Variant report

Variant	esv34901
Chromosome Location	chr9:12283944-12589068
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	chr9:12328968-12329168	HepG2	liver:	n/a	n/a
2	BACH1	chr9:12292536-12292567	H1-hESC	embryonic stem cell:	n/a	n/a
3	BACH1	chr9:12469180-12469392	H1-hESC	embryonic stem cell:	n/a	n/a
4	BACH1	chr9:12497880-12498136	H1-hESC	embryonic stem cell:	n/a	n/a
5	BACH1	chr9:12465730-12465736	H1-hESC	embryonic stem cell:	n/a	n/a
6	BACH1	chr9:12567176-12567212	H1-hESC	embryonic stem cell:	n/a	n/a
7	BATF	chr9:12329455-12329670	GM12878	blood:	n/a	n/a
8	BCLAF1	chr9:12329426-12329668	GM12878	blood:	n/a	n/a
9	BHLHE40	chr9:12328884-12329725	HepG2	liver:	n/a	n/a
10	BHLHE40	chr9:12328995-12329158	K562	blood:	n/a	n/a
11	BHLHE40	chr9:12414650-12414651	HepG2	liver:	n/a	n/a
12	BHLHE40	chr9:12329021-12329257	GM12878	blood:	n/a	n/a
13	BRCA1	chr9:12368889-12368916	GM12878	blood:	n/a	n/a
14	CEBPB	chr9:12447534-12447781	A549	lung:	n/a	chr9:12447635-12447646
15	CEBPB	chr9:12447532-12447761	IMR90	lung:	n/a	chr9:12447635-12447646
16	CEBPB	chr9:12537932-12538011	K562	blood:	n/a	chr9:12537992-12538003
17	CEBPB	chr9:12553807-12553971	HepG2	liver:	n/a	chr9:12553921-12553932 chr9:12553919-12553930
18	CEBPB	chr9:12367335-12367535	HepG2	liver:	n/a	chr9:12367443-12367454
19	CEBPB	chr9:12450499-12450835	HepG2	liver:	n/a	chr9:12450652-12450663
20	CEBPB	chr9:12473244-12473438	A549	lung:	n/a	n/a
21	CEBPB	chr9:12503780-12504174	MCF-7	breast:	n/a	chr9:12503986-12503998
22	CEBPB	chr9:12447570-12447769	H1-hESC	embryonic stem cell:	n/a	chr9:12447635-12447646
23	CEBPB	chr9:12503775-12504054	MCF-7	breast:	n/a	chr9:12503986-12503998
24	CEBPB	chr9:12473238-12473507	IMR90	lung:	n/a	n/a
25	CEBPB	chr9:12288039-12288167	HepG2	liver:	n/a	n/a
26	CEBPB	chr9:12553870-12554030	IMR90	lung:	n/a	chr9:12553921-12553932 chr9:12553919-12553930
27	CEBPB	chr9:12539775-12539867	HepG2	liver:	n/a	n/a
28	CEBPB	chr9:12537944-12538164	HepG2	liver:	n/a	chr9:12538015-12538032 chr9:12537992-12538003 chr9:12538016-12538029
29	CEBPB	chr9:12491079-12491286	A549	lung:	n/a	n/a
30	CEBPB	chr9:12447528-12447785	HepG2	liver:	n/a	chr9:12447635-12447646
31	CHD1	chr9:12314638-12314797	GM12878	blood:	n/a	n/a
32	CHD2	chr9:12319226-12319370	GM12878	blood:	n/a	n/a
33	CHD2	chr9:12314733-12314838	GM12878	blood:	n/a	n/a
34	CTCF	chr9:12329520-12329670	A549	lung:	n/a	n/a
35	CTCF	chr9:12329500-12329650	HCFaa	heart:	n/a	n/a
36	CTCF	chr9:12426300-12426450	HRE	kidney:	n/a	chr9:12426384-12426405
37	CTCF	chr9:12465020-12465170	Hela-S3	cervix:	n/a	chr9:12465092-12465113 chr9:12465098-12465114 chr9:12465097-12465115 chr9:12465100-12465110
38	CTCF	chr9:12329520-12329670	AG09319	gingival:	n/a	n/a
39	CTCF	chr9:12426360-12426510	HRE	kidney:	n/a	chr9:12426384-12426405
40	CTCF	chr9:12465020-12465170	HMEC	breast:	n/a	chr9:12465092-12465113 chr9:12465098-12465114 chr9:12465097-12465115 chr9:12465100-12465110
41	CTCF	chr9:12465000-12465150	MCF-7	breast:	n/a	chr9:12465092-12465113 chr9:12465098-12465114 chr9:12465097-12465115 chr9:12465100-12465110
42	CTCF	chr9:12426302-12426522	LNCaP	prostate:	n/a	chr9:12426384-12426405
43	CTCF	chr9:12426360-12426510	NHDF-neo	bronchial:	n/a	chr9:12426384-12426405
44	CTCF	chr9:12464960-12465110	HEK293	kidney:	n/a	chr9:12465100-12465110
45	CTCF	chr9:12329309-12329662	MCF-7	breast:	n/a	n/a
46	CTCF	chr9:12329500-12329650	K562	blood:	n/a	n/a
47	CTCF	chr9:12554700-12554850	GM06990	blood:	n/a	chr9:12554829-12554847 chr9:12554832-12554845
48	CTCF	chr9:12465353-12465469	GM10248	blood:	n/a	n/a
49	CTCF	chr9:12554600-12554750	A549	lung:	n/a	n/a
50	CTCF	chr9:12465022-12465202	Gliobla	brain:	n/a	chr9:12465092-12465113 chr9:12465098-12465114 chr9:12465097-12465115 chr9:12465100-12465110

No.	Distal block	Cell Line	Cell type
1	chr1:186649939..186650766-chr9:12429991..12430491,2	Hela-S3	cervix:
2	chr9:12425929..12426463-chr9:12464660..12465379,2	MCF-7	breast:
3	chr9:10855600..10856394-chr9:12425953..12426703,2	MCF-7	breast:
4	chr1:149223798..149224416-chr9:12526808..12527328,4	MCF-7	breast:
5	chr9:12425929..12426463-chr9:12464660..12465379,2	MCF-7	breast:
6	chr9:12494239..12495105-chr9:12503977..12504835,2	MCF-7	breast:
7	chr6:116381055..116381867-chr9:12405688..12406208,2	Hela-S3	cervix:
8	chr9:12494239..12495105-chr9:12503977..12504835,2	MCF-7	breast:
9	chr9:12526692..12528486-chr9:12531576..12533111,2	MCF-7	breast:
10	chr8:43095234..43095797-chr9:12480274..12480774,2	MCF-7	breast:
11	chr9:12495478..12497603-chr9:12499554..12502350,2	MCF-7	breast:
12	chr9:12554435..12555308-chr9:12639713..12640600,2	MCF-7	breast:
13	chr9:10855828..10856443-chr9:12329128..12329639,2	MCF-7	breast:
14	chr9:12495478..12497603-chr9:12499554..12502350,2	MCF-7	breast:
15	chr9:10365979..10366914-chr9:12329143..12329893,2	MCF-7	breast:
16	chr9:12526692..12528486-chr9:12531576..12533111,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TYRP1-4	chr9:12287320-12288238	NONHSAT130222

Variant related genes	Relation type
ENSG00000231491	TF binding region
RNU2-47P	TF binding region
ENSG00000206737	chromatin interactions

Extended variants
information (count: 4577 )
Associated
traits (count: 106 )

Variant overlapped rSNPs/rCNVs (count:4577 , 50 per page) page: 1 2 3 4 5 6 7 ... 92

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs7853256	chr9:12283944-12283945	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs570522080	chr9:12283968-12283969	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs34824379	chr9:12283973-12283974	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs12342082	chr9:12284003-12284004	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs375796200	chr9:12284126-12284127	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs75198008	chr9:12284139-12284140	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs541669739	chr9:12284152-12284153	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs77241848	chr9:12284155-12284156	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs146046048	chr9:12284206-12284207	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs572025282	chr9:12284211-12284212	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs376894630	chr9:12284232-12284233	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs140186196	chr9:12284236-12284237	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs12351366	chr9:12284252-12284253	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs78813827	chr9:12284282-12284283	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs75673591	chr9:12284285-12284286	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs562927619	chr9:12284290-12284291	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs531962258	chr9:12284300-12284301	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs139346557	chr9:12284391-12284392	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs186398561	chr9:12284400-12284401	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs12380267	chr9:12284426-12284427	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs527997035	chr9:12284435-12284436	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs149913317	chr9:12284456-12284457	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs569975158	chr9:12284489-12284490	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs35033906	chr9:12284526-12284527	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs570474602	chr9:12284561-12284562	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs377685258	chr9:12284581-12284582	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs535406671	chr9:12284600-12284601	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs144941110	chr9:12284603-12284604	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs149044506	chr9:12284609-12284610	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs10809748	chr9:12284611-12284612	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs142262385	chr9:12284665-12284666	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs71306715	chr9:12284666-12284667	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs398040367	chr9:12284686-12284687	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs535605936	chr9:12284687-12284688	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs555153340	chr9:12284746-12284747	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs565592490	chr9:12284788-12284789	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs534650838	chr9:12284792-12284793	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs190559160	chr9:12284839-12284840	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs577205080	chr9:12284874-12284875	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs181475977	chr9:12284909-12284910	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs565569148	chr9:12284935-12284936	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs145781600	chr9:12284969-12284970	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs576474220	chr9:12284995-12284996	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs542399347	chr9:12285013-12285014	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs534701451	chr9:12285018-12285019	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs186372617	chr9:12285035-12285036	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs190870020	chr9:12285065-12285066	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs557608851	chr9:12285105-12285106	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs527988488	chr9:12285118-12285119	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs34860556	chr9:12285122-12285123	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:106)

Disease	PMID	Source
Disorders of sex development	21048976	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
Chronic lymphocytic leukemia	21546498	CNVD
abnormal development	18461090	CNVD
Glioblastoma multiforme	21080181	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
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
Intellectual disability	22102821	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
Breast cancer	21364760	CNVD
Myelofibrosis	22110671	CNVD
Glioblastoma	19074898	CNVD
Malignant melanoma	19074898	CNVD
Prostate cancer	16573809	CNVD
Metanephric adenoma	20802469	CNVD
Cancer	20164920	CNVD
Developmental delay	21147756	CNVD
small cell lung cancer	21764851	CNVD
Glioblastoma multiforme	22286061	CNVD
Glioma	17123091	CNVD
Lung cancer	16773561	CNVD
Colorectal cancer	16272173	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Gastric cancer	16891809	CNVD
Mental retardation	17847001	CNVD
Cutaneous squamous cell carcinomas	17420988	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Pilocytic astrocytoma	18670637	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Breast cancer	21611746	CNVD
Melanoma	22183965	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Autism	20858261	CNVD
Epilepsy	20858261	CNVD
Mental retardation	20858261	CNVD
Chordoma	21215367	CNVD
Renal cell carcinoma	21215367	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:270 , 50 per page) page: 1 2 3 4 5 6

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12283000-12284000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:12284000-12284400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:12284400-12284600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr9:12284600-12285400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr9:12285400-12285600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:12285600-12285800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr9:12289600-12290200	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr9:12289600-12290200	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr9:12289600-12290200	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr9:12289600-12290200	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr9:12289600-12290400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr9:12289800-12290200	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr9:12289800-12290200	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr9:12289800-12290200	Enhancers	Brain Germinal Matrix	brain
15	chr9:12289800-12290400	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr9:12289800-12290400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:12289800-12290600	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr9:12290000-12290600	Enhancers	Brain Cingulate Gyrus	brain
19	chr9:12290000-12290600	Enhancers	Brain Hippocampus Middle	brain
20	chr9:12290000-12291000	Enhancers	Brain Substantia Nigra	brain
21	chr9:12290200-12290800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr9:12292200-12293000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr9:12294200-12294600	Active TSS	Fetal Lung	lung
24	chr9:12302000-12302400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr9:12314400-12317200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr9:12318800-12319800	Enhancers	Adipose Nuclei	Adipose
27	chr9:12324000-12324400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr9:12324400-12329000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr9:12328800-12329000	Enhancers	Liver	Liver
30	chr9:12328800-12329000	Enhancers	Pancreas	Pancrea
31	chr9:12329000-12329200	Enhancers	Adipose Nuclei	Adipose
32	chr9:12329000-12329200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr9:12329000-12329200	Enhancers	Fetal Muscle Trunk	muscle
34	chr9:12329000-12329400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr9:12329000-12329400	Flanking Active TSS	Liver	Liver
36	chr9:12329000-12329600	Active TSS	ES-I3 Cell Line	embryonic stem cell
37	chr9:12329000-12329600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr9:12329000-12329600	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr9:12329000-12329600	Flanking Active TSS	Pancreas	Pancrea
40	chr9:12329000-12329600	Active TSS	HepG2	liver
41	chr9:12329200-12329400	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr9:12329200-12329400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr9:12329200-12329600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr9:12329200-12329600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr9:12329200-12329600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr9:12329200-12329600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr9:12329200-12329600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr9:12329200-12329600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr9:12329200-12329600	Flanking Active TSS	Adipose Nuclei	Adipose
50	chr9:12329200-12329600	Active TSS	Brain Angular Gyrus	brain

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