Variant report

Variant	esv3389734
Chromosome Location	chr6:53783968-53784315
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:53783899-53783980	LNCaP	prostate:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53656949..53662173-chr6:53781368..53784554,5	MCF-7	breast:

Variant related genes	Relation type
LRRC1	TF binding region
ENSG00000228614	chromatin interactions
ENSG00000137269	chromatin interactions

Extended variants
information (count: 20 )
Associated
traits (count: 79 )

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs200770019	chr6:53784019-53784020	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs57302181	chr6:53784028-53784029	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs2494085	chr6:53784029-53784030	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	mRNA abundance
4	rs70980879	chr6:53784053-53784054	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs374992102	chr6:53784054-53784055	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs146065480	chr6:53784101-53784102	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs529350395	chr6:53784128-53784129	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs189719709	chr6:53784159-53784160	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs536286866	chr6:53784175-53784176	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs9474683	chr6:53784235-53784236	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs59246960	chr6:53784268-53784269	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs371290750	chr6:53784275-53784276	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs45473902	chr6:53784276-53784277	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	mRNA abundance
14	rs538737288	chr6:53784283-53784284	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs9474684	chr6:53784288-53784289	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs59865937	chr6:53784291-53784292	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs562020383	chr6:53784292-53784293	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs569292129	chr6:53784296-53784297	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs575420124	chr6:53784308-53784309	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs180993604	chr6:53784313-53784314	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:79)

Disease	PMID	Source
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Leukemia	21518781	CNVD
Cancer	21637783	CNVD
Facial dysmorphism	22105932	CNVD
Medulloblastoma	21979893	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Endometrial cancer	22040021	CNVD
Acute myeloid leukemia	16864856	CNVD
Breast cancer	21264507	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Bladder cancer	19088036	CNVD
Wilms tumour	21544195	CNVD
Uveal melanoma	21693616	CNVD
Biliary cancer	19435499	CNVD
Malaria	21533027	CNVD
Retinoblastoma	19183342	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	21858162	CNVD
Ewing''s sarcoma	17952124	CNVD
Autism	21448237	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Autism	22495311	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Urothelial carcinoma	18382360	CNVD
Cancer	21183584	CNVD
Hodgkin''s lymphoma	17606441	CNVD
small cell lung cancer	20016488	CNVD
Gastric cancer	17908304	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Neuroblastoma	16790693	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Osteosarcoma	16790693	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Lung cancer	18438408	CNVD
Neuroblastoma	18923191	CNVD
Breast cancer	17603634	CNVD
Neurocytoma	17123091	CNVD
Systemic lupus erythematosus	17503323	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Breast cancer	16608533	CNVD
Melanoma	18172304	CNVD
Esophageal adenocarcinoma	18820669	CNVD
Neuroblastoma	19686582	CNVD
Neuroblastoma	17289879	CNVD
Breast cancer	17899364	CNVD
Breast cancer	17133270	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
Glioblastoma multiforme	22286061	CNVD
Colorectal cancer	16912164	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	21364760	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53759200-53787600	Weak transcription	Spleen	Spleen
2	chr6:53759200-53794400	Weak transcription	Right Ventricle	heart
3	chr6:53759400-53786400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr6:53759600-53789800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:53760400-53789400	Weak transcription	Stomach Mucosa	stomach
6	chr6:53760400-53791200	Weak transcription	Hela-S3	cervix
7	chr6:53760600-53793600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr6:53761000-53785400	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr6:53761400-53787400	Weak transcription	HMEC	breast
10	chr6:53761400-53791200	Weak transcription	Colon Smooth Muscle	Colon
11	chr6:53761600-53790800	Weak transcription	Fetal Heart	heart
12	chr6:53761800-53786800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:53762000-53791200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr6:53762000-53791600	Weak transcription	Fetal Lung	lung
15	chr6:53762200-53786800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:53764400-53784600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr6:53768600-53785000	Weak transcription	Primary B cells from cord blood	blood
18	chr6:53768800-53796000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr6:53769000-53785400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:53769200-53790400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr6:53769600-53785200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr6:53769800-53784400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:53769800-53784400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr6:53770000-53795800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr6:53770600-53787400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr6:53771200-53785000	Weak transcription	Left Ventricle	heart
27	chr6:53772000-53784200	Weak transcription	Colonic Mucosa	Colon
28	chr6:53772000-53784400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:53772000-53787600	Weak transcription	Pancreas	Pancrea
30	chr6:53772000-53803000	Weak transcription	Lung	lung
31	chr6:53776000-53786600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr6:53776000-53790600	Weak transcription	Brain Germinal Matrix	brain
33	chr6:53776200-53786400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:53776400-53786600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:53776600-53785200	Weak transcription	Ovary	ovary
36	chr6:53776600-53789200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr6:53776800-53791000	Weak transcription	HUVEC	blood vessel
38	chr6:53777600-53790600	Strong transcription	Fetal Thymus	thymus
39	chr6:53778000-53787800	Strong transcription	Dnd41	blood
40	chr6:53778000-53791800	Weak transcription	Small Intestine	intestine
41	chr6:53779200-53787600	Weak transcription	Aorta	Aorta
42	chr6:53779400-53787600	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr6:53779600-53784400	Weak transcription	Fetal Stomach	stomach
44	chr6:53779600-53784800	Weak transcription	Fetal Muscle Trunk	muscle
45	chr6:53779600-53785400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr6:53779600-53787400	Weak transcription	Esophagus	oesophagus
47	chr6:53779600-53791400	Weak transcription	Placenta	Placenta
48	chr6:53779800-53785400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr6:53780200-53784400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr6:53780200-53790400	Weak transcription	Gastric	stomach

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