-19554864	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs369579873	chr3:19554866-19554867	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs374707531	chr3:19554867-19554868	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs377303001	chr3:19554868-19554869	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs528622143	chr3:19554875-19554876	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs113132967	chr3:19554959-19554960	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs562088212	chr3:19555177-19555178	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs529536219	chr3:19555192-19555193	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs548200369	chr3:19555236-19555237	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs191607715	chr3:19555245-19555246	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs6549944	chr3:19555271-19555272	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs182890218	chr3:19555280-19555281	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs570672054	chr3:19555305-19555306	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs534855938	chr3:19555379-19555380	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs139710080	chr3:19555397-19555398	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs186112432	chr3:19555454-19555455	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs377204904	chr3:19555455-19555456	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs535352148	chr3:19555468-19555469	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs144416545	chr3:19555495-19555496	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs371596315	chr3:19555496-19555497	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs190922500	chr3:19555497-19555498	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs563704475	chr3:19555539-19555540	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs183448589	chr3:19555584-19555585	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs539931632	chr3:19555598-19555599	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs557867971	chr3:19555641-19555642	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs572995109	chr3:19555682-19555683	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs540452286	chr3:19555709-19555710	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:73)

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
Acute lymphoblastic leukemia	22237106	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:229 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19540200-19557200	Weak transcription	Primary B cells from cord blood	blood
2	chr3:19549200-19555800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr3:19550000-19557600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr3:19550400-19566200	Weak transcription	Brain Germinal Matrix	brain
5	chr3:19551800-19559200	Weak transcription	Primary B cells from peripheral blood	blood
6	chr3:19552800-19564200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:19553200-19565200	Weak transcription	Pancreas	Pancrea
8	chr3:19553600-19567400	Weak transcription	Fetal Brain Female	brain
9	chr3:19554400-19555200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:19555200-19557600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:19557200-19557600	Strong transcription	Primary B cells from cord blood	blood
12	chr3:19557600-19558800	Weak transcription	Primary B cells from cord blood	blood
13	chr3:19557600-19561200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:19557600-19561200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:19558800-19559000	Enhancers	Primary B cells from cord blood	blood
16	chr3:19559000-19559400	Weak transcription	Primary B cells from cord blood	blood
17	chr3:19559200-19561200	Enhancers	Primary B cells from peripheral blood	blood
18	chr3:19559400-19561400	Enhancers	Primary B cells from cord blood	blood
19	chr3:19560400-19560800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr3:19560400-19560800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:19561200-19561800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:19561200-19564000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:19561200-19572600	Weak transcription	Primary B cells from peripheral blood	blood
24	chr3:19561400-19571000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr3:19561400-19572800	Weak transcription	Primary B cells from cord blood	blood
26	chr3:19561800-19562800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:19562800-19563800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:19563800-19564000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:19564000-19564200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
30	chr3:19564000-19566200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:19564200-19567400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:19564200-19569200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:19566200-19566600	Enhancers	Brain Germinal Matrix	brain
34	chr3:19566200-19566800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:19566600-19577000	Weak transcription	Brain Germinal Matrix	brain
36	chr3:19566800-19567200	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:19567200-19570000	Enhancers	Fetal Brain Male	brain
38	chr3:19567200-19571000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:19567400-19569000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr3:19567400-19569800	Enhancers	Fetal Brain Female	brain
41	chr3:19569000-19571200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:19569200-19571200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:19571000-19571200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr3:19571000-19571800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:19571200-19575000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr3:19571800-19575000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:19572600-19576200	Enhancers	Primary B cells from peripheral blood	blood
48	chr3:19572800-19576800	Enhancers	Primary B cells from cord blood	blood
49	chr3:19575000-19575600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:19575000-19578600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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