Variant report

Variant	nsv520423
Chromosome Location	chr9:79047117-79065299
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	ARID3A	chr9:79062412-79062746	HepG2	liver:	n/a	n/a
2	ARID3A	chr9:79049946-79050170	HepG2	liver:	n/a	n/a
3	ARID3A	chr9:79062536-79062729	K562	blood:	n/a	n/a
4	ATF2	chr9:79056302-79057120	GM12878	blood:	n/a	n/a
5	ATF2	chr9:79053608-79054305	GM12878	blood:	n/a	n/a
6	ATF2	chr9:79056279-79057268	GM12878	blood:	n/a	n/a
7	ATF2	chr9:79053668-79054176	GM12878	blood:	n/a	n/a
8	BATF	chr9:79053726-79054163	GM12878	blood:	n/a	n/a
9	BATF	chr9:79053859-79054130	GM12878	blood:	n/a	n/a
10	BATF	chr9:79056388-79056752	GM12878	blood:	n/a	chr9:79056569-79056579
11	BATF	chr9:79056369-79057111	GM12878	blood:	n/a	chr9:79056871-79056881 chr9:79056569-79056579
12	BCL11A	chr9:79056353-79056802	GM12878	blood:	n/a	n/a
13	BCL11A	chr9:79053880-79054156	GM12878	blood:	n/a	n/a
14	BCL11A	chr9:79053717-79054138	GM12878	blood:	n/a	n/a
15	BCL11A	chr9:79056434-79056791	GM12878	blood:	n/a	n/a
16	BCL3	chr9:79056396-79056997	GM12878	blood:	n/a	n/a
17	BCL3	chr9:79053720-79054130	GM12878	blood:	n/a	n/a
18	BCLAF1	chr9:79056291-79057255	GM12878	blood:	n/a	n/a
19	BCLAF1	chr9:79053673-79054242	GM12878	blood:	n/a	n/a
20	BCLAF1	chr9:79053691-79054175	GM12878	blood:	n/a	n/a
21	BCLAF1	chr9:79056254-79056988	GM12878	blood:	n/a	n/a
22	BHLHE40	chr9:79056383-79057124	GM12878	blood:	n/a	n/a
23	BHLHE40	chr9:79059480-79059570	K562	blood:	n/a	n/a
24	BHLHE40	chr9:79053749-79054208	GM12878	blood:	n/a	n/a
25	CEBPB	chr9:79053687-79054205	GM12878	blood:	n/a	n/a
26	CEBPB	chr9:79062489-79062670	K562	blood:	n/a	n/a
27	CEBPB	chr9:79055289-79055557	HepG2	liver:	n/a	chr9:79055438-79055449
28	CEBPB	chr9:79048806-79049138	IMR90	lung:	n/a	n/a
29	CEBPB	chr9:79062452-79062657	HepG2	liver:	n/a	n/a
30	CEBPB	chr9:79062459-79062727	H1-hESC	embryonic stem cell:	n/a	n/a
31	CEBPB	chr9:79062401-79062742	Hela-S3	cervix:	n/a	n/a
32	CEBPB	chr9:79056281-79057126	GM12878	blood:	n/a	n/a
33	CHD1	chr9:79056525-79057056	GM12878	blood:	n/a	n/a
34	CHD2	chr9:79056468-79056763	GM12878	blood:	n/a	n/a
35	CTCF	chr9:79062520-79062670	K562	blood:	n/a	chr9:79062573-79062586 chr9:79062570-79062588 chr9:79062573-79062582 chr9:79062573-79062586
36	CTCF	chr9:79062500-79062650	GM12864	blood:	n/a	chr9:79062573-79062586 chr9:79062570-79062588 chr9:79062573-79062582 chr9:79062573-79062586
37	CTCF	chr9:79062406-79062756	SK-N-SH_RA	brain:	n/a	chr9:79062573-79062586 chr9:79062570-79062588 chr9:79062573-79062582 chr9:79062573-79062586
38	CTCF	chr9:79062460-79062610	HCT-116	colon:	n/a	chr9:79062573-79062586 chr9:79062570-79062588 chr9:79062573-79062582 chr9:79062573-79062586
39	CTCF	chr9:79062500-79062650	HBMEC	blood vessel:	n/a	chr9:79062573-79062586 chr9:79062570-79062588 chr9:79062573-79062582 chr9:79062573-79062586
40	CTCF	chr9:79062520-79062670	WERI-Rb-1	eye:	n/a	chr9:79062573-79062586 chr9:79062570-79062588 chr9:79062573-79062582 chr9:79062573-79062586
41	CTCF	chr9:79062460-79062610	HAc	cerebellar:	n/a	chr9:79062573-79062586 chr9:79062570-79062588 chr9:79062573-79062582 chr9:79062573-79062586
42	CTCF	chr9:79062500-79062650	HMF	breast:	n/a	chr9:79062573-79062586 chr9:79062570-79062588 chr9:79062573-79062582 chr9:79062573-79062586
43	CTCF	chr9:79062480-79062630	GM12870	blood:	n/a	chr9:79062573-79062586 chr9:79062570-79062588 chr9:79062573-79062582 chr9:79062573-79062586
44	CTCF	chr9:79062520-79062670	HRE	kidney:	n/a	chr9:79062573-79062586 chr9:79062570-79062588 chr9:79062573-79062582 chr9:79062573-79062586
45	CTCF	chr9:79062500-79062650	HFF-Myc	foreskin:	n/a	chr9:79062573-79062586 chr9:79062570-79062588 chr9:79062573-79062582 chr9:79062573-79062586
46	CTCF	chr9:79062560-79062710	A549	lung:	n/a	chr9:79062573-79062586 chr9:79062570-79062588 chr9:79062573-79062582 chr9:79062573-79062586
47	CTCF	chr9:79062760-79062910	GM12867	blood:	n/a	n/a
48	CTCF	chr9:79062324-79062845	MCF-7	breast:	n/a	chr9:79062573-79062586 chr9:79062570-79062588 chr9:79062573-79062582 chr9:79062573-79062586
49	CTCF	chr9:79062480-79062630	GM12874	blood:	n/a	chr9:79062573-79062586 chr9:79062570-79062588 chr9:79062573-79062582 chr9:79062573-79062586
50	CTCF	chr9:79062553-79062629	NHEK	skin:	n/a	chr9:79062573-79062586 chr9:79062570-79062588 chr9:79062573-79062582 chr9:79062573-79062586

No.	Distal block	Cell Line	Cell type
1	chr9:79062485..79063050-chr9:79074982..79075830,2	K562	blood:
2	chr9:79062474..79063044-chr9:79273108..79273738,2	K562	blood:
3	chr9:79061368..79063776-chr9:79272393..79274903,3	MCF-7	breast:
4	chr9:79062067..79063554-chr9:79273134..79274136,17	MCF-7	breast:
5	chr9:79057975..79060162-chr9:79063071..79066178,3	MCF-7	breast:
6	chr9:79062570..79065209-chr9:79073838..79075635,2	MCF-7	breast:
7	chr9:79062552..79063515-chr9:79319220..79320201,4	K562	blood:
8	chr9:79062119..79063115-chr9:79277138..79277991,2	MCF-7	breast:
9	chr9:79062041..79063533-chr9:79272880..79274341,6	MCF-7	breast:
10	chr9:79059311..79060843-chr9:79133319..79135511,2	MCF-7	breast:
11	chr9:79057879..79060217-chr9:79273582..79275232,2	MCF-7	breast:
12	chr9:79057975..79060162-chr9:79063071..79066178,3	MCF-7	breast:
13	chr9:79018063..79018678-chr9:79058921..79059562,2	MCF-7	breast:
14	chr9:79056464..79059191-chr9:79073425..79075482,2	MCF-7	breast:
15	chr9:79058598..79061580-chr9:79067952..79069510,2	MCF-7	breast:

Variant related genes	Relation type
GCNT1	TF binding region
ENSG00000187210	chromatin interactions

Extended variants
information (count: 730 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:730 , 50 per page) page: 1 2 3 4 5 6 7 ... 15

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs6560519	chr9:79047117-79047118	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs145848492	chr9:79047123-79047124	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs368538597	chr9:79047167-79047168	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs563551098	chr9:79047215-79047216	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs544367068	chr9:79047238-79047239	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs569496082	chr9:79047260-79047261	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs115686910	chr9:79047320-79047321	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs564160065	chr9:79047338-79047339	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs545733394	chr9:79047346-79047347	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs558905453	chr9:79047382-79047383	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs199687726	chr9:79047412-79047413	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs369601089	chr9:79047414-79047415	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs371170960	chr9:79047444-79047445	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs113772217	chr9:79047453-79047454	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs554377610	chr9:79047465-79047466	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs375298468	chr9:79047498-79047499	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs189858926	chr9:79047511-79047512	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs138310200	chr9:79047535-79047536	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs4745548	chr9:79047559-79047560	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
20	rs547176854	chr9:79047568-79047569	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs182507900	chr9:79047578-79047579	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs141908547	chr9:79047588-79047589	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs533553367	chr9:79047589-79047590	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs535627093	chr9:79047652-79047653	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs539334344	chr9:79047697-79047698	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs368362698	chr9:79047722-79047723	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs552938398	chr9:79047735-79047736	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs138732459	chr9:79047760-79047761	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs79493834	chr9:79047768-79047769	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs555014924	chr9:79047840-79047841	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs12350292	chr9:79047890-79047891	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs532035130	chr9:79047923-79047924	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs576712167	chr9:79047940-79047941	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs113388050	chr9:79047956-79047957	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs149314436	chr9:79047995-79047996	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs576658815	chr9:79048016-79048017	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs545670370	chr9:79048060-79048061	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs559243181	chr9:79048073-79048074	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs192928069	chr9:79048074-79048075	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs541468780	chr9:79048094-79048095	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs561777441	chr9:79048098-79048099	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs79729378	chr9:79048115-79048116	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs12552376	chr9:79048155-79048156	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs563714855	chr9:79048174-79048175	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs532785183	chr9:79048179-79048180	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs4745549	chr9:79048219-79048220	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs375489874	chr9:79048225-79048226	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs185027715	chr9:79048228-79048229	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs566393504	chr9:79048253-79048254	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs188742120	chr9:79048289-79048290	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:61)

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
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
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
Glioblastoma multiforme	21750150	CNVD
Cancer	21183584	CNVD
Bipolar disorder	18458673	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Intellectual disability	22102821	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Wilms tumour	21544195	CNVD
Melanoma	17363583	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:221 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79046000-79047200	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr9:79046200-79047200	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr9:79046200-79048600	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr9:79046400-79047600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:79046400-79047800	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr9:79046400-79047800	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr9:79046400-79048000	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr9:79047000-79047200	Weak transcription	HepG2	liver
9	chr9:79047000-79047400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr9:79047000-79047800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr9:79047000-79048000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr9:79047200-79049200	Enhancers	HepG2	liver
13	chr9:79047400-79047600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr9:79047400-79049400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:79047600-79048400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr9:79047800-79048000	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr9:79048000-79048200	Enhancers	H9 Cell Line	embryonic stem cell
18	chr9:79048000-79049400	Enhancers	Muscle Satellite Cultured Cells	--
19	chr9:79048000-79049400	Enhancers	NH-A	brain
20	chr9:79048000-79049400	Enhancers	Osteobl	bone
21	chr9:79048200-79048600	Enhancers	Esophagus	oesophagus
22	chr9:79048200-79049200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr9:79048200-79049200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr9:79048200-79049200	Enhancers	A549	lung
25	chr9:79048200-79049200	Enhancers	GM12878-XiMat	blood
26	chr9:79048200-79049400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr9:79048400-79048600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr9:79048400-79048600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr9:79048400-79048600	Enhancers	Colonic Mucosa	Colon
30	chr9:79048400-79048800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr9:79048400-79049000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr9:79048400-79049200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr9:79048400-79049200	Enhancers	HMEC	breast
34	chr9:79048400-79049400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr9:79048600-79049200	Enhancers	NHDF-Ad	bronchial
36	chr9:79048600-79049400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr9:79049200-79050200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr9:79049200-79050200	Weak transcription	HepG2	liver
39	chr9:79049200-79050400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr9:79049400-79055400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr9:79049400-79055400	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr9:79049400-79055400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr9:79049400-79055400	Weak transcription	Osteobl	bone
44	chr9:79049400-79056400	Weak transcription	NH-A	brain
45	chr9:79049800-79050600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr9:79049800-79050600	Enhancers	Stomach Mucosa	stomach
47	chr9:79050200-79050400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr9:79050200-79051400	Enhancers	HepG2	liver
49	chr9:79050400-79050800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr9:79050800-79052200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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