Variant report

Variant	esv3335270
Chromosome Location	chr3:141377810-141378085
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	SRF	chr3:141377901-141378378	ECC-1	luminal epithelium:	n/a	chr3:141378144-141378162
2	SRF	chr3:141378058-141378243	HepG2	liver:	n/a	chr3:141378144-141378162
3	SRF	chr3:141377976-141378295	ECC-1	luminal epithelium:	n/a	chr3:141378144-141378162
4	SRF	chr3:141377997-141378242	H1-hESC	embryonic stem cell:	n/a	chr3:141378144-141378162
5	SRF	chr3:141377996-141378332	H1-hESC	embryonic stem cell:	n/a	chr3:141378144-141378162
6	SRF	chr3:141378016-141378231	HepG2	liver:	n/a	chr3:141378144-141378162

No.	Distal block	Cell Line	Cell type
1	chr3:141376839..141379290-chr3:141593720..141595646,2	MCF-7	breast:
2	chr3:141377266..141379551-chr3:141385595..141387849,2	MCF-7	breast:
3	chr3:141361177..141363053-chr3:141377745..141380110,2	MCF-7	breast:
4	chr3:141286560..141289498-chr3:141377973..141379933,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242104	TF binding region
ENSG00000069849	chromatin interactions

Extended variants
information (count: 26 )
Associated
traits (count: 53 )

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs545921359	chr3:141377814-141377815	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs75386028	chr3:141377838-141377839	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs6440026	chr3:141377851-141377852	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs544372110	chr3:141377861-141377862	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs570289639	chr3:141377870-141377871	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs6807566	chr3:141377906-141377907	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs6795034	chr3:141377910-141377911	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs145583668	chr3:141377924-141377925	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs150264607	chr3:141377940-141377941	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs4067544	chr3:141377949-141377950	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs4067545	chr3:141377950-141377951	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs4067539	chr3:141377952-141377953	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs4067540	chr3:141377953-141377954	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs3856752	chr3:141377954-141377955	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs4067541	chr3:141377955-141377956	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs3856753	chr3:141377957-141377958	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs112941621	chr3:141377958-141377959	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs369599599	chr3:141377959-141377960	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs112941984	chr3:141377973-141377974	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs183614180	chr3:141377977-141377978	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs71153911	chr3:141377978-141377979	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs375497506	chr3:141377981-141377982	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs373191131	chr3:141377999-141378000	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs188707586	chr3:141378009-141378010	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs527269845	chr3:141378019-141378020	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs6795341	chr3:141378054-141378055	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:53)

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
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
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
microdeletion syndrome	22180640	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Basal cell lymphoma	21115979	CNVD
Ovarian cancer	22174824	CNVD
Colorectal cancer	18645599	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Hepatocellular carcinoma	16750200	CNVD
Lung cancer	16740712	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Blepharophimosis-ptosis-epicanthus inversus syndrome	22067867	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
abnormal development	18461090	CNVD
Cancer	21129771	CNVD
Ovarian cancer	23621864	CNVD
Congenital anomalies of the kidney and urinary tract	20605837	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	21785460	CNVD

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141376200-141378200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:141377000-141378400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
3	chr3:141377600-141378000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:141377600-141379400	Active TSS	Aorta	Aorta
5	chr3:141377600-141379600	Active TSS	Colon Smooth Muscle	Colon
6	chr3:141377600-141379600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
7	chr3:141377600-141379800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr3:141377600-141379800	Active TSS	Rectal Smooth Muscle	rectum
9	chr3:141377800-141378000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
10	chr3:141377800-141378200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
11	chr3:141377800-141378200	Bivalent Enhancer	Fetal Lung	lung
12	chr3:141377800-141378200	Bivalent Enhancer	HepG2	liver
13	chr3:141377800-141378600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:141377800-141378800	Enhancers	Fetal Heart	heart
15	chr3:141378000-141378200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
16	chr3:141378000-141378200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:141378000-141378200	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
18	chr3:141378000-141378200	Bivalent/Poised TSS	Placenta	Placenta
19	chr3:141378000-141378200	Bivalent/Poised TSS	Fetal Stomach	stomach
20	chr3:141378000-141378200	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
21	chr3:141378000-141378200	Flanking Bivalent TSS/Enh	NHDF-Ad	bronchial
22	chr3:141378000-141378400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
23	chr3:141378000-141378400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:141378000-141378400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:141378000-141378400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
26	chr3:141378000-141378400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:141378000-141378400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:141378000-141378400	Bivalent Enhancer	Liver	Liver
29	chr3:141378000-141378400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
30	chr3:141378000-141378600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
31	chr3:141378000-141378600	Enhancers	Fetal Kidney	kidney
32	chr3:141378000-141378600	Bivalent Enhancer	Fetal Muscle Leg	muscle
33	chr3:141378000-141378600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
34	chr3:141378000-141379000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:141378000-141379400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
36	chr3:141378000-141379400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:141378000-141380000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell

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