Variant report

Variant	esv3448882
Chromosome Location	chr20:23362387-23362949
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	chr20:23362600-23362750	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:23344681..23346860-chr20:23360081..23363046,2	MCF-7	breast:

Variant related genes	Relation type
RNA5SP479	TF binding region
ENSG00000125812	chromatin interactions

Extended variants
information (count: 23 )
Associated
traits (count: 56 )

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs570109807	chr20:23362408-23362409	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs529373619	chr20:23362434-23362435	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs192251782	chr20:23362464-23362465	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs183969572	chr20:23362468-23362469	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs535044369	chr20:23362525-23362526	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs554090885	chr20:23362535-23362536	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs569549155	chr20:23362571-23362572	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs188352253	chr20:23362577-23362578	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs558299628	chr20:23362586-23362587	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs73901819	chr20:23362589-23362590	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs576726443	chr20:23362676-23362677	Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs12625468	chr20:23362678-23362679	Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
13	rs555091873	chr20:23362680-23362681	Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs374927265	chr20:23362697-23362698	Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs571686002	chr20:23362707-23362708	Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs7269627	chr20:23362727-23362728	Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
17	rs574755526	chr20:23362777-23362778	Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs533481429	chr20:23362783-23362784	Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs12625489	chr20:23362825-23362826	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
20	rs563741463	chr20:23362842-23362843	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs529534233	chr20:23362849-23362850	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs560182936	chr20:23362850-23362851	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs549474422	chr20:23362863-23362864	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:56)

Disease	PMID	Source
Wilms tumour	21544195	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	16272173	CNVD
Melanoma	18172304	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Oral cancer	19627613	CNVD
colon cancer	17210682	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	21080181	CNVD
Thyroid cancer	19087340	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Colorectal cancer	19359472	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Human rectal carcinomas	16397240	CNVD
Olfactory neuroblastoma	18408657	CNVD
Central neurocytomas	17123091	CNVD
Colorectal cancer	16272173	CNVD
Medulloblastoma	21979893	CNVD
Gastric cancer	17908304	CNVD
Urothelial carcinoma	21177765	CNVD
Acute myeloid leukemia	20729466	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Ewing''s sarcoma	17952124	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Colorectal cancer	21645411	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Autism	22495311	CNVD
Renal cell carcinoma	18765545	CNVD
Alagille syndrome	17576883	CNVD
Anaplastic large cell lymphoma	18179710	CNVD
Prostate cancer	18632612	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Cancer	21183584	CNVD
Myxofibrosarcoma	16751306	CNVD
Pancreatic endocrine tumor	17639061	CNVD
Breast cancer	16608533	CNVD
Bladder cancer	21909424	CNVD
Esophageal cancer	21851588	CNVD
Breast cancer	17133270	CNVD
Thrombophilia	17576883	CNVD
Myelofibrosis	22110671	CNVD
Mental retardation	21062444	CNVD
Hepatocellular carcinoma	22174799	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
Chordoma	18071362	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
small cell lung cancer	17426248	CNVD

Chromatin state (count:162 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23344000-23392600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr20:23344800-23362400	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr20:23345000-23362600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr20:23346600-23363200	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr20:23346800-23362600	Weak transcription	Right Atrium	heart
6	chr20:23347200-23362400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr20:23347800-23362600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr20:23348000-23374200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr20:23348200-23384800	Weak transcription	Stomach Mucosa	stomach
10	chr20:23348600-23362400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr20:23348600-23363000	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr20:23348800-23363000	Strong transcription	GM12878-XiMat	blood
13	chr20:23348800-23366400	Strong transcription	Dnd41	blood
14	chr20:23349200-23363000	Strong transcription	Adipose Nuclei	Adipose
15	chr20:23349400-23363200	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr20:23349600-23363600	Strong transcription	Liver	Liver
17	chr20:23349600-23366000	Strong transcription	HepG2	liver
18	chr20:23349800-23362800	Strong transcription	Osteobl	bone
19	chr20:23349800-23363000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr20:23349800-23364200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr20:23350000-23363000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr20:23350000-23363600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr20:23350400-23362600	Strong transcription	Placenta	Placenta
24	chr20:23351200-23371000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr20:23351200-23374000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr20:23351400-23374000	Weak transcription	Fetal Brain Male	brain
27	chr20:23352200-23367800	Weak transcription	Small Intestine	intestine
28	chr20:23352800-23362800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr20:23352800-23376400	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr20:23353000-23365400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr20:23353000-23378200	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr20:23353400-23372400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr20:23353400-23374200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr20:23354400-23389000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr20:23354400-23399800	Weak transcription	Hela-S3	cervix
36	chr20:23354600-23374200	Weak transcription	Rectal Smooth Muscle	rectum
37	chr20:23354600-23375200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr20:23354800-23362800	Weak transcription	Spleen	Spleen
39	chr20:23354800-23371000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr20:23354800-23373600	Weak transcription	Colonic Mucosa	Colon
41	chr20:23356600-23365400	Weak transcription	Gastric	stomach
42	chr20:23356600-23374200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr20:23356800-23368800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr20:23357000-23371200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr20:23357200-23364200	Strong transcription	A549	lung
46	chr20:23357400-23363200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr20:23357800-23370000	Weak transcription	Brain Substantia Nigra	brain
48	chr20:23358000-23362400	Weak transcription	Colon Smooth Muscle	Colon
49	chr20:23358000-23362600	Weak transcription	Psoas Muscle	Psoas
50	chr20:23358000-23366800	Weak transcription	K562	blood

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