Variant report

Variant	esv3413622
Chromosome Location	chr3:112054745-112055084
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112050155..112051724-chr3:112053726..112056411,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091972	chromatin interactions

Extended variants
information (count: 15 )
Associated
traits (count: 56 )

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs377534353	chr3:112054753-112054754	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs139668233	chr3:112054754-112054755	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs201119808	chr3:112054776-112054777	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs374482918	chr3:112054806-112054807	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs202016458	chr3:112054829-112054830	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs201908678	chr3:112054842-112054843	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs111769389	chr3:112054875-112054876	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs72950292	chr3:112054939-112054940	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs550276035	chr3:112054964-112054965	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs62264124	chr3:112055023-112055024	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs374338782	chr3:112055029-112055030	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs186807735	chr3:112055042-112055043	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs13063879	chr3:112055056-112055057	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs13086524	chr3:112055062-112055063	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs13086533	chr3:112055068-112055069	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:56)

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
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
Breast cancer	16608533	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Developmental delay	22180640	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21858162	CNVD
Multiple myeloma	17550852	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Basal cell lymphoma	21115979	CNVD
Attention deficit hyperactivity disorder	22180640	CNVD

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112051600-112054800	Active TSS	Brain Cingulate Gyrus	brain
2	chr3:112051800-112055400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
3	chr3:112052600-112062400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:112052600-112066400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:112052800-112076200	Weak transcription	Right Ventricle	heart
6	chr3:112053000-112056400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
7	chr3:112053000-112057200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:112053200-112062200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:112053200-112066400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:112053200-112076400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:112053400-112055800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr3:112053400-112057200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:112053400-112057600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr3:112053600-112054800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr3:112053600-112056600	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr3:112053800-112056200	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
17	chr3:112053800-112056200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:112053800-112056800	Weak transcription	HMEC	breast
19	chr3:112053800-112057000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:112053800-112057000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:112053800-112063800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr3:112053800-112064200	Weak transcription	Fetal Intestine Large	intestine
23	chr3:112054000-112054800	Enhancers	Primary T cells from cord blood	blood
24	chr3:112054000-112054800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:112054000-112055200	Enhancers	Fetal Intestine Small	intestine
26	chr3:112054000-112056400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr3:112054000-112057200	Enhancers	Adipose Nuclei	Adipose
28	chr3:112054000-112065800	Weak transcription	Fetal Kidney	kidney
29	chr3:112054000-112068600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr3:112054200-112054800	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
31	chr3:112054200-112054800	Flanking Active TSS	Brain Germinal Matrix	brain
32	chr3:112054200-112054800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
33	chr3:112054200-112054800	Genic enhancers	Fetal Thymus	thymus
34	chr3:112054200-112054800	Enhancers	Ovary	ovary
35	chr3:112054200-112054800	Enhancers	Right Atrium	heart
36	chr3:112054200-112054800	Enhancers	Small Intestine	intestine
37	chr3:112054200-112055000	Genic enhancers	H1 Cell Line	embryonic stem cell
38	chr3:112054200-112055000	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
39	chr3:112054200-112055000	Flanking Active TSS	Fetal Brain Female	brain
40	chr3:112054200-112055000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr3:112054200-112055200	Weak transcription	Placenta	Placenta
42	chr3:112054200-112055400	Enhancers	Fetal Lung	lung
43	chr3:112054200-112055400	Enhancers	Fetal Stomach	stomach
44	chr3:112054200-112055800	Enhancers	Primary B cells from peripheral blood	blood
45	chr3:112054200-112056600	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr3:112054200-112063800	Weak transcription	Fetal Muscle Trunk	muscle
47	chr3:112054200-112064000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr3:112054400-112054800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr3:112054400-112054800	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:112054400-112054800	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast

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