Variant report

Variant	esv8967
Chromosome Location	chr3:49197550-49198293
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:76)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:76 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49198008-49198471	GM12891	blood:	n/a	n/a
2	POLR2A	chr3:49198049-49198404	GM12892	blood:	n/a	n/a
3	POLR2A	chr3:49198069-49198500	K562	blood:	n/a	n/a
4	POLR2A	chr3:49197446-49197785	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr3:49198039-49198411	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:49197967-49198493	U87	brain:	n/a	n/a
7	POLR2A	chr3:49197996-49198435	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr3:49197504-49197737	HCT-116	colon:	n/a	n/a
9	POLR2A	chr3:49198120-49199205	HepG2	liver:	n/a	n/a
10	POLR2A	chr3:49197944-49198480	GM12892	blood:	n/a	n/a
11	POLR2A	chr3:49197990-49198468	GM12891	blood:	n/a	n/a
12	POLR2A	chr3:49197475-49197797	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr3:49197576-49197633	GM12878	blood:	n/a	n/a
14	POLR2A	chr3:49197959-49199338	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr3:49197498-49197732	A549	lung:	n/a	n/a
16	POLR2A	chr3:49198091-49198419	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr3:49198042-49198453	K562	blood:	n/a	n/a
18	POLR2A	chr3:49197538-49197701	HepG2	liver:	n/a	n/a
19	POLR2A	chr3:49197955-49203552	SK-N-MC	brain:	n/a	n/a
20	POLR2A	chr3:49197411-49197808	GM12892	blood:	n/a	n/a
21	POLR2A	chr3:49197493-49197747	GM12878	blood:	n/a	n/a
22	POLR2A	chr3:49197426-49197697	PANC-1	pancreas:	n/a	n/a
23	POLR2A	chr3:49198196-49198375	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr3:49197470-49197598	K562	blood:	n/a	n/a
25	POLR2A	chr3:49197989-49198460	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr3:49198119-49198358	SK-N-SH	brain:	n/a	n/a
27	POLR2A	chr3:49197529-49197730	A549	lung:	n/a	n/a
28	POLR2A	chr3:49198285-49198354	A549	lung:	n/a	n/a
29	POLR2A	chr3:49197489-49197727	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr3:49197525-49197712	A549	lung:	n/a	n/a
31	POLR2A	chr3:49197552-49197756	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr3:49197633-49197638	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr3:49197536-49197865	GM12878	blood:	n/a	n/a
34	POLR2A	chr3:49197442-49197768	GM12892	blood:	n/a	n/a
35	POLR2A	chr3:49197991-49198468	GM12892	blood:	n/a	n/a
36	POLR2A	chr3:49197973-49198354	U87	brain:	n/a	n/a
37	POLR2A	chr3:49197504-49197720	A549	lung:	n/a	n/a
38	POLR2A	chr3:49197529-49197734	MCF-7	breast:	n/a	n/a
39	POLR2A	chr3:49198029-49198473	HCT-116	colon:	n/a	n/a
40	POLR2A	chr3:49197553-49197740	SK-N-SH	brain:	n/a	n/a
41	POLR2A	chr3:49198116-49198377	GM12878	blood:	n/a	n/a
42	POLR2A	chr3:49197517-49197768	HL-60	blood:	n/a	n/a
43	POLR2A	chr3:49197411-49197852	GM12878	blood:	n/a	n/a
44	POLR2A	chr3:49198032-49198448	HCT-116	colon:	n/a	n/a
45	POLR2A	chr3:49198185-49198408	HepG2	liver:	n/a	n/a
46	POLR2A	chr3:49197410-49197739	SK-N-SH	brain:	n/a	n/a
47	POLR2A	chr3:49197475-49197819	K562	blood:	n/a	n/a
48	POLR2A	chr3:49198060-49198498	GM12878	blood:	n/a	n/a
49	POLR2A	chr3:49198086-49198443	K562	blood:	n/a	n/a
50	POLR2A	chr3:49198158-49198334	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49166454..49167956-chr3:49197730..49200400,2	K562	blood:
2	chr3:49198168..49200645-chr3:49211215..49212732,2	K562	blood:
3	chr3:49197673..49199686-chr3:49449232..49451070,2	K562	blood:
4	chr3:49195403..49197616-chr3:49208526..49210728,2	K562	blood:
5	chr3:49057940..49060006-chr3:49197956..49200673,2	MCF-7	breast:
6	chr3:49063218..49064787-chr3:49194853..49197640,2	K562	blood:
7	chr3:49195402..49201533-chr3:49207296..49212401,9	MCF-7	breast:
8	chr3:49168509..49171088-chr3:49198215..49200498,3	K562	blood:
9	chr3:49043216..49045196-chr3:49196235..49197868,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000270441	TF binding region
ENSG00000178252	chromatin interactions
ENSG00000185909	chromatin interactions
ENSG00000172037	chromatin interactions
ENSG00000145022	chromatin interactions
ENSG00000178057	chromatin interactions
ENSG00000207605	chromatin interactions
ENSG00000178149	chromatin interactions
ENSG00000067560	chromatin interactions

Extended variants
information (count: 27 )
Associated
traits (count: 99 )

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs575695923	chr3:49197560-49197561	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs549784386	chr3:49197564-49197565	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs181711990	chr3:49197640-49197641	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs369201950	chr3:49197695-49197696	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
5	rs377686590	chr3:49197723-49197724	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
6	rs551852208	chr3:49197740-49197741	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
7	rs13079694	chr3:49197761-49197762	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
8	rs201598039	chr3:49197764-49197765	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
9	rs112637219	chr3:49197792-49197793	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
10	rs112233751	chr3:49197800-49197801	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
11	rs111688071	chr3:49197839-49197840	Weak transcription Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
12	rs112317186	chr3:49197855-49197856	Weak transcription Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
13	rs111437667	chr3:49197863-49197864	Weak transcription Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
14	rs112900220	chr3:49197916-49197917	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
15	rs111656661	chr3:49197924-49197925	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
16	rs111983565	chr3:49197931-49197932	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
17	rs567059052	chr3:49197972-49197973	Weak transcription Strong transcription	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
18	rs112811318	chr3:49197982-49197983	Weak transcription Strong transcription	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
19	rs112897987	chr3:49197985-49197986	Weak transcription Strong transcription	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
20	rs112665851	chr3:49198006-49198007	Weak transcription Strong transcription	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
21	rs111330120	chr3:49198023-49198024	Weak transcription Strong transcription	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
22	rs566996533	chr3:49198067-49198068	Weak transcription Strong transcription	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
23	rs201123944	chr3:49198072-49198073	Weak transcription Strong transcription	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
24	rs55713230	chr3:49198091-49198092	Weak transcription Strong transcription	Chromatin interactive region	7 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
25	rs562408921	chr3:49198144-49198145	Weak transcription Strong transcription	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
26	rs534137852	chr3:49198205-49198206	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
27	rs555491551	chr3:49198236-49198237	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:99)

Disease	PMID	Source
Lynch syndrome	18415027	CNVD
Renal cell carcinoma	18592004	CNVD
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
Glioblastoma multiforme	21080181	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Esophageal cancer	20955586	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Melanoma	20688739	CNVD
Acute myeloid leukemia	21251322	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Kartagener syndrome	16639409	CNVD
Biliary cancer	19435499	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	16397240	CNVD
Breast cancer	22032731	CNVD
Non-small cell lung cancer	20864512	CNVD
Colorectal cancer	16912164	CNVD
Non-small cell lung cancer	19010865	CNVD
Colorectal cancer	16272173	CNVD
Non-muscle invasive bladder neoplasm	19445696	CNVD
Acute myeloid leukemia	17268525	CNVD
Salivary gland tumor	18059337	CNVD
Gastric cancer	16891809	CNVD
Night blindness	17160897	CNVD
Cancer	17160897	CNVD
Breast cancer	20409316	CNVD
Lung cancer	17297452	CNVD
Multiple myeloma	16616336	CNVD
Effusion lymphoma	18079361	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Neuroblastoma	20406844	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	21045282	CNVD
Urothelial cell carcinoma	18451213	CNVD
Neuroblastoma	17327916	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Melanoma	17363583	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medullary thyroid carcinoma	18765511	CNVD
abnormal development	18461090	CNVD
Developmental delay	21147756	CNVD
Urothelial carcinoma	21177765	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:128 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49172200-49200400	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:49186200-49198800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr3:49186800-49198800	Weak transcription	Pancreas	Pancrea
4	chr3:49191000-49198800	Weak transcription	Ovary	ovary
5	chr3:49191000-49199800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:49191400-49198800	Weak transcription	Gastric	stomach
7	chr3:49191400-49199000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:49191600-49200200	Weak transcription	Esophagus	oesophagus
9	chr3:49192000-49198000	Weak transcription	Thymus	Thymus
10	chr3:49192200-49198600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:49194400-49198200	Weak transcription	Brain Germinal Matrix	brain
12	chr3:49194400-49199000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr3:49194600-49198200	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr3:49194600-49198800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr3:49194800-49198200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr3:49195000-49198200	Weak transcription	Fetal Brain Female	brain
17	chr3:49195000-49198200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr3:49195000-49199600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:49195200-49199400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:49195200-49200400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:49195200-49202400	Weak transcription	Fetal Kidney	kidney
22	chr3:49195400-49198800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr3:49195400-49200400	Weak transcription	Brain Angular Gyrus	brain
24	chr3:49195600-49198200	Weak transcription	Primary B cells from peripheral blood	blood
25	chr3:49195600-49198200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:49195600-49198600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:49195600-49198600	Weak transcription	Fetal Muscle Leg	muscle
28	chr3:49195600-49198800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:49195600-49198800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr3:49195600-49198800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr3:49195600-49199000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:49195600-49199400	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr3:49195600-49199400	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr3:49195600-49200200	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr3:49195600-49200200	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr3:49195600-49200400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:49195600-49200400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr3:49195600-49200400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr3:49195600-49200400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr3:49195600-49202200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr3:49195800-49198000	Weak transcription	Fetal Intestine Small	intestine
42	chr3:49195800-49198200	Weak transcription	Brain Substantia Nigra	brain
43	chr3:49195800-49198800	Weak transcription	Fetal Intestine Large	intestine
44	chr3:49195800-49199600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr3:49196000-49197600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:49196000-49198200	Weak transcription	Fetal Thymus	thymus
47	chr3:49196000-49202400	Strong transcription	Fetal Stomach	stomach
48	chr3:49196200-49200200	Weak transcription	Fetal Lung	lung
49	chr3:49196400-49198800	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr3:49196400-49199200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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