Variant report

Variant	nsv1015495
Chromosome Location	chr9:12300488-12452015
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	BATF	chr9:12329455-12329670	GM12878	blood:	n/a	n/a
3	BCLAF1	chr9:12329426-12329668	GM12878	blood:	n/a	n/a
4	BHLHE40	chr9:12328995-12329158	K562	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	BRCA1	chr9:12368889-12368916	GM12878	blood:	n/a	n/a
9	CEBPB	chr9:12450499-12450835	HepG2	liver:	n/a	chr9:12450652-12450663
10	CEBPB	chr9:12367335-12367535	HepG2	liver:	n/a	chr9:12367443-12367454
11	CEBPB	chr9:12447570-12447769	H1-hESC	embryonic stem cell:	n/a	chr9:12447635-12447646
12	CEBPB	chr9:12447534-12447781	A549	lung:	n/a	chr9:12447635-12447646
13	CEBPB	chr9:12447528-12447785	HepG2	liver:	n/a	chr9:12447635-12447646
14	CEBPB	chr9:12447532-12447761	IMR90	lung:	n/a	chr9:12447635-12447646
15	CHD1	chr9:12314638-12314797	GM12878	blood:	n/a	n/a
16	CHD2	chr9:12314733-12314838	GM12878	blood:	n/a	n/a
17	CHD2	chr9:12319226-12319370	GM12878	blood:	n/a	n/a
18	CTCF	chr9:12441217-12441234	Lung_OC	lung:	n/a	n/a
19	CTCF	chr9:12329480-12329630	GM12801	blood:	n/a	n/a
20	CTCF	chr9:12329800-12329950	AG09319	gingival:	n/a	n/a
21	CTCF	chr9:12329460-12329610	HAc	cerebellar:	n/a	n/a
22	CTCF	chr9:12329428-12329702	Kidney_OC	kidney:	n/a	n/a
23	CTCF	chr9:12426302-12426522	LNCaP	prostate:	n/a	chr9:12426384-12426405
24	CTCF	chr9:12426320-12426470	NHEK	skin:	n/a	chr9:12426384-12426405
25	CTCF	chr9:12329520-12329670	HRPEpiC	eye:	n/a	n/a
26	CTCF	chr9:12366160-12366310	AG04450	lung:	n/a	n/a
27	CTCF	chr9:12329480-12329630	MCF-7	breast:	n/a	n/a
28	CTCF	chr9:12329440-12329590	WI-38	lung:	n/a	n/a
29	CTCF	chr9:12329520-12329670	HVMF	connective:	n/a	n/a
30	CTCF	chr9:12329434-12329717	LNCaP	prostate:	n/a	n/a
31	CTCF	chr9:12329500-12329650	SK-N-SH_RA	brain:	n/a	n/a
32	CTCF	chr9:12329500-12329650	WERI-Rb-1	eye:	n/a	n/a
33	CTCF	chr9:12426220-12426370	BE2_C	brain:	n/a	n/a
34	CTCF	chr9:12329349-12329714	ECC-1	luminal epithelium:	n/a	n/a
35	CTCF	chr9:12426280-12426430	HEEpiC	esophagus:	n/a	chr9:12426384-12426405
36	CTCF	chr9:12426340-12426490	WERI-Rb-1	eye:	n/a	chr9:12426384-12426405
37	CTCF	chr9:12329280-12329352	GM12892	blood:	n/a	n/a
38	CTCF	chr9:12329500-12329650	HMF	breast:	n/a	n/a
39	CTCF	chr9:12426340-12426490	HPAF	blood vessel:	n/a	chr9:12426384-12426405
40	CTCF	chr9:12329353-12329696	A549	lung:	n/a	n/a
41	CTCF	chr9:12329436-12329697	Pancreas_OC	pancreas:	n/a	n/a
42	CTCF	chr9:12329480-12329630	AG09319	gingival:	n/a	n/a
43	CTCF	chr9:12329480-12329630	GM12866	blood:	n/a	n/a
44	CTCF	chr9:12329500-12329650	Caco-2	colon:	n/a	n/a
45	CTCF	chr9:12329500-12329650	GM12873	blood:	n/a	n/a
46	CTCF	chr9:12329480-12329630	GM06990	blood:	n/a	n/a
47	CTCF	chr9:12329243-12329716	GM12891	blood:	n/a	n/a
48	CTCF	chr9:12439300-12439450	GM12867	blood:	n/a	n/a
49	CTCF	chr9:12450200-12450270	GM10248	blood:	n/a	n/a
50	CTCF	chr9:12329460-12329610	BE2_C	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:10855600..10856394-chr9:12425953..12426703,2	MCF-7	breast:
2	chr9:10365979..10366914-chr9:12329143..12329893,2	MCF-7	breast:
3	chr1:186649939..186650766-chr9:12429991..12430491,2	Hela-S3	cervix:
4	chr9:12425929..12426463-chr9:12464660..12465379,2	MCF-7	breast:
5	chr6:116381055..116381867-chr9:12405688..12406208,2	Hela-S3	cervix:
6	chr9:10855828..10856443-chr9:12329128..12329639,2	MCF-7	breast:

Variant related genes	Relation type
RNU2-47P	TF binding region

Extended variants
information (count: 2503 )
Associated
traits (count: 101 )

Variant overlapped rSNPs/rCNVs (count:2503 , 50 per page) page: 1 2 3 4 5 6 7 ... 51

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs372986878	chr9:12300775-12300776	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs151062630	chr9:12300787-12300788	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs7850595	chr9:12300788-12300789	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs74989230	chr9:12300797-12300798	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs140966083	chr9:12300811-12300812	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs553824082	chr9:12300832-12300833	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs114489021	chr9:12300869-12300870	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs529486368	chr9:12300874-12300875	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs549232249	chr9:12300884-12300885	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs376111643	chr9:12300925-12300926	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs377671181	chr9:12300928-12300929	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs534274575	chr9:12300937-12300938	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs557371176	chr9:12300948-12300949	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs183365806	chr9:12300967-12300968	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs563756960	chr9:12302036-12302037	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs574098756	chr9:12302038-12302039	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs1928884	chr9:12302048-12302049	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs375524769	chr9:12302103-12302104	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs528682482	chr9:12302176-12302177	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs551623093	chr9:12302193-12302194	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs367682984	chr9:12302210-12302211	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs138290838	chr9:12302224-12302225	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs530476172	chr9:12302243-12302244	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs78322594	chr9:12302254-12302255	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs184731127	chr9:12302268-12302269	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs189540640	chr9:12302278-12302279	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs180743345	chr9:12302317-12302318	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs566646789	chr9:12302352-12302353	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs190921276	chr9:12314402-12314403	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs564016166	chr9:12314422-12314423	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs573407570	chr9:12314428-12314429	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs183067327	chr9:12314431-12314432	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs573545770	chr9:12314441-12314442	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs4358892	chr9:12314484-12314485	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs111766491	chr9:12314508-12314509	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs558915074	chr9:12314519-12314520	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs553954810	chr9:12314539-12314540	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs188196329	chr9:12314548-12314549	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs551526215	chr9:12314554-12314555	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs1928880	chr9:12314565-12314566	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs545305265	chr9:12314583-12314584	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs545650295	chr9:12314592-12314593	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs530736379	chr9:12314618-12314619	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs374491117	chr9:12314620-12314621	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs569979552	chr9:12314631-12314632	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs563410988	chr9:12314644-12314645	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs115698361	chr9:12314653-12314654	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs567597487	chr9:12314655-12314656	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs535460843	chr9:12314671-12314672	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs549392746	chr9:12314694-12314695	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:101)

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
Chordoma	21215367	CNVD
Renal cell carcinoma	21215367	CNVD

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12302000-12302400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:12314400-12317200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:12318800-12319800	Enhancers	Adipose Nuclei	Adipose
4	chr9:12324000-12324400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr9:12324400-12329000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr9:12328800-12329000	Enhancers	Liver	Liver
7	chr9:12328800-12329000	Enhancers	Pancreas	Pancrea
8	chr9:12329000-12329200	Enhancers	Adipose Nuclei	Adipose
9	chr9:12329000-12329200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr9:12329000-12329200	Enhancers	Fetal Muscle Trunk	muscle
11	chr9:12329000-12329400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr9:12329000-12329400	Flanking Active TSS	Liver	Liver
13	chr9:12329000-12329600	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr9:12329000-12329600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr9:12329000-12329600	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr9:12329000-12329600	Flanking Active TSS	Pancreas	Pancrea
17	chr9:12329000-12329600	Active TSS	HepG2	liver
18	chr9:12329200-12329400	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr9:12329200-12329400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
20	chr9:12329200-12329600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr9:12329200-12329600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr9:12329200-12329600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr9:12329200-12329600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:12329200-12329600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr9:12329200-12329600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr9:12329200-12329600	Flanking Active TSS	Adipose Nuclei	Adipose
27	chr9:12329200-12329600	Active TSS	Brain Angular Gyrus	brain
28	chr9:12329200-12329600	Active TSS	Brain Cingulate Gyrus	brain
29	chr9:12329200-12329600	Active TSS	Brain Hippocampus Middle	brain
30	chr9:12329200-12329600	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr9:12329200-12329600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr9:12329200-12329600	Active TSS	Brain Substantia Nigra	brain
33	chr9:12329200-12329600	Active TSS	Fetal Kidney	kidney
34	chr9:12329200-12329600	Enhancers	Fetal Lung	lung
35	chr9:12329200-12329600	Flanking Active TSS	Fetal Muscle Trunk	muscle
36	chr9:12329200-12329600	Enhancers	Gastric	stomach
37	chr9:12329200-12329600	Enhancers	Lung	lung
38	chr9:12329200-12329600	Active TSS	Right Atrium	heart
39	chr9:12329200-12329600	Active TSS	Stomach Smooth Muscle	stomach
40	chr9:12329200-12329600	Enhancers	HUVEC	blood vessel
41	chr9:12329400-12329600	Active TSS	Liver	Liver
42	chr9:12329400-12329600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr9:12329400-12329600	Enhancers	Fetal Muscle Leg	muscle
44	chr9:12334000-12334200	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr9:12340600-12341000	Enhancers	Liver	Liver
46	chr9:12350800-12352400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr9:12351600-12352800	Enhancers	Fetal Brain Male	brain
48	chr9:12354400-12354600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr9:12354600-12357400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr9:12357400-12357600	Genic enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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