Variant report

Variant	nsv892188
Chromosome Location	chr9:6999846-7026860
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	ATF1	chr9:7011743-7011938	K562	blood:	n/a	n/a
2	CEBPB	chr9:7001647-7001868	IMR90	lung:	n/a	chr9:7001766-7001783 chr9:7001769-7001782
3	CEBPB	chr9:7001595-7001907	K562	blood:	n/a	chr9:7001766-7001783 chr9:7001769-7001782
4	CHD2	chr9:7006711-7006764	GM12878	blood:	n/a	n/a
5	CTCF	chr9:7008040-7008190	GM12871	blood:	n/a	n/a
6	E2F4	chr9:7014900-7015160	MCF10A-Er-Src	breast:	n/a	n/a
7	E2F4	chr9:7009393-7009858	MCF10A-Er-Src	breast:	n/a	n/a
8	EP300	chr9:7009268-7009280	GM12878	blood:	n/a	n/a
9	FAM48A	chr9:7000681-7000765	GM12878	blood:	n/a	n/a
10	FAM48A	chr9:7014453-7014484	GM12878	blood:	n/a	n/a
11	FOXA1	chr9:7005352-7005680	HepG2	liver:	n/a	n/a
12	GATA2	chr9:7018479-7018763	SH-SY5Y	brain:	n/a	n/a
13	GATA2	chr9:7004772-7005003	SH-SY5Y	brain:	n/a	n/a
14	GATA3	chr9:7019861-7020157	SH-SY5Y	brain:	n/a	chr9:7020026-7020036
15	GATA3	chr9:7018391-7018743	MCF-7	breast:	n/a	n/a
16	GATA3	chr9:7004703-7004936	SH-SY5Y	brain:	n/a	n/a
17	GATA3	chr9:7018426-7018647	SH-SY5Y	brain:	n/a	n/a
18	GATA3	chr9:6999865-7000273	MCF-7	breast:	n/a	n/a
19	GATA3	chr9:7021697-7021894	SH-SY5Y	brain:	n/a	n/a
20	GATA3	chr9:7000257-7000583	SH-SY5Y	brain:	n/a	chr9:7000439-7000455 chr9:7000439-7000455
21	IKZF1	chr9:7011861-7012031	GM12878	blood:	n/a	n/a
22	KAP1	chr9:7009073-7009491	K562	blood:	n/a	n/a
23	MAFF	chr9:6999893-7000155	K562	blood:	n/a	chr9:6999990-7000008
24	MAFF	chr9:6999828-7000159	HepG2	liver:	n/a	chr9:6999990-7000008
25	MAFK	chr9:6999829-7000160	IMR90	lung:	n/a	chr9:6999986-7000006 chr9:6999991-7000006
26	MAFK	chr9:6999843-7000151	HepG2	liver:	n/a	chr9:6999986-7000006 chr9:6999991-7000006
27	MAFK	chr9:6999821-7000161	HepG2	liver:	n/a	chr9:6999986-7000006 chr9:6999991-7000006
28	MAX	chr9:7011385-7012131	NB4	blood:	n/a	chr9:7011922-7011932
29	MAZ	chr9:7008465-7008582	HepG2	liver:	n/a	n/a
30	MYC	chr9:7008825-7008852	NB4	blood:	n/a	n/a
31	MYC	chr9:7011526-7012109	NB4	blood:	n/a	chr9:7011922-7011932
32	NFIC	chr9:7008309-7008823	ECC-1	luminal epithelium:	n/a	n/a
33	NRF1	chr9:7000119-7000124	GM12878	blood:	n/a	n/a
34	PAX5	chr9:7011988-7012186	GM12878	blood:	n/a	n/a
35	PAX5	chr9:7011938-7012221	GM12878	blood:	n/a	n/a
36	PAX5	chr9:7011953-7012228	GM12878	blood:	n/a	n/a
37	PAX5	chr9:7011864-7012271	GM12878	blood:	n/a	n/a
38	POLR2A	chr9:7008566-7008663	HepG2	liver:	n/a	n/a
39	POLR2A	chr9:7011339-7011476	MCF10A-Er-Src	breast:	n/a	n/a
40	POLR2A	chr9:7001516-7001712	K562	blood:	n/a	n/a
41	POLR2A	chr9:7017613-7017919	H1-neurons	neurons:	n/a	n/a
42	POLR2A	chr9:7011694-7012200	HL-60	blood:	n/a	n/a
43	POLR2A	chr9:7017604-7017990	H1-neurons	neurons:	n/a	n/a
44	POLR2A	chr9:7011548-7012261	HL-60	blood:	n/a	n/a
45	POLR2A	chr9:7013971-7014144	MCF10A-Er-Src	breast:	n/a	n/a
46	POLR2A	chr9:7010058-7010341	MCF10A-Er-Src	breast:	n/a	n/a
47	POLR2A	chr9:7008759-7008760	MCF-7	breast:	n/a	n/a
48	POLR2A	chr9:7013979-7014105	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr9:7011768-7011938	A549	lung:	n/a	n/a
50	POLR2A	chr9:7008309-7008421	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:35003633..35004245-chr9:7020432..7021432,2	K562	blood:
2	chr9:7001163..7002731-chr9:7004777..7006309,2	K562	blood:
3	chr9:7001163..7002731-chr9:7004777..7006309,2	K562	blood:
4	chr9:6996659..6998506-chr9:6999056..7001855,2	K562	blood:

Variant related genes	Relation type
KDM4C	TF binding region

Extended variants
information (count: 1476 )
Associated
traits (count: 104 )

Variant overlapped rSNPs/rCNVs (count:1476 , 50 per page) page: 1 2 3 4 5 6 7 ... 30

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs10122718	chr9:6999846-6999847	Weak transcription Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs547484549	chr9:6999860-6999861	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs559389158	chr9:6999885-6999886	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs567422588	chr9:6999898-6999899	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs79467106	chr9:6999924-6999925	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs76473840	chr9:6999925-6999926	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs201022160	chr9:6999951-6999952	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs2792241	chr9:6999953-6999954	Weak transcription Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
9	rs149102138	chr9:6999958-6999959	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs116614068	chr9:6999963-6999964	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs538608818	chr9:7000020-7000021	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs556511883	chr9:7000043-7000044	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs574900998	chr9:7000062-7000063	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs192784962	chr9:7000086-7000087	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs4742280	chr9:7000087-7000088	Weak transcription Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs552477849	chr9:7000153-7000154	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs573373094	chr9:7000192-7000193	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs540504540	chr9:7000202-7000203	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs10815506	chr9:7000206-7000207	Weak transcription Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs199547201	chr9:7000276-7000277	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs146539966	chr9:7000297-7000298	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs141249867	chr9:7000317-7000318	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs562831693	chr9:7000348-7000349	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs185522379	chr9:7000360-7000361	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs549295422	chr9:7000374-7000375	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs538053446	chr9:7000376-7000377	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs10116747	chr9:7000409-7000410	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs545029314	chr9:7000413-7000414	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs60838219	chr9:7000428-7000429	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs7854608	chr9:7000438-7000439	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
31	rs533840264	chr9:7000442-7000443	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs575312281	chr9:7000448-7000449	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs538313009	chr9:7000474-7000475	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs10975960	chr9:7000480-7000481	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs568508164	chr9:7000488-7000489	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs535881284	chr9:7000494-7000495	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs190828240	chr9:7000495-7000496	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs573485558	chr9:7000520-7000521	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs576766927	chr9:7000531-7000532	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs367949737	chr9:7000538-7000539	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs192524204	chr9:7000579-7000580	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs2792240	chr9:7000595-7000596	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
43	rs10975961	chr9:7000653-7000654	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs544671446	chr9:7000654-7000655	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs145053827	chr9:7000665-7000666	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs114308178	chr9:7000668-7000669	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs542280876	chr9:7000712-7000713	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs115208493	chr9:7000737-7000738	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs2792239	chr9:7000759-7000760	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs2792238	chr9:7000769-7000770	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:104)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
Intracranial aneurysm	16715129	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Disorders of sex development	22290220	CNVD
Glioblastoma multiforme	21080181	CNVD
Sudden cardiac death	19188705	CNVD
Non-small cell lung cancer	21829676	CNVD
Acute myeloid leukemia	16864856	CNVD
Cancer	21183584	CNVD
Non-small cell lung cancer	21952639	CNVD
Disorders of sex development	21048976	CNVD
Neuroblastoma	18923191	CNVD
Intellectual disability	22102821	CNVD
abnormal development	18461090	CNVD
Honadal dysgenesis	21048976	CNVD
Medulloblastoma	21979893	CNVD
Lung cancer	16740712	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Oral squamous cell carcinoma	17134496	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
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
Pleomorphic xanthoastrocytoma	20730472	CNVD
microdeletion syndrome	16199537	CNVD
Non-syndromic sensorineural hearing loss	21987784	CNVD
Cancer	20164919	CNVD
Chronic myeloid leukemia	21384125	CNVD
Ovarian cancer	21720365	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
small cell lung cancer	20016488	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Developmental delay	21147756	CNVD
Lung cancer	18438408	CNVD
XY gonadal dysgenesis	20685758	CNVD
Urothelial carcinoma	21177765	CNVD
Oral cancer	21386901	CNVD
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Myelodysplastic syndrome	21251322	CNVD
Breast cancer	21785460	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21858162	CNVD
Renal cell carcinoma	21668985	CNVD
Autism	22495311	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Myelofibrosis	22110671	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Hepatocellular carcinoma	18803288	CNVD
Breast cancer	21364760	CNVD
Metastatic melanoma	18483359	CNVD
Glioblastoma	19074898	CNVD
Malignant melanoma	19074898	CNVD
Prostate cancer	16573809	CNVD
Metanephric adenoma	20802469	CNVD
Medulloblastoma	16783165	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD
Autism	20858261	CNVD
Epilepsy	20858261	CNVD
Mental retardation	20858261	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Renal cell carcinoma	21215367	CNVD
Cancer	21215367	CNVD

Chromatin state (count:701 , 50 per page) page: 1 2 3 4 5 6 7 ... 15

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6972000-7013200	Weak transcription	Fetal Kidney	kidney
2	chr9:6976200-7011800	Weak transcription	Psoas Muscle	Psoas
3	chr9:6977000-7008200	Strong transcription	Primary B cells from cord blood	blood
4	chr9:6977800-7008200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr9:6978800-7008200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:6979600-7008000	Weak transcription	NHEK	skin
7	chr9:6979800-7018600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr9:6980200-7008400	Strong transcription	Primary B cells from peripheral blood	blood
9	chr9:6980800-7004200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr9:6981400-7008000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr9:6981400-7011200	Weak transcription	HUVEC	blood vessel
12	chr9:6982600-7000200	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr9:6982600-7008200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr9:6982600-7008200	Weak transcription	NHLF	lung
15	chr9:6982800-7004200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr9:6983000-7008600	Weak transcription	Fetal Brain Female	brain
17	chr9:6983400-7010200	Weak transcription	Stomach Mucosa	stomach
18	chr9:6983800-7008200	Weak transcription	A549	lung
19	chr9:6984000-7018200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr9:6985200-7007800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr9:6985200-7008200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr9:6985600-7008000	Weak transcription	K562	blood
23	chr9:6985600-7008200	Weak transcription	Right Ventricle	heart
24	chr9:6985600-7008400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr9:6985600-7011200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr9:6985600-7019200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr9:6985600-7035600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr9:6986800-7015600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr9:6987200-7008000	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr9:6987200-7008000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr9:6987200-7008200	Weak transcription	Colon Smooth Muscle	Colon
32	chr9:6987200-7008200	Weak transcription	NHDF-Ad	bronchial
33	chr9:6987200-7008400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr9:6987400-7008000	Weak transcription	Brain Angular Gyrus	brain
35	chr9:6987400-7008600	Weak transcription	Hela-S3	cervix
36	chr9:6987600-7008000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr9:6987600-7008000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr9:6987600-7008000	Weak transcription	Fetal Muscle Leg	muscle
39	chr9:6987600-7008000	Weak transcription	HepG2	liver
40	chr9:6987600-7008200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr9:6987600-7008400	Weak transcription	Osteobl	bone
42	chr9:6987800-7004000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr9:6988800-7008200	Weak transcription	Aorta	Aorta
44	chr9:6988800-7008200	Weak transcription	Small Intestine	intestine
45	chr9:6989200-7008000	Weak transcription	Dnd41	blood
46	chr9:6991600-7008000	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr9:6994600-7008000	Weak transcription	Colonic Mucosa	Colon
48	chr9:6994600-7008000	Weak transcription	Spleen	Spleen
49	chr9:6995000-7008000	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr9:6995400-7008600	Weak transcription	HMEC	breast

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