Variant report

Variant	esv1799921
Chromosome Location	chr3:47259253-47283105
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:14)
LncRNA
region (count:19)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:47266423..47269047-chr3:47271285..47273402,2	K562	blood:
2	chr3:47266423..47269047-chr3:47271285..47273402,2	K562	blood:
3	chr3:47276538..47278116-chr3:47285524..47288270,2	K562	blood:
4	chr3:47276902..47279384-chr3:47323090..47325567,2	K562	blood:
5	chr3:47254260..47256683-chr3:47261651..47264367,2	MCF-7	breast:
6	chr3:47276373..47278773-chr3:47281395..47283848,2	K562	blood:
7	chr3:47261367..47263490-chr3:47277485..47279613,2	K562	blood:
8	chr3:47276373..47278773-chr3:47281395..47283848,2	K562	blood:
9	chr3:47206330..47207935-chr3:47269635..47272422,2	K562	blood:
10	chr3:47280979..47281768-chr3:188326015..188326796,2	MCF-7	breast:
11	chr3:47279696..47282501-chr3:47283361..47286390,3	K562	blood:
12	chr3:47261367..47263490-chr3:47277485..47279613,2	K562	blood:
13	chr3:47256140..47258456-chr3:47263578..47266012,2	K562	blood:
14	chr3:47256438..47258456-chr3:47263578..47265840,2	K562	blood:

(count:19 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLHL18-1	chr3:47279894-47280059	ENSG00000227398
2	lnc-KLHL18-1	chr3:47273257-47273353	ENSG00000227398
3	lnc-KLHL18-1	chr3:47280950-47281684	NONHSAT089488
4	lnc-KLHL18-1	chr3:47279894-47280059	ENSG00000227398.3
5	lnc-KLHL18-1	chr3:47281105-47281684	NONHSAT089479
6	lnc-KLHL18-1	chr3:47281105-47281684	ENSG00000227398
7	lnc-NBEAL2-2	chr3:47259473-47260609	refGeneNc_4033_NR_033373
8	lnc-KLHL18-1	chr3:47281105-47281684	NONHSAT089478
9	lnc-KLHL18-1	chr3:47279894-47280059	NONHSAT089478
10	lnc-KLHL18-1	chr3:47277547-47277649	ENSG00000227398.3
11	lnc-KLHL18-1	chr3:47277544-47277649	NONHSAT089479
12	lnc-KLHL18-1	chr3:47273257-47273348	NONHSAT089479
13	lnc-KLHL18-1	chr3:47273257-47273353	ENSG00000227398.3
14	lnc-KLHL18-1	chr3:47277547-47277649	NONHSAT089478
15	lnc-KLHL18-4	chr3:47263633-47264866	NONHSAT089485
16	lnc-KLHL18-1	chr3:47277547-47277649	ENSG00000227398
17	lnc-KLHL18-1	chr3:47279894-47280059	NONHSAT089479
18	lnc-KLHL18-1	chr3:47273257-47273353	NONHSAT089478
19	lnc-KLHL18-1	chr3:47281105-47281684	ENSG00000227398.3

No data

Variant related genes	Relation type
ENSG00000114648	chromatin interactions
ENSG00000088727	chromatin interactions
BTRC	miRNA target sites
C4orf43	miRNA target sites
BMPR2	miRNA target sites
NUP205	miRNA target sites

Extended variants
information (count: 820 )
Associated
traits (count: 101 )

Variant overlapped rSNPs/rCNVs (count:820 , 50 per page) page: 1 2 3 4 5 6 7 ... 17

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs181945724	chr3:47259258-47259259	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs34183712	chr3:47259383-47259384	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs570680178	chr3:47259428-47259429	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs534794477	chr3:47259432-47259433	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs542091183	chr3:47259441-47259442	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs553023808	chr3:47259447-47259448	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs11925560	chr3:47259460-47259461	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
8	rs544990178	chr3:47259529-47259530	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
9	rs535148415	chr3:47259584-47259585	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
10	rs199557659	chr3:47259592-47259593	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
11	rs78467588	chr3:47259616-47259617	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
12	rs556540090	chr3:47259628-47259629	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
13	rs574862102	chr3:47259635-47259636	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
14	rs539171068	chr3:47259703-47259704	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
15	rs141069458	chr3:47259743-47259744	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
16	rs200418837	chr3:47259744-47259745	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
17	rs573137596	chr3:47259804-47259805	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
18	rs12488371	chr3:47259922-47259923	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs6767868	chr3:47259945-47259946	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs112311244	chr3:47259957-47259958	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
21	rs185701962	chr3:47260128-47260129	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
22	rs6808117	chr3:47260190-47260191	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs78848076	chr3:47260194-47260195	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
24	rs189882098	chr3:47260195-47260196	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
25	rs181655342	chr3:47260231-47260232	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
26	rs142737318	chr3:47260293-47260294	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
27	rs5848825	chr3:47260338-47260339	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
28	rs147356714	chr3:47260494-47260495	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
29	rs185650464	chr3:47260539-47260540	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
30	rs546767105	chr3:47260562-47260563	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
31	rs568113727	chr3:47260594-47260595	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
32	rs535759126	chr3:47260652-47260653	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs367807198	chr3:47260708-47260709	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs558862630	chr3:47260723-47260724	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs137865682	chr3:47260734-47260735	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs371642335	chr3:47260803-47260804	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs373369459	chr3:47260819-47260820	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs539033858	chr3:47260822-47260823	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs557471918	chr3:47260860-47260861	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs572892401	chr3:47260987-47260988	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs533605158	chr3:47261040-47261041	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs555937687	chr3:47261106-47261107	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs74792588	chr3:47261127-47261128	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs544943518	chr3:47261131-47261132	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs530865478	chr3:47261155-47261156	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs149537357	chr3:47261191-47261192	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs543612490	chr3:47261213-47261214	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs374358041	chr3:47261229-47261230	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs578095403	chr3:47261312-47261313	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs377738461	chr3:47261368-47261369	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:101)

Disease	PMID	Source
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
Glioblastoma multiforme	21080181	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
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Esophageal cancer	20955586	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Melanoma	20688739	CNVD
Acute myeloid leukemia	21251322	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Kartagener syndrome	16639409	CNVD
Biliary cancer	19435499	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	16397240	CNVD
Breast cancer	22032731	CNVD
Non-small cell lung cancer	20864512	CNVD
Colorectal cancer	16912164	CNVD
Non-small cell lung cancer	19010865	CNVD
Colorectal cancer	16272173	CNVD
Non-muscle invasive bladder neoplasm	19445696	CNVD
Acute myeloid leukemia	17268525	CNVD
Salivary gland tumor	18059337	CNVD
Gastric cancer	16891809	CNVD
Night blindness	17160897	CNVD
Cancer	17160897	CNVD
Breast cancer	20409316	CNVD
Lung cancer	17297452	CNVD
Multiple myeloma	16616336	CNVD
Effusion lymphoma	18079361	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Neuroblastoma	20406844	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	21045282	CNVD
Urothelial cell carcinoma	18451213	CNVD
Neuroblastoma	17327916	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Melanoma	17363583	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Adrenocortical carcinoma	18281524	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
Medullary thyroid carcinoma	18765511	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Autism	21865298	CNVD

Chromatin state (count:203 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47208200-47276600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:47223800-47269200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr3:47245400-47266600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:47247000-47269400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:47262800-47266200	Weak transcription	Primary B cells from cord blood	blood
6	chr3:47262800-47287400	Weak transcription	Primary T cells from cord blood	blood
7	chr3:47263000-47263200	Weak transcription	Fetal Muscle Leg	muscle
8	chr3:47263000-47275600	Weak transcription	HSMMtube	muscle
9	chr3:47263200-47263400	Enhancers	Fetal Muscle Leg	muscle
10	chr3:47263200-47263600	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr3:47263400-47263800	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr3:47263400-47268000	Weak transcription	Fetal Muscle Leg	muscle
13	chr3:47263600-47276600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:47264200-47322200	Weak transcription	Gastric	stomach
15	chr3:47265200-47266800	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr3:47265400-47267000	Enhancers	Hela-S3	cervix
17	chr3:47265600-47265800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:47265600-47266400	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr3:47265800-47283800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:47266200-47266600	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr3:47266200-47266600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr3:47266200-47270000	Enhancers	Primary B cells from cord blood	blood
23	chr3:47266200-47270200	Enhancers	Adipose Nuclei	Adipose
24	chr3:47266400-47266600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:47266400-47266800	Enhancers	Primary hematopoietic stem cells	blood
26	chr3:47266400-47266800	Enhancers	GM12878-XiMat	blood
27	chr3:47266400-47267000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:47266400-47267000	Enhancers	K562	blood
29	chr3:47266400-47267200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:47266400-47267200	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr3:47266400-47267400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:47266400-47267600	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr3:47266400-47267600	Enhancers	Duodenum Mucosa	Duodenum
34	chr3:47266400-47268400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr3:47266600-47266800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:47266600-47267600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:47266600-47267800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
38	chr3:47266600-47268800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr3:47266600-47269200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:47266600-47269200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr3:47266600-47270400	Enhancers	Primary B cells from peripheral blood	blood
42	chr3:47266800-47267200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
43	chr3:47266800-47267200	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr3:47266800-47267200	Enhancers	NHEK	skin
45	chr3:47266800-47267600	Flanking Active TSS	GM12878-XiMat	blood
46	chr3:47266800-47276400	Weak transcription	Fetal Intestine Small	intestine
47	chr3:47267000-47267400	Active TSS	Brain Hippocampus Middle	brain
48	chr3:47267000-47270400	Weak transcription	Brain Germinal Matrix	brain
49	chr3:47267000-47280400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:47267200-47269200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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