Variant report

Variant	nsv972653
Chromosome Location	chr9:21811294-21811794
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	chr9:21811760-21811910	HCFaa	heart:	n/a	n/a
2	GATA3	chr9:21811642-21811842	SH-SY5Y	brain:	n/a	n/a
3	POLR2A	chr9:21811743-21812209	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr9:21811283-21811846	HepG2	liver:	n/a	n/a
5	POLR2A	chr9:21810371-21811333	MCF-7	breast:	n/a	n/a
6	POLR2A	chr9:21811700-21812294	HCT-116	colon:	n/a	n/a
7	POLR2A	chr9:21811501-21811781	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr9:21811409-21811781	HCT-116	colon:	n/a	n/a
9	POLR2A	chr9:21811630-21812336	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr9:21811752-21814285	A549	lung:	n/a	n/a
11	POLR2A	chr9:21811483-21812507	MCF-7	breast:	n/a	n/a
12	POLR2A	chr9:21811561-21814235	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:21811237..21820561-chr9:21988636..21997115,18	MCF-7	breast:
2	chr9:21811532..21820564-chr9:21988281..21997291,17	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266732	TF binding region
ENSG00000240498	chromatin interactions
ENSG00000266446	chromatin interactions
ENSG00000147889	chromatin interactions

Extended variants
information (count: 31 )
Associated
traits (count: 163 )

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs562920463	chr9:21811294-21811295	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
2	rs200584071	chr9:21811335-21811336	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
3	rs149998965	chr9:21811339-21811340	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
4	rs118132633	chr9:21811348-21811349	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
5	rs551757096	chr9:21811356-21811357	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
6	rs576074370	chr9:21811398-21811399	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
7	rs545303081	chr9:21811405-21811406	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
8	rs7859886	chr9:21811441-21811442	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs539421207	chr9:21811442-21811443	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
10	rs34749428	chr9:21811449-21811450	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
11	rs115995531	chr9:21811450-21811451	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
12	rs397893493	chr9:21811459-21811460	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
13	rs561267110	chr9:21811507-21811508	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
14	rs530086578	chr9:21811513-21811514	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
15	rs543948765	chr9:21811522-21811523	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
16	rs192013227	chr9:21811523-21811524	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
17	rs375766709	chr9:21811528-21811529	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
18	rs7860126	chr9:21811533-21811534	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs79254031	chr9:21811547-21811548	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
20	rs73429337	chr9:21811565-21811566	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs571380804	chr9:21811589-21811590	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
22	rs527584655	chr9:21811601-21811602	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
23	rs529006959	chr9:21811695-21811696	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
24	rs566939659	chr9:21811709-21811710	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
25	rs535881065	chr9:21811722-21811723	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
26	rs556105862	chr9:21811725-21811726	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
27	rs569699385	chr9:21811751-21811752	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
28	rs538720516	chr9:21811752-21811753	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
29	rs558892840	chr9:21811756-21811757	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
30	rs114764774	chr9:21811784-21811785	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
31	rs541766013	chr9:21811785-21811786	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:163)

Disease	PMID	Source
Glioblastoma multiforme	21080181	CNVD
Medulloblastoma	21979893	CNVD
Breast cancer	16608533	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Breast cancer	16272173	CNVD
Hepatocellular carcinoma	16750200	CNVD
Breast cancer	17133270	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Cervical cancer	21063398	CNVD
Retinoblastoma	22278416	CNVD
Splenic marginal zone lymphoma	18492102	CNVD
Melanoma	18172304	CNVD
Biliary cancer	19435499	CNVD
Gastric cancer	21586687	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myopathy	18421352	CNVD
Neuroblastoma	18664255	CNVD
Acute lymphoblastic leukemia	18957548	CNVD
Myeloproliferative neoplasm	17564968	CNVD
Malignant meningioma	17937814	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Glioma	21971842	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	17603634	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Oligodendroglial tumors	17285580	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chordoma	18071362	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chordoma	21602918	CNVD
Renal cell carcinoma	18592004	CNVD
Developmental delay	19490664	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
microdeletion syndrome	16199537	CNVD
Non-syndromic sensorineural hearing loss	21987784	CNVD
Cancer	20164919	CNVD
Ovarian cancer	21720365	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Lung cancer	18438408	CNVD
Urothelial carcinoma	21177765	CNVD
Oral cancer	21386901	CNVD
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Chronic myeloid leukemia	21384125	CNVD
Breast cancer	21785460	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21858162	CNVD
Renal cell carcinoma	21668985	CNVD
Myelodysplastic syndrome	21251322	CNVD
Autism	22495311	CNVD
Hepatocellular carcinoma	18803288	CNVD
Metanephric adenoma	20802469	CNVD
Developmental delay	21147756	CNVD
Pilocytic astrocytoma	18670637	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Melanoma	22183965	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Non-small cell lung cancer	19010865	CNVD
Myoepithelioma	18604193	CNVD
Cancer	22183965	CNVD
Glioblastoma multiforme	21569311	CNVD
Myelofibrosis	22110671	CNVD
Ewing''s sarcoma	22429812	CNVD
Neuroblastoma	21899760	CNVD
Glioblastoma multiforme	19435819	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Cutaneous T-cell lymphoma	21881587	CNVD
Glioblastoma multiforme	22291905	CNVD
Lung cancer	21911935	CNVD
Primary central nervous system lymphoma	21088137	CNVD
head and neck squamous cell carcinoma	21798897	CNVD
Cancer	21253487	CNVD
Glioblastoma multiforme	22286061	CNVD
Intracranial ependymoma	16609018	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Glioblastoma multiforme	21922591	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
T-cell acute lymphoblastic leukemia	19406988	CNVD
Urothelial cell carcinoma	18451213	CNVD
Glioma	17123091	CNVD
Mental retardation	17124404	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Acute lymphoblastic leukemia	18768390	CNVD
Leukemia	19602459	CNVD
Acute monocytic leukemia	16498392	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Leukemia	18688285	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Acute myeloid leukemia	19651601	CNVD
Coronary Disease	20032323	CNVD
Squamous cell cancer	20885788	CNVD
Hirschsprung''s Disease	21712996	CNVD
Cancer	21732550	CNVD
Gastric cancer	22539939	CNVD
Cancer	21183584	CNVD
T-cell lymphomas	19863542	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Metastatic melanoma	18483359	CNVD
Non-small cell lung cancer	20864512	CNVD
Cervical cancer	21062161	CNVD
Acute myeloid leukemia	16864856	CNVD
Glioblastoma	17090523	CNVD
Lung cancer	16773561	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Colorectal cancer	16774939	CNVD
Bladder cancer	19088036	CNVD
Colorectal cancer	16272173	CNVD
Melanoma	16977458	CNVD
Glioblastoma multiforme	17369134	CNVD
Chagasic megaesophagus	20163722	CNVD
Melanoma	19566914	CNVD
Squamous cell cancer	19047905	CNVD
Lung adenocarcinoma	19525976	CNVD
Lung cancer	19525976	CNVD
Hodgkin''s lymphoma	18179710	CNVD
Glioma	20126413	CNVD
Melanoma	17363583	CNVD
Glioblastoma multiforme	19115005	CNVD
Glioblastoma multiforme	21138945	CNVD
Adenoid cystic carcinoma	18332873	CNVD
Cancer	20581869	CNVD
Glioblastoma multiforme	21525872	CNVD
Multiple myeloma	17550852	CNVD
Oral cancer	22144094	CNVD
Lung cancer	21569311	CNVD
Barrett''s syndrome	19417022	CNVD
Cancer	20164920	CNVD
Breast cancer	17142309	CNVD
Ependymoma	18628472	CNVD
Ewing''s sarcoma	18628472	CNVD
Glioblastoma multiforme	18628472	CNVD
Breast cancer	21364760	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Lung squamous cell carcinoma	22363434	CNVD
Cancer	17699850	CNVD
Ovarian cancer	17699850	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Ewing''s sarcoma	17952124	CNVD
Lung adenocarcinoma	17982442	CNVD
Autism	20858261	CNVD
Epilepsy	20858261	CNVD
Mental retardation	20858261	CNVD

Chromatin state (count:139 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21804000-21814200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr9:21804000-21817600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:21804000-21838200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr9:21804200-21813200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr9:21804200-21813200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr9:21804400-21813200	Weak transcription	Colonic Mucosa	Colon
7	chr9:21804400-21816000	Weak transcription	Fetal Kidney	kidney
8	chr9:21804800-21813600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr9:21805000-21812000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr9:21805000-21813200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr9:21805000-21816200	Weak transcription	Fetal Brain Male	brain
12	chr9:21805200-21812800	Strong transcription	Fetal Stomach	stomach
13	chr9:21805200-21813200	Weak transcription	Psoas Muscle	Psoas
14	chr9:21805200-21813400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr9:21805400-21812600	Strong transcription	Fetal Intestine Large	intestine
16	chr9:21805800-21813200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr9:21805800-21813200	Weak transcription	Brain Angular Gyrus	brain
18	chr9:21806000-21812400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr9:21806000-21812600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr9:21806000-21817600	Genic enhancers	HMEC	breast
21	chr9:21806200-21813200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr9:21806400-21812200	Strong transcription	Fetal Intestine Small	intestine
23	chr9:21806400-21812400	Strong transcription	HepG2	liver
24	chr9:21806400-21812800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr9:21806400-21813200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr9:21806400-21813200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr9:21806400-21819800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr9:21806600-21812200	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr9:21806600-21812400	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr9:21806600-21815800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:21806600-21841200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr9:21806800-21811600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr9:21806800-21812000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr9:21806800-21812000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr9:21806800-21812800	Strong transcription	Primary T cells from cord blood	blood
36	chr9:21806800-21813200	Weak transcription	Brain Cingulate Gyrus	brain
37	chr9:21806800-21815800	Weak transcription	Brain Germinal Matrix	brain
38	chr9:21807000-21812000	Strong transcription	Fetal Muscle Leg	muscle
39	chr9:21807000-21813600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr9:21807200-21811400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr9:21807200-21812000	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr9:21807200-21812800	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr9:21807200-21813200	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr9:21807200-21813400	Strong transcription	Fetal Muscle Trunk	muscle
45	chr9:21807400-21812200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr9:21807400-21812200	Strong transcription	Thymus	Thymus
47	chr9:21807400-21812400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr9:21807400-21813200	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr9:21807400-21813200	Weak transcription	Brain Substantia Nigra	brain
50	chr9:21807600-21812000	Strong transcription	Primary T helper cells fromperipheralblood	blood

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