Variant report

Variant	esv3515132
Chromosome Location	chr9:71736982-71744630
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:18)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:71649472..71654369-chr9:71735388..71737779,6	MCF-7	breast:
2	chr9:71733168..71738729-chr9:71786929..71793777,10	MCF-7	breast:
3	chr9:71735373..71738833-chr9:71764136..71766985,4	MCF-7	breast:
4	chr1:149223425..149225310-chr9:71736139..71738412,2	MCF-7	breast:
5	chr9:71727081..71728601-chr9:71737166..71739059,2	MCF-7	breast:
6	chr9:71696609..71699452-chr9:71736834..71738699,2	MCF-7	breast:
7	chr9:71720044..71724145-chr9:71733178..71738087,7	MCF-7	breast:
8	chr1:62208097..62208620-chr9:71736404..71737107,2	Hela-S3	cervix:
9	chr9:71734142..71739001-chr9:71788032..71795507,11	MCF-7	breast:
10	chr9:71736483..71737290-chr9:71808170..71808758,2	MCF-7	breast:
11	chr9:71734182..71738595-chr9:71741906..71745315,7	MCF-7	breast:
12	chr9:71736310..71738206-chr9:71797242..71798901,2	MCF-7	breast:
13	chr9:71743905..71746446-chr9:71805495..71808231,2	MCF-7	breast:
14	chr9:71649857..71652024-chr9:71744170..71747063,2	MCF-7	breast:
15	chr9:71733940..71739343-chr9:71741877..71748941,25	MCF-7	breast:
16	chr9:71736348..71739276-chr9:71751743..71753516,2	MCF-7	breast:
17	chr11:65666788..65667405-chr9:71737195..71738062,2	Hela-S3	cervix:
18	chr9:71743521..71745547-chr9:71821447..71823888,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TJP2-1	chr9:71736400-71737148	ENSG00000227410.1

No data

Variant related genes	Relation type
ENSG00000206737	chromatin interactions
ENSG00000270236	chromatin interactions
ENSG00000165060	chromatin interactions
ENSG00000119139	chromatin interactions
ENSG00000132849	chromatin interactions

Extended variants
information (count: 247 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:247 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs537220196	chr9:71737003-71737004	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	Chromatin interactive region lncRNA	5 gene(s)	Overlapped CNVs	n/a
2	rs547230245	chr9:71737083-71737084	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	Chromatin interactive region lncRNA	5 gene(s)	Overlapped CNVs	n/a
3	rs182232799	chr9:71737097-71737098	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	Chromatin interactive region lncRNA	5 gene(s)	Overlapped CNVs	n/a
4	rs577677844	chr9:71737116-71737117	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
5	rs150901548	chr9:71737121-71737122	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
6	rs555833595	chr9:71737141-71737142	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
7	rs568979869	chr9:71737143-71737144	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription	Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
8	rs560162401	chr9:71737204-71737205	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
9	rs572087789	chr9:71737208-71737209	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
10	rs542987864	chr9:71737287-71737288	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
11	rs139728670	chr9:71737288-71737289	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
12	rs543958049	chr9:71737373-71737374	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
13	rs531833867	chr9:71737408-71737409	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
14	rs144379034	chr9:71737409-71737410	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
15	rs186891177	chr9:71737412-71737413	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
16	rs118055398	chr9:71737413-71737414	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
17	rs11145355	chr9:71737414-71737415	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
18	rs560248263	chr9:71737427-71737428	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
19	rs368588529	chr9:71737430-71737431	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
20	rs77399146	chr9:71737438-71737439	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
21	rs529676535	chr9:71737483-71737484	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
22	rs557962310	chr9:71737533-71737534	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
23	rs184061045	chr9:71737549-71737550	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
24	rs577792641	chr9:71737627-71737628	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
25	rs569887982	chr9:71737652-71737653	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
26	rs188499230	chr9:71737664-71737665	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
27	rs78016328	chr9:71737679-71737680	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
28	rs4278214	chr9:71737684-71737685	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription	Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs538776930	chr9:71737685-71737686	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
30	rs149672010	chr9:71737705-71737706	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
31	rs74749405	chr9:71737743-71737744	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
32	rs542979598	chr9:71737752-71737753	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
33	rs74646159	chr9:71737764-71737765	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
34	rs554971748	chr9:71737792-71737793	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
35	rs576713586	chr9:71737828-71737829	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
36	rs114863213	chr9:71737851-71737852	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
37	rs540970203	chr9:71737863-71737864	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
38	rs565505871	chr9:71737867-71737868	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
39	rs148905726	chr9:71737878-71737879	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
40	rs115712160	chr9:71737880-71737881	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
41	rs532246336	chr9:71737902-71737903	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
42	rs369452767	chr9:71737906-71737907	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
43	rs559460438	chr9:71737913-71737914	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
44	rs114241970	chr9:71737922-71737923	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
45	rs548131568	chr9:71737985-71737986	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
46	rs143624780	chr9:71738000-71738001	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
47	rs530883036	chr9:71738065-71738066	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
48	rs147640588	chr9:71738086-71738087	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
49	rs570349009	chr9:71738121-71738122	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs111340106	chr9:71738123-71738124	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:57)

Disease	PMID	Source
Breast cancer	17133270	CNVD
Chordoma	18071362	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
Renal cell carcinoma	18592004	CNVD
Developmental delay	19490664	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
Medulloblastoma	21979893	CNVD
microdeletion syndrome	16199537	CNVD
Ovarian cancer	21720365	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Cancer	20164919	CNVD
Urothelial carcinoma	21177765	CNVD
Renal cell carcinoma	21668985	CNVD
Autism	22495311	CNVD
Melanoma	18172304	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Melanoma	22183965	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Cancer	16751803	CNVD
Myelofibrosis	22110671	CNVD
lymphocytic leukemia	21291569	CNVD
Leukemia	17361228	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Glioblastoma	16823260	CNVD
Leukemia	18688285	CNVD
Non-small cell lung cancer	21044232	CNVD
Brain cancer	20823417	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Astrocytoma	17387387	CNVD
Glioblastoma multiforme	21080181	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Renal cell carcinoma	19461508	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Heart disease	21282601	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Lung cancer	18438408	CNVD
small cell lung cancer	20016488	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Acute myeloid leukemia	21251322	CNVD
Breast cancer	17899364	CNVD
Mantle cell lymphoma	19029149	CNVD
Hepatocellular carcinoma	16750200	CNVD
Acute myeloid leukemia	20729466	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Breast cancer	17603634	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Oral cancer	21386901	CNVD
Epilepsy	22083797	CNVD
Glioblastoma multiforme	21750150	CNVD
Cancer	21183584	CNVD
Bipolar disorder	18458673	CNVD

Chromatin state (count:411 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71729800-71745600	Weak transcription	K562	blood
2	chr9:71734800-71737800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr9:71734800-71737800	Active TSS	H9 Cell Line	embryonic stem cell
4	chr9:71735000-71737600	Active TSS	Pancreas	Pancrea
5	chr9:71735000-71737800	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr9:71735000-71737800	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr9:71735000-71738200	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr9:71735000-71738200	Active TSS	Fetal Intestine Large	intestine
9	chr9:71735200-71737400	Active TSS	Primary T cells from cord blood	blood
10	chr9:71735200-71738000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr9:71735200-71738000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr9:71735200-71738200	Active TSS	H1 Cell Line	embryonic stem cell
13	chr9:71735200-71738200	Active TSS	Fetal Intestine Small	intestine
14	chr9:71735200-71738400	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr9:71735400-71737400	Active TSS	Rectal Smooth Muscle	rectum
16	chr9:71735400-71737400	Active TSS	Stomach Smooth Muscle	stomach
17	chr9:71735400-71737600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr9:71735400-71737600	Active TSS	Esophagus	oesophagus
19	chr9:71735400-71737600	Active TSS	Fetal Kidney	kidney
20	chr9:71735400-71737800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr9:71735400-71738000	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr9:71735600-71737200	Active TSS	Stomach Mucosa	stomach
23	chr9:71735600-71737400	Active TSS	Brain Cingulate Gyrus	brain
24	chr9:71735600-71737400	Active TSS	Duodenum Mucosa	Duodenum
25	chr9:71735600-71737400	Active TSS	A549	lung
26	chr9:71735600-71737600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr9:71735600-71737600	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr9:71735600-71737600	Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr9:71735600-71737600	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr9:71735600-71737600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr9:71735600-71737600	Active TSS	Brain Anterior Caudate	brain
32	chr9:71735600-71737600	Active TSS	Placenta Amnion	Placenta Amnion
33	chr9:71735600-71737600	Active TSS	Right Ventricle	heart
34	chr9:71735600-71737600	Active TSS	Thymus	Thymus
35	chr9:71735600-71737800	Active TSS	HUES64 Cell Line	embryonic stem cell
36	chr9:71735600-71738000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
37	chr9:71735800-71737000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr9:71735800-71737200	Active TSS	HSMM	muscle
39	chr9:71735800-71737400	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr9:71735800-71737600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr9:71735800-71737600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr9:71735800-71737600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
43	chr9:71735800-71737600	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr9:71735800-71737600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr9:71735800-71737600	Active TSS	Left Ventricle	heart
46	chr9:71735800-71737600	Active TSS	Ovary	ovary
47	chr9:71735800-71737600	Active TSS	Rectal Mucosa Donor 31	rectum
48	chr9:71735800-71737600	Active TSS	Sigmoid Colon	Sigmoid Colon
49	chr9:71735800-71737600	Active TSS	Hela-S3	cervix
50	chr9:71735800-71737600	Active TSS	Osteobl	bone

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