Variant report

Variant	esv2758181
Chromosome Location	chr9:12235048-12621991
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	chr9:12604207-12604421	H1-hESC	embryonic stem cell:	n/a	chr9:12604278-12604292
3	BACH1	chr9:12497880-12498136	H1-hESC	embryonic stem cell:	n/a	n/a
4	BACH1	chr9:12567176-12567212	H1-hESC	embryonic stem cell:	n/a	n/a
5	BACH1	chr9:12469180-12469392	H1-hESC	embryonic stem cell:	n/a	n/a
6	BACH1	chr9:12292536-12292567	H1-hESC	embryonic stem cell:	n/a	n/a
7	BACH1	chr9:12465730-12465736	H1-hESC	embryonic stem cell:	n/a	n/a
8	BATF	chr9:12329455-12329670	GM12878	blood:	n/a	n/a
9	BCLAF1	chr9:12329426-12329668	GM12878	blood:	n/a	n/a
10	BHLHE40	chr9:12414650-12414651	HepG2	liver:	n/a	n/a
11	BHLHE40	chr9:12329021-12329257	GM12878	blood:	n/a	n/a
12	BHLHE40	chr9:12612186-12612202	GM12878	blood:	n/a	n/a
13	BHLHE40	chr9:12328884-12329725	HepG2	liver:	n/a	n/a
14	BHLHE40	chr9:12328995-12329158	K562	blood:	n/a	n/a
15	BRCA1	chr9:12368889-12368916	GM12878	blood:	n/a	n/a
16	CEBPB	chr9:12607483-12607778	IMR90	lung:	n/a	chr9:12607616-12607627 chr9:12607571-12607582
17	CEBPB	chr9:12447532-12447761	IMR90	lung:	n/a	chr9:12447635-12447646
18	CEBPB	chr9:12473244-12473438	A549	lung:	n/a	n/a
19	CEBPB	chr9:12503780-12504174	MCF-7	breast:	n/a	chr9:12503986-12503998
20	CEBPB	chr9:12537944-12538164	HepG2	liver:	n/a	chr9:12538015-12538032 chr9:12537992-12538003 chr9:12538016-12538029
21	CEBPB	chr9:12447528-12447785	HepG2	liver:	n/a	chr9:12447635-12447646
22	CEBPB	chr9:12473238-12473507	IMR90	lung:	n/a	n/a
23	CEBPB	chr9:12447570-12447769	H1-hESC	embryonic stem cell:	n/a	chr9:12447635-12447646
24	CEBPB	chr9:12491079-12491286	A549	lung:	n/a	n/a
25	CEBPB	chr9:12367335-12367535	HepG2	liver:	n/a	chr9:12367443-12367454
26	CEBPB	chr9:12537932-12538011	K562	blood:	n/a	chr9:12537992-12538003
27	CEBPB	chr9:12553870-12554030	IMR90	lung:	n/a	chr9:12553921-12553932 chr9:12553919-12553930
28	CEBPB	chr9:12288039-12288167	HepG2	liver:	n/a	n/a
29	CEBPB	chr9:12553807-12553971	HepG2	liver:	n/a	chr9:12553921-12553932 chr9:12553919-12553930
30	CEBPB	chr9:12503775-12504054	MCF-7	breast:	n/a	chr9:12503986-12503998
31	CEBPB	chr9:12447534-12447781	A549	lung:	n/a	chr9:12447635-12447646
32	CEBPB	chr9:12539775-12539867	HepG2	liver:	n/a	n/a
33	CEBPB	chr9:12607448-12607767	HepG2	liver:	n/a	chr9:12607616-12607627 chr9:12607571-12607582
34	CEBPB	chr9:12450499-12450835	HepG2	liver:	n/a	chr9:12450652-12450663
35	CHD1	chr9:12314638-12314797	GM12878	blood:	n/a	n/a
36	CHD2	chr9:12314733-12314838	GM12878	blood:	n/a	n/a
37	CHD2	chr9:12319226-12319370	GM12878	blood:	n/a	n/a
38	CTCF	chr9:12465080-12465230	HBMEC	blood vessel:	n/a	chr9:12465092-12465113 chr9:12465098-12465114 chr9:12465097-12465115 chr9:12465100-12465110
39	CTCF	chr9:12329460-12329610	HFF	foreskin:	n/a	n/a
40	CTCF	chr9:12329520-12329670	GM12868	blood:	n/a	n/a
41	CTCF	chr9:12329520-12329670	A549	lung:	n/a	n/a
42	CTCF	chr9:12329423-12329765	A549	lung:	n/a	n/a
43	CTCF	chr9:12329500-12329650	K562	blood:	n/a	n/a
44	CTCF	chr9:12554780-12554930	HVMF	connective:	n/a	chr9:12554829-12554847 chr9:12554832-12554845
45	CTCF	chr9:12464960-12465110	HCT-116	colon:	n/a	chr9:12465100-12465110
46	CTCF	chr9:12329500-12329650	AG04449	skin:	n/a	n/a
47	CTCF	chr9:12464640-12464790	GM12868	blood:	n/a	n/a
48	CTCF	chr9:12465160-12465310	A549	lung:	n/a	n/a
49	CTCF	chr9:12554720-12554870	HUVEC	blood vessel:	n/a	chr9:12554829-12554847 chr9:12554832-12554845
50	CTCF	chr9:12554720-12554870	SAEC	small airway:	n/a	chr9:12554829-12554847 chr9:12554832-12554845

No.	Distal block	Cell Line	Cell type
1	chr9:12554435..12555308-chr9:12639713..12640600,2	MCF-7	breast:
2	chr9:12526692..12528486-chr9:12531576..12533111,2	MCF-7	breast:
3	chr9:10855600..10856394-chr9:12425953..12426703,2	MCF-7	breast:
4	chr9:12268631..12271178-chr9:12273434..12276211,2	K562	blood:
5	chr1:149223798..149224416-chr9:12526808..12527328,4	MCF-7	breast:
6	chr9:12494239..12495105-chr9:12503977..12504835,2	MCF-7	breast:
7	chr9:12268631..12271178-chr9:12273434..12276211,2	K562	blood:
8	chr6:116381055..116381867-chr9:12405688..12406208,2	Hela-S3	cervix:
9	chr9:12526692..12528486-chr9:12531576..12533111,2	MCF-7	breast:
10	chr9:12607055..12609983-chr9:12671838..12674027,2	K562	blood:
11	chr9:12495478..12497603-chr9:12499554..12502350,2	MCF-7	breast:
12	chr9:10855828..10856443-chr9:12329128..12329639,2	MCF-7	breast:
13	chr16:89002000..89004763-chr9:12244429..12246932,2	MCF-7	breast:
14	chr1:186649939..186650766-chr9:12429991..12430491,2	Hela-S3	cervix:
15	chr9:12425929..12426463-chr9:12464660..12465379,2	MCF-7	breast:
16	chr8:43095234..43095797-chr9:12480274..12480774,2	MCF-7	breast:
17	chr9:12615022..12617476-chr9:12617492..12619010,2	MCF-7	breast:
18	chr9:12425929..12426463-chr9:12464660..12465379,2	MCF-7	breast:
19	chr9:12495478..12497603-chr9:12499554..12502350,2	MCF-7	breast:
20	chr9:10365979..10366914-chr9:12329143..12329893,2	MCF-7	breast:
21	chr9:12615022..12617476-chr9:12617492..12619010,2	MCF-7	breast:
22	chr9:12494239..12495105-chr9:12503977..12504835,2	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
ENSG00000261226	chromatin interactions
ENSG00000206737	chromatin interactions

Extended variants
information (count: 5733 )
Associated
traits (count: 108 )

Variant overlapped rSNPs/rCNVs (count:5733 , 50 per page) page: 1 2 3 4 5 6 7 ... 115

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs946453	chr9:12235226-12235227	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs59539787	chr9:12235243-12235244	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs76780532	chr9:12235250-12235251	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs545229394	chr9:12235266-12235267	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs565478227	chr9:12235286-12235287	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs368720079	chr9:12235306-12235307	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs372162513	chr9:12235321-12235322	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs147300150	chr9:12235352-12235353	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs528889468	chr9:12235362-12235363	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs371390976	chr9:12235369-12235370	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs184687841	chr9:12235404-12235405	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs546666674	chr9:12235429-12235430	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs566437742	chr9:12235433-12235434	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs57234100	chr9:12235436-12235437	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs189104100	chr9:12235437-12235438	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs117793314	chr9:12235462-12235463	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs537681030	chr9:12235464-12235465	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs554419124	chr9:12235499-12235500	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs78210800	chr9:12235509-12235510	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs191959861	chr9:12235544-12235545	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs74701843	chr9:12235567-12235568	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs563670855	chr9:12235581-12235582	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs184991740	chr9:12235585-12235586	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs545505671	chr9:12235592-12235593	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs190962155	chr9:12241211-12241212	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs148655514	chr9:12241220-12241221	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs570770668	chr9:12241222-12241223	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs539760876	chr9:12241224-12241225	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs555713248	chr9:12241225-12241226	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs180961323	chr9:12241249-12241250	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs368946190	chr9:12241261-12241262	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs535468016	chr9:12241262-12241263	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs142889908	chr9:12241309-12241310	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs572151858	chr9:12241324-12241325	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs147688592	chr9:12241369-12241370	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs185311247	chr9:12241394-12241395	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs577971284	chr9:12241410-12241411	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs543758730	chr9:12241414-12241415	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs563611960	chr9:12241417-12241418	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs576352325	chr9:12241430-12241431	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs79422830	chr9:12241459-12241460	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs190417008	chr9:12241465-12241466	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs183049648	chr9:12241477-12241478	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs142379488	chr9:12241533-12241534	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs188082610	chr9:12241537-12241538	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs7042933	chr9:12241558-12241559	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
47	rs10809740	chr9:12241585-12241586	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
48	rs146353964	chr9:12241589-12241590	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs191682903	chr9:12241631-12241632	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs548965371	chr9:12241637-12241638	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:108)

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
Acute myeloid leukemia	21251322	CNVD
Breast cancer	21611746	CNVD
Melanoma	22183965	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Autism	20858261	CNVD
Epilepsy	20858261	CNVD
Mental retardation	20858261	CNVD
Chordoma	21215367	CNVD
Renal cell carcinoma	21215367	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:334 , 50 per page) page: 1 2 3 4 5 6 7

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12235200-12235600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr9:12241200-12242000	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr9:12241400-12243200	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr9:12241600-12242000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr9:12241600-12242000	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr9:12241600-12242000	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr9:12241600-12242000	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr9:12241600-12242000	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr9:12242600-12242800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
10	chr9:12260800-12261200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr9:12271200-12271600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr9:12271200-12274800	Enhancers	Rectal Smooth Muscle	rectum
13	chr9:12271200-12275200	Enhancers	Fetal Brain Male	brain
14	chr9:12271400-12271600	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr9:12271400-12272000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr9:12271400-12273400	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr9:12271600-12272000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr9:12271600-12272000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr9:12271600-12272600	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr9:12271600-12272800	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr9:12271600-12274400	Enhancers	Colon Smooth Muscle	Colon
22	chr9:12271600-12276600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr9:12271600-12277600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr9:12272000-12272400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr9:12272000-12273000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:12272400-12272800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr9:12272400-12273000	Enhancers	Brain Cingulate Gyrus	brain
28	chr9:12272400-12273400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr9:12272400-12274000	Enhancers	Fetal Stomach	stomach
30	chr9:12272600-12272800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr9:12272600-12273200	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr9:12272600-12273200	Enhancers	Brain Angular Gyrus	brain
33	chr9:12272800-12273200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr9:12273000-12273600	Enhancers	Fetal Brain Female	brain
35	chr9:12273200-12275800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:12273400-12276200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr9:12273600-12274600	Weak transcription	Fetal Brain Female	brain
38	chr9:12274000-12275200	Enhancers	Brain Hippocampus Middle	brain
39	chr9:12274600-12275000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr9:12274800-12275000	Enhancers	Brain Angular Gyrus	brain
41	chr9:12274800-12275000	Enhancers	Fetal Brain Female	brain
42	chr9:12275800-12277600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr9:12276200-12276400	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr9:12276400-12277000	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr9:12276600-12277000	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr9:12280800-12281000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr9:12283000-12284000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr9:12284000-12284400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr9:12284400-12284600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr9:12284600-12285400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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