Variant report

Variant	esv3426402
Chromosome Location	chr3:119472162-119475860
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	GATA3	chr3:119474275-119474461	SH-SY5Y	brain:	n/a	n/a
2	POLR2A	chr3:119473636-119473651	MCF-7	breast:	n/a	n/a
3	STAT3	chr3:119475214-119475345	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000239994	TF binding region

Extended variants
information (count: 121 )
Associated
traits (count: 58 )

Variant overlapped rSNPs/rCNVs (count:121 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs9810454	chr3:119472174-119472175	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs536432698	chr3:119472194-119472195	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
3	rs556973723	chr3:119472218-119472219	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
4	rs9810210	chr3:119472243-119472244	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
5	rs540009758	chr3:119472283-119472284	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
6	rs138935249	chr3:119472285-119472286	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
7	rs559352459	chr3:119472312-119472313	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
8	rs181843025	chr3:119472316-119472317	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
9	rs2472663	chr3:119472327-119472328	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs186129200	chr3:119472411-119472412	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs142863420	chr3:119472416-119472417	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs190838798	chr3:119472417-119472418	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs567086190	chr3:119472436-119472437	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs369733258	chr3:119472498-119472499	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs373512000	chr3:119472546-119472547	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs143441258	chr3:119472594-119472595	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs147409373	chr3:119472608-119472609	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs377297841	chr3:119472644-119472645	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs551593613	chr3:119472645-119472646	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs563793738	chr3:119472674-119472675	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs530859302	chr3:119472680-119472681	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs554693484	chr3:119472681-119472682	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs548942276	chr3:119472720-119472721	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs567254968	chr3:119472746-119472747	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs534617198	chr3:119472802-119472803	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs546842441	chr3:119472824-119472825	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs571360154	chr3:119472855-119472856	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs574057338	chr3:119472874-119472875	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs183041993	chr3:119472993-119472994	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs188125913	chr3:119473009-119473010	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs547548416	chr3:119473038-119473039	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs34490729	chr3:119473051-119473052	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs373320115	chr3:119473056-119473057	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs536282666	chr3:119473079-119473080	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs139701738	chr3:119473104-119473105	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs572842424	chr3:119473107-119473108	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs541768288	chr3:119473115-119473116	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs528452361	chr3:119473116-119473117	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs559955410	chr3:119473127-119473128	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs578139062	chr3:119473270-119473271	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs545138030	chr3:119473333-119473334	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs556811220	chr3:119473337-119473338	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs563658838	chr3:119473339-119473340	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs530895215	chr3:119473346-119473347	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs549030010	chr3:119473383-119473384	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs548487554	chr3:119473387-119473388	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs528420364	chr3:119473390-119473391	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs190717270	chr3:119473424-119473425	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs113841311	chr3:119473436-119473437	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs75191042	chr3:119473441-119473442	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:58)

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
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
microdeletion syndrome	22180640	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
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	16608533	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Developmental delay	22180640	CNVD
Multiple myeloma	17550852	CNVD
Basal cell lymphoma	21115979	CNVD
Ovarian cancer	22174824	CNVD
lymphocytic leukemia	21291569	CNVD
small cell lung cancer	20016488	CNVD
Cancer	20164920	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Non-syndromic sensorineural hearing loss	21987784	CNVD
Glioblastoma multiforme	22286061	CNVD
Neurodevelopmental disorder	22521361	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119435400-119478200	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:119450600-119474200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:119451000-119473400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:119451200-119475200	Weak transcription	Fetal Brain Male	brain
5	chr3:119457600-119472200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:119459600-119472200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr3:119463200-119476000	Weak transcription	Spleen	Spleen
8	chr3:119465600-119474400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:119470000-119474400	Strong transcription	Ovary	ovary
10	chr3:119470200-119472400	Strong transcription	Duodenum Smooth Muscle	Duodenum
11	chr3:119470600-119474600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
12	chr3:119470800-119473400	Weak transcription	Pancreas	Pancrea
13	chr3:119470800-119473600	Weak transcription	Aorta	Aorta
14	chr3:119471000-119472600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr3:119471000-119472800	Weak transcription	Brain Anterior Caudate	brain
16	chr3:119471000-119479400	Weak transcription	Brain Substantia Nigra	brain
17	chr3:119471200-119472400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:119471200-119472800	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:119471200-119474800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:119471200-119475200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:119471200-119475800	Weak transcription	Brain Angular Gyrus	brain
22	chr3:119471400-119474200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr3:119471800-119472200	Weak transcription	Fetal Kidney	kidney
24	chr3:119472200-119474400	Strong transcription	Fetal Kidney	kidney
25	chr3:119472200-119474400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
26	chr3:119472400-119472600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr3:119472400-119473800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:119472600-119473000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
29	chr3:119472600-119474400	Strong transcription	Brain Inferior Temporal Lobe	brain
30	chr3:119472800-119473000	ZNF genes & repeats	Brain Hippocampus Middle	brain
31	chr3:119472800-119473800	Strong transcription	Brain Anterior Caudate	brain
32	chr3:119473000-119479400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:119473400-119473800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:119473400-119473800	Strong transcription	Pancreas	Pancrea
35	chr3:119473600-119473800	ZNF genes & repeats	Aorta	Aorta
36	chr3:119473800-119474000	Weak transcription	Aorta	Aorta
37	chr3:119473800-119476600	Weak transcription	Brain Anterior Caudate	brain
38	chr3:119473800-119484800	Weak transcription	Pancreas	Pancrea
39	chr3:119474400-119476000	Weak transcription	Fetal Kidney	kidney
40	chr3:119474400-119478200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:119474400-119478800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr3:119474400-119493400	Weak transcription	Ovary	ovary
43	chr3:119474600-119477000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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