Variant report

Variant	esv2756677
Chromosome Location	chr9:12243400-12440000
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:499)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:499 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

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	BATF	chr9:12329455-12329670	GM12878	blood:	n/a	n/a
4	BCLAF1	chr9:12329426-12329668	GM12878	blood:	n/a	n/a
5	BHLHE40	chr9:12414650-12414651	HepG2	liver:	n/a	n/a
6	BHLHE40	chr9:12328884-12329725	HepG2	liver:	n/a	n/a
7	BHLHE40	chr9:12329021-12329257	GM12878	blood:	n/a	n/a
8	BHLHE40	chr9:12328995-12329158	K562	blood:	n/a	n/a
9	BRCA1	chr9:12368889-12368916	GM12878	blood:	n/a	n/a
10	CEBPB	chr9:12288039-12288167	HepG2	liver:	n/a	n/a
11	CEBPB	chr9:12367335-12367535	HepG2	liver:	n/a	chr9:12367443-12367454
12	CHD1	chr9:12314638-12314797	GM12878	blood:	n/a	n/a
13	CHD2	chr9:12319226-12319370	GM12878	blood:	n/a	n/a
14	CHD2	chr9:12314733-12314838	GM12878	blood:	n/a	n/a
15	CTCF	chr9:12329500-12329650	AG04450	lung:	n/a	n/a
16	CTCF	chr9:12329423-12329765	A549	lung:	n/a	n/a
17	CTCF	chr9:12329180-12329330	HRE	kidney:	n/a	n/a
18	CTCF	chr9:12329480-12329630	NHEK	skin:	n/a	n/a
19	CTCF	chr9:12329460-12329610	HVMF	connective:	n/a	n/a
20	CTCF	chr9:12401600-12401750	NHDF-neo	bronchial:	n/a	n/a
21	CTCF	chr9:12329480-12329630	HA-sp	spinal cord:	n/a	n/a
22	CTCF	chr9:12426300-12426450	HPAF	blood vessel:	n/a	chr9:12426384-12426405
23	CTCF	chr9:12426300-12426450	NHDF-neo	bronchial:	n/a	chr9:12426384-12426405
24	CTCF	chr9:12426300-12426450	HMEC	breast:	n/a	chr9:12426384-12426405
25	CTCF	chr9:12329322-12329716	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr9:12329480-12329630	GM12864	blood:	n/a	n/a
27	CTCF	chr9:12426298-12426529	LNCaP	prostate:	n/a	chr9:12426384-12426405
28	CTCF	chr9:12329480-12329630	WERI-Rb-1	eye:	n/a	n/a
29	CTCF	chr9:12329800-12329950	AG04449	skin:	n/a	n/a
30	CTCF	chr9:12329520-12329670	HRPEpiC	eye:	n/a	n/a
31	CTCF	chr9:12329460-12329610	AG04450	lung:	n/a	n/a
32	CTCF	chr9:12329500-12329650	GM12873	blood:	n/a	n/a
33	CTCF	chr9:12426320-12426470	NB4	blood:	n/a	chr9:12426384-12426405
34	CTCF	chr9:12329451-12329695	Lung_OC	lung:	n/a	n/a
35	CTCF	chr9:12329520-12329670	HCM	heart:	n/a	n/a
36	CTCF	chr9:12329309-12329364	MCF-7	breast:	n/a	n/a
37	CTCF	chr9:12426342-12426459	Hela-S3	cervix:	n/a	chr9:12426384-12426405
38	CTCF	chr9:12329480-12329630	GM12865	blood:	n/a	n/a
39	CTCF	chr9:12329520-12329670	GM12867	blood:	n/a	n/a
40	CTCF	chr9:12329520-12329670	GM12870	blood:	n/a	n/a
41	CTCF	chr9:12329500-12329650	WERI-Rb-1	eye:	n/a	n/a
42	CTCF	chr9:12319380-12319530	MCF-7	breast:	n/a	n/a
43	CTCF	chr9:12329460-12329610	HFF	foreskin:	n/a	n/a
44	CTCF	chr9:12329480-12329630	RPTEC	kidney:	n/a	n/a
45	CTCF	chr9:12329420-12329696	MCF-7	breast:	n/a	n/a
46	CTCF	chr9:12328920-12329070	WERI-Rb-1	eye:	n/a	n/a
47	CTCF	chr9:12426260-12426410	SK-N-SH_RA	brain:	n/a	chr9:12426384-12426405
48	CTCF	chr9:12426500-12426650	SK-N-SH_RA	brain:	n/a	n/a
49	CTCF	chr9:12329407-12329722	Gliobla	brain:	n/a	n/a
50	CTCF	chr9:12329460-12329610	HCT-116	colon:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:12268631..12271178-chr9:12273434..12276211,2	K562	blood:
2	chr9:10855600..10856394-chr9:12425953..12426703,2	MCF-7	breast:
3	chr9:10855828..10856443-chr9:12329128..12329639,2	MCF-7	breast:
4	chr6:116381055..116381867-chr9:12405688..12406208,2	Hela-S3	cervix:
5	chr9:12268631..12271178-chr9:12273434..12276211,2	K562	blood:
6	chr9:12425929..12426463-chr9:12464660..12465379,2	MCF-7	breast:
7	chr9:10365979..10366914-chr9:12329143..12329893,2	MCF-7	breast:
8	chr1:186649939..186650766-chr9:12429991..12430491,2	Hela-S3	cervix:
9	chr16:89002000..89004763-chr9:12244429..12246932,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

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

No data

Variant related genes	Relation type
ENSG00000231491	TF binding region
RNU2-47P	TF binding region
ENSG00000261226	chromatin interactions

Extended variants
information (count: 3008 )
Associated
traits (count: 107 )

Variant overlapped rSNPs/rCNVs (count:3008 , 50 per page) page: 1 2 3 4 5 6 7 ... 61

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs375728816	chr9:12244439-12244440	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs367860407	chr9:12244454-12244455	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs7866722	chr9:12244458-12244459	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs567019684	chr9:12244461-12244462	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs539186943	chr9:12244502-12244503	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs115944769	chr9:12244519-12244520	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs187633690	chr9:12244527-12244528	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs192378425	chr9:12244610-12244611	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs140819313	chr9:12244614-12244615	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs369302910	chr9:12244625-12244626	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs182761403	chr9:12244643-12244644	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs574333033	chr9:12244648-12244649	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs539880671	chr9:12244661-12244662	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs114316704	chr9:12244688-12244689	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs77387421	chr9:12244720-12244721	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs188083965	chr9:12244721-12244722	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs545561830	chr9:12244723-12244724	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs562565626	chr9:12244737-12244738	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs10809742	chr9:12244743-12244744	Inactive region	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs541742394	chr9:12244759-12244760	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs571560500	chr9:12244767-12244768	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs374589047	chr9:12244772-12244773	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs111529794	chr9:12244783-12244784	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs192901181	chr9:12244786-12244787	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs534056419	chr9:12244817-12244818	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs547020530	chr9:12244852-12244853	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs566929770	chr9:12244854-12244855	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs532668266	chr9:12244868-12244869	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs552774945	chr9:12244875-12244876	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs553877885	chr9:12244944-12244945	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs538464136	chr9:12244961-12244962	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs554951823	chr9:12244975-12244976	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs568779474	chr9:12245046-12245047	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs184681997	chr9:12245071-12245072	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs533496337	chr9:12245095-12245096	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs553055003	chr9:12245165-12245166	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs553370297	chr9:12245200-12245201	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs189122175	chr9:12245209-12245210	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs545473253	chr9:12245225-12245226	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs556257914	chr9:12245233-12245234	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs576148764	chr9:12245243-12245244	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs144689982	chr9:12245245-12245246	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs576612943	chr9:12245255-12245256	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs561789176	chr9:12245257-12245258	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs191975731	chr9:12245275-12245276	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs527591669	chr9:12245283-12245284	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs185007248	chr9:12245303-12245304	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs551117611	chr9:12245315-12245316	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs560495682	chr9:12245350-12245351	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs373479920	chr9:12245491-12245492	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:107)

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

Chromatin state (count:160 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12260800-12261200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:12271200-12271600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:12271200-12274800	Enhancers	Rectal Smooth Muscle	rectum
4	chr9:12271200-12275200	Enhancers	Fetal Brain Male	brain
5	chr9:12271400-12271600	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr9:12271400-12272000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr9:12271400-12273400	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr9:12271600-12272000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:12271600-12272000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr9:12271600-12272600	Enhancers	Duodenum Smooth Muscle	Duodenum
11	chr9:12271600-12272800	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr9:12271600-12274400	Enhancers	Colon Smooth Muscle	Colon
13	chr9:12271600-12276600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr9:12271600-12277600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr9:12272000-12272400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr9:12272000-12273000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr9:12272400-12272800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr9:12272400-12273000	Enhancers	Brain Cingulate Gyrus	brain
19	chr9:12272400-12273400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr9:12272400-12274000	Enhancers	Fetal Stomach	stomach
21	chr9:12272600-12272800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr9:12272600-12273200	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr9:12272600-12273200	Enhancers	Brain Angular Gyrus	brain
24	chr9:12272800-12273200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:12273000-12273600	Enhancers	Fetal Brain Female	brain
26	chr9:12273200-12275800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr9:12273400-12276200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr9:12273600-12274600	Weak transcription	Fetal Brain Female	brain
29	chr9:12274000-12275200	Enhancers	Brain Hippocampus Middle	brain
30	chr9:12274600-12275000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr9:12274800-12275000	Enhancers	Brain Angular Gyrus	brain
32	chr9:12274800-12275000	Enhancers	Fetal Brain Female	brain
33	chr9:12275800-12277600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr9:12276200-12276400	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr9:12276400-12277000	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr9:12276600-12277000	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr9:12280800-12281000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr9:12283000-12284000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr9:12284000-12284400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr9:12284400-12284600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr9:12284600-12285400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr9:12285400-12285600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr9:12285600-12285800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr9:12289600-12290200	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr9:12289600-12290200	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr9:12289600-12290200	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr9:12289600-12290200	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr9:12289600-12290400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr9:12289800-12290200	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr9:12289800-12290200	Enhancers	iPS-15b Cell Line	embryonic stem cell

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