Variant report

Variant	esv3392416
Chromosome Location	chr3:100056925-100057181
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	POLR2A	chr3:100056941-100056973	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr3:100057025-100057182	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:100056720-100057772	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:100055925..100057917-chr3:100076174..100079116,2	MCF-7	breast:
2	chr3:100051539..100055958-chr3:100056037..100061247,9	MCF-7	breast:
3	chr3:100056838..100058599-chr3:100119834..100121558,2	MCF-7	breast:

Variant related genes	Relation type
NIT2	TF binding region
ENSG00000154174	chromatin interactions
ENSG00000114021	chromatin interactions
ENSG00000206535	chromatin interactions

Extended variants
information (count: 11 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs563730364	chr3:100056963-100056964	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
2	rs559357635	chr3:100056989-100056990	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
3	rs111389443	chr3:100056994-100056995	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
4	rs183769775	chr3:100057000-100057001	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
5	rs552468491	chr3:100057007-100057008	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
6	rs564299146	chr3:100057029-100057030	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
7	rs186326668	chr3:100057053-100057054	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
8	rs34409241	chr3:100057062-100057063	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
9	rs190418981	chr3:100057091-100057092	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
10	rs72941434	chr3:100057109-100057110	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs114208385	chr3:100057124-100057125	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:57)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Renal cell carcinoma	21668985	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Hirschsprung''s Disease	21712996	CNVD
Hepatocellular carcinoma	16750200	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
Neurodevelopmental disorder	22521361	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
small cell lung cancer	20016488	CNVD
Ductal carcinoma	22052326	CNVD
Myelofibrosis	22110671	CNVD
T-cell acute lymphoblastic leukemia	19406988	CNVD
Breast cancer	16608533	CNVD
Amyotrophic lateral sclerosis	20685689	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:133 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100054000-100065000	Weak transcription	Spleen	Spleen
2	chr3:100054200-100081000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:100054400-100067600	Weak transcription	Psoas Muscle	Psoas
4	chr3:100054600-100057000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:100054600-100057000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:100054600-100057200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:100054600-100057200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:100054600-100057400	Weak transcription	Primary T cells from cord blood	blood
9	chr3:100054600-100058000	Weak transcription	Fetal Brain Male	brain
10	chr3:100054600-100058000	Weak transcription	Fetal Brain Female	brain
11	chr3:100054600-100058200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr3:100054600-100058400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:100054600-100058600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr3:100054600-100058600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr3:100054600-100058800	Weak transcription	Aorta	Aorta
16	chr3:100054600-100059400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:100054600-100059800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:100054600-100060200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr3:100054600-100063000	Weak transcription	Brain Substantia Nigra	brain
20	chr3:100054600-100064200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr3:100054600-100064400	Weak transcription	Thymus	Thymus
22	chr3:100054600-100102600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr3:100054800-100057000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:100054800-100057000	Weak transcription	Fetal Lung	lung
25	chr3:100054800-100057000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr3:100054800-100057200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:100054800-100057200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:100054800-100057200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:100054800-100057200	Weak transcription	Primary B cells from cord blood	blood
30	chr3:100054800-100057200	Weak transcription	HSMM	muscle
31	chr3:100054800-100057200	Weak transcription	Osteobl	bone
32	chr3:100054800-100057400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:100054800-100057400	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr3:100054800-100057600	Weak transcription	Primary B cells from peripheral blood	blood
35	chr3:100054800-100057600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:100054800-100057600	Weak transcription	Adipose Nuclei	Adipose
37	chr3:100054800-100057600	Weak transcription	Brain Hippocampus Middle	brain
38	chr3:100054800-100057600	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr3:100054800-100057800	Enhancers	Liver	Liver
40	chr3:100054800-100057800	Weak transcription	Gastric	stomach
41	chr3:100054800-100057800	Weak transcription	Ovary	ovary
42	chr3:100054800-100057800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr3:100054800-100057800	Weak transcription	NHDF-Ad	bronchial
44	chr3:100054800-100058000	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr3:100054800-100058000	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr3:100054800-100058000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:100054800-100058000	Weak transcription	Fetal Thymus	thymus
48	chr3:100054800-100058000	Weak transcription	Left Ventricle	heart
49	chr3:100054800-100058000	Weak transcription	Lung	lung
50	chr3:100054800-100058000	Weak transcription	Placenta Amnion	Placenta Amnion

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