Variant report

Variant	esv11442
Chromosome Location	chr2:54342963-54343528
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:54196743..54198781-chr2:54341566..54344110,2	K562	blood:
2	chr16:20912054..20912881-chr2:54342309..54343237,2	Hela-S3	cervix:
3	chr2:54343136..54344762-chr2:54350422..54352755,2	K562	blood:
4	chr2:54341806..54344770-chr2:54784235..54787039,2	MCF-7	breast:
5	chr2:54340617..54344494-chr2:54480899..54484108,3	K562	blood:
6	chr15:76603595..76604138-chr2:54342354..54343006,2	HCT-116	colon:
7	chr2:54341520..54343821-chr2:54682367..54684141,3	MCF-7	breast:
8	chr2:54341307..54344135-chr2:54557168..54559182,2	K562	blood:
9	chr18:12947857..12948364-chr2:54342415..54343083,2	Hela-S3	cervix:
10	chr2:54341443..54343043-chr2:54557751..54559883,2	MCF-7	breast:
11	chr2:54342079..54343052-chr5:109024930..109025777,2	Hela-S3	cervix:
12	chr19:48281526..48282040-chr2:54342571..54343371,2	NB4	blood:
13	chr2:54342236..54343923-chr2:54879380..54882162,2	MCF-7	breast:
14	chr2:54343141..54345901-chr2:54421855..54423562,2	K562	blood:
15	chr17:79849578..79850209-chr2:54342411..54343037,2	Hela-S3	cervix:
16	chr2:54341216..54345253-chr2:54347980..54351307,5	MCF-7	breast:
17	chr2:54342420..54344092-chr20:46285600..46287785,2	MCF-7	breast:
18	chr2:54341515..54343973-chr2:55337394..55340042,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000112893	chromatin interactions
ENSG00000178021	chromatin interactions
ENSG00000115310	chromatin interactions
ENSG00000102897	chromatin interactions
ENSG00000178980	chromatin interactions
ENSG00000170634	chromatin interactions
ENSG00000115306	chromatin interactions
ENSG00000140374	chromatin interactions
ENSG00000196562	chromatin interactions
ENSG00000068878	chromatin interactions
ENSG00000177994	chromatin interactions
ENSG00000085415	chromatin interactions
ENSG00000141552	chromatin interactions

Extended variants
information (count: 33 )
Associated
traits (count: 64 )

Variant overlapped rSNPs/rCNVs (count:33 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs2287640	chr2:54342974-54342975	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	13 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs556496112	chr2:54342977-54342978	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
3	rs576680539	chr2:54342982-54342983	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
4	rs7573491	chr2:54343012-54343013	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	12 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
5	rs559286244	chr2:54343028-54343029	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	12 gene(s)	Overlapped CNVs	n/a
6	rs9807941	chr2:54343039-54343040	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
7	rs572520718	chr2:54343041-54343042	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
8	rs116827186	chr2:54343042-54343043	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
9	rs561294827	chr2:54343046-54343047	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
10	rs529317278	chr2:54343049-54343050	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
11	rs543873084	chr2:54343069-54343070	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
12	rs562372545	chr2:54343074-54343075	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
13	rs531388051	chr2:54343090-54343091	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
14	rs9808326	chr2:54343108-54343109	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	9 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
15	rs571202478	chr2:54343110-54343111	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
16	rs141471032	chr2:54343122-54343123	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
17	rs527531823	chr2:54343138-54343139	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
18	rs547084169	chr2:54343147-54343148	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
19	rs567219118	chr2:54343156-54343157	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
20	rs190326699	chr2:54343162-54343163	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
21	rs182099634	chr2:54343184-54343185	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
22	rs9808489	chr2:54343192-54343193	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	9 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs539233738	chr2:54343213-54343214	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
24	rs59005281	chr2:54343240-54343241	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
25	rs145308584	chr2:54343263-54343264	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
26	rs79440554	chr2:54343290-54343291	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
27	rs372285146	chr2:54343304-54343305	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
28	rs2161084	chr2:54343348-54343349	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
29	rs554690032	chr2:54343356-54343357	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
30	rs564500743	chr2:54343423-54343424	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
31	rs574757183	chr2:54343468-54343469	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
32	rs2042143	chr2:54343514-54343515	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	7 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
33	rs563430728	chr2:54343516-54343517	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:64)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17387387	CNVD
Neuroblastoma	17533364	CNVD
Neuroblastoma	18923191	CNVD
Endometrial cancer	22040021	CNVD
Adrenal tumor	17535989	CNVD
Breast cancer	21264507	CNVD
Basal cell lymphoma	17053054	CNVD
Medulloblastoma	17522785	CNVD
Cancer	23418310	CNVD
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Breast cancer	21785460	CNVD
Lung cancer	18438408	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21508638	CNVD
Neurodevelopmental disorder	22521361	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Williams Syndrome	20824207	CNVD
Breast cancer	16272173	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Ovarian cancer	21720365	CNVD
abnormal development	18461090	CNVD
Lung adenocarcinoma	17086460	CNVD
Retinoblastoma	22278416	CNVD
Cancer	21183584	CNVD
Breast cancer	16397240	CNVD
Lung cancer	17086460	CNVD
Chronic lymphocytic leukemia	17053054	CNVD
Hereditary non-polyposis colorectal cancer	19566914	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Developmental delay	21147756	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:210 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54341800-54343000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:54341800-54343200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:54341800-54343200	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr2:54341800-54343200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:54341800-54343200	Active TSS	K562	blood
6	chr2:54341800-54343400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:54341800-54343400	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr2:54341800-54343400	Active TSS	GM12878-XiMat	blood
9	chr2:54341800-54343600	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr2:54341800-54343600	Active TSS	Muscle Satellite Cultured Cells	--
11	chr2:54341800-54343600	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr2:54341800-54343600	Active TSS	A549	lung
13	chr2:54341800-54344000	Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr2:54342000-54343200	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr2:54342000-54343200	Active TSS	Fetal Brain Female	brain
16	chr2:54342000-54343400	Active TSS	H1 Cell Line	embryonic stem cell
17	chr2:54342000-54343400	Active TSS	H9 Cell Line	embryonic stem cell
18	chr2:54342000-54343400	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr2:54342000-54343400	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr2:54342000-54343400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:54342000-54343400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:54342000-54343400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:54342000-54343400	Active TSS	Left Ventricle	heart
24	chr2:54342000-54343400	Active TSS	HSMM	muscle
25	chr2:54342000-54343400	Active TSS	NHDF-Ad	bronchial
26	chr2:54342000-54343600	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr2:54342000-54343600	Active TSS	NHLF	lung
28	chr2:54342200-54343200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr2:54342200-54343200	Active TSS	Dnd41	blood
30	chr2:54342200-54343400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr2:54342200-54343400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr2:54342200-54343400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:54342200-54343400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr2:54342200-54343400	Active TSS	Aorta	Aorta
35	chr2:54342200-54343400	Active TSS	Colonic Mucosa	Colon
36	chr2:54342200-54343400	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr2:54342200-54343400	Active TSS	Fetal Muscle Trunk	muscle
38	chr2:54342200-54343400	Active TSS	Fetal Stomach	stomach
39	chr2:54342200-54343400	Active TSS	Fetal Thymus	thymus
40	chr2:54342200-54343400	Active TSS	Psoas Muscle	Psoas
41	chr2:54342200-54343400	Active TSS	Right Ventricle	heart
42	chr2:54342200-54343400	Active TSS	Thymus	Thymus
43	chr2:54342200-54343400	Active TSS	HSMMtube	muscle
44	chr2:54342200-54343600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:54342200-54343600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr2:54342200-54343600	Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr2:54342200-54343600	Active TSS	Brain Cingulate Gyrus	brain
48	chr2:54342200-54343600	Active TSS	Brain Germinal Matrix	brain
49	chr2:54342200-54343600	Active TSS	Brain Hippocampus Middle	brain
50	chr2:54342200-54343600	Active TSS	Fetal Muscle Leg	muscle

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