Variant report

Variant	esv999299
Chromosome Location	chr3:158348460-158358157
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	CBX3	chr3:158351252-158351561	K562	blood:	n/a	n/a
2	CTCF	chr3:158350723-158350757	Pancreas_OC	pancreas:	n/a	n/a
3	CTCF	chr3:158348360-158348510	GM12865	blood:	n/a	n/a
4	FOXA2	chr3:158352622-158352986	A549	lung:	n/a	n/a
5	FOXA2	chr3:158352501-158353133	A549	lung:	n/a	n/a
6	KAP1	chr3:158351251-158351528	K562	blood:	n/a	n/a
7	POLR2A	chr3:158355300-158355543	K562	blood:	n/a	n/a
8	POLR2A	chr3:158356528-158357606	K562	blood:	n/a	n/a
9	POLR2A	chr3:158351598-158354991	K562	blood:	n/a	n/a
10	POLR2A	chr3:158345592-158351341	K562	blood:	n/a	n/a
11	POLR2A	chr3:158357820-158357951	K562	blood:	n/a	n/a
12	POLR2A	chr3:158355968-158356274	K562	blood:	n/a	n/a
13	POLR2A	chr3:158351945-158352695	H1-hESC	embryonic stem cell:	n/a	n/a
14	TEAD4	chr3:158351187-158351521	H1-hESC	embryonic stem cell:	n/a	n/a
15	YY1	chr3:158352110-158352414	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
GFM1	TF binding region
ENSG00000243165	TF binding region

Extended variants
information (count: 237 )
Associated
traits (count: 60 )

Variant overlapped rSNPs/rCNVs (count:237 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs187750830	chr3:158348474-158348475	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs566338154	chr3:158348526-158348527	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs536842381	chr3:158348538-158348539	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs192225306	chr3:158348561-158348562	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs543489678	chr3:158348567-158348568	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs550424554	chr3:158348589-158348590	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs527883376	chr3:158348620-158348621	Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs201252658	chr3:158348623-158348624	Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs558341097	chr3:158348626-158348627	Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs560342209	chr3:158348649-158348650	Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs148111115	chr3:158348659-158348660	Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs551817685	chr3:158348668-158348669	Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs185041733	chr3:158348737-158348738	Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs112387648	chr3:158348757-158348758	Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs373911770	chr3:158348786-158348787	Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs187890271	chr3:158348806-158348807	Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs367723773	chr3:158348836-158348837	Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs192176938	chr3:158348856-158348857	Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs142825752	chr3:158348872-158348873	Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs550272953	chr3:158348877-158348878	Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs565346847	chr3:158348888-158348889	Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs146092571	chr3:158348960-158348961	Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs184387259	chr3:158348998-158348999	Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs371168136	chr3:158349029-158349030	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs115184489	chr3:158349030-158349031	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs548533646	chr3:158349046-158349047	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs189656872	chr3:158349176-158349177	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs537213300	chr3:158349182-158349183	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs148079541	chr3:158349233-158349234	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs374861990	chr3:158349238-158349239	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs558238489	chr3:158349281-158349282	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs576987889	chr3:158349289-158349290	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs115251677	chr3:158349291-158349292	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs60378784	chr3:158349312-158349313	Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs552539184	chr3:158349316-158349317	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs368945975	chr3:158349377-158349378	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs377762501	chr3:158349389-158349390	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs7619478	chr3:158349397-158349398	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs542082639	chr3:158349406-158349407	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs563411078	chr3:158349467-158349468	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs141970865	chr3:158349501-158349502	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs545451320	chr3:158349519-158349520	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs545641171	chr3:158349538-158349539	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs565383556	chr3:158349544-158349545	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs531077268	chr3:158349545-158349546	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs369578971	chr3:158349552-158349553	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs372246539	chr3:158349571-158349572	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs547854095	chr3:158349603-158349604	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs557157495	chr3:158349617-158349618	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs559768734	chr3:158349626-158349627	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:60)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Breast cancer	22032731	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Basal cell lymphoma	21115979	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Hepatocellular carcinoma	16750200	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Basal cell lymphoma	17170743	CNVD
Breast cancer	16608533	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Acute myeloid leukemia	20729466	CNVD
Non-small cell lung cancer	19010865	CNVD
abnormal development	18461090	CNVD
Prostate cancer	18632612	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Colorectal cancer	16272173	CNVD
Prostate cancer	16547154	CNVD
Breast cancer	21364760	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Cancer	20164919	CNVD
Ovarian cancer	21781307	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD
Non-syndromic sensorineural hearing loss	19587683	CNVD

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158348600-158349000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:158349000-158351800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:158349400-158351400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:158349600-158349800	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr3:158349600-158350200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr3:158349600-158350200	Enhancers	Brain Germinal Matrix	brain
7	chr3:158349600-158350400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:158349600-158350400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:158349600-158350600	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr3:158349800-158350200	Enhancers	H1 Cell Line	embryonic stem cell
11	chr3:158349800-158350200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:158349800-158350200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr3:158349800-158350200	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr3:158349800-158350600	Enhancers	H9 Cell Line	embryonic stem cell
15	chr3:158350000-158350200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:158350000-158350400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:158350000-158350400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:158350000-158350600	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr3:158350000-158350600	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr3:158350200-158350400	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr3:158350200-158351800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr3:158350200-158352000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr3:158350400-158352000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr3:158350600-158351800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr3:158350600-158352000	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:158350600-158352000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr3:158350600-158352200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr3:158351800-158352000	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr3:158351800-158352400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:158351800-158352400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
31	chr3:158352000-158352200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr3:158352000-158352200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr3:158352000-158352200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr3:158352000-158352200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
35	chr3:158352000-158352200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
36	chr3:158352000-158352400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
37	chr3:158352000-158352400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr3:158352000-158352400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:158352000-158352400	Enhancers	Fetal Brain Female	brain
40	chr3:158352000-158352600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:158352000-158353000	Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr3:158352200-158352400	Flanking Active TSS	H9 Cell Line	embryonic stem cell
43	chr3:158352200-158352400	Active TSS	iPS-15b Cell Line	embryonic stem cell
44	chr3:158352200-158352400	Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr3:158352200-158352600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:158352200-158352600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr3:158352200-158353000	Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr3:158352200-158353200	Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr3:158352200-158353200	Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr3:158352400-158352600	Active TSS	H1 Cell Line	embryonic stem cell

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