Variant report

Variant	nsv593073
Chromosome Location	chr3:195949541-195950176
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EGR1	chr3:195950169-195950411	K562	blood:	n/a	n/a
2	FOS	chr3:195949849-195950067	MCF10A-Er-Src	breast:	n/a	n/a
3	FOXA1	chr3:195950075-195950450	T-47D	breast:	n/a	n/a
4	FOXA1	chr3:195950082-195950467	T-47D	breast:	n/a	n/a
5	FOXP2	chr3:195950134-195950262	PFSK-1	brain:	n/a	n/a
6	RCOR1	chr3:195949959-195950100	K562	blood:	n/a	n/a
7	RCOR1	chr3:195949953-195950374	K562	blood:	n/a	n/a
8	ZNF143	chr3:195950010-195950145	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:195807479..195809245-chr3:195949684..195952002,2	MCF-7	breast:
2	chr3:195943354..195945789-chr3:195947655..195950538,2	K562	blood:
3	chr3:195945138..195947988-chr3:195949670..195951213,2	MCF-7	breast:
4	chr3:195947010..195950626-chr3:195954155..195955751,3	K562	blood:

No data

Variant related genes	Relation type
SLC51A	TF binding region
ENSG00000163959	chromatin interactions
ENSG00000072274	chromatin interactions

Extended variants
information (count: 20 )
Associated
traits (count: 83 )

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs9840089	chr3:195949541-195949542	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs554708645	chr3:195949598-195949599	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs536274631	chr3:195949634-195949635	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs1543975	chr3:195949655-195949656	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs149892944	chr3:195949675-195949676	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs532723999	chr3:195949710-195949711	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs544489661	chr3:195949716-195949717	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs375659198	chr3:195949747-195949748	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs79398212	chr3:195949755-195949756	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs548134417	chr3:195949760-195949761	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs566863530	chr3:195949771-195949772	Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs527755270	chr3:195949939-195949940	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
13	rs566697697	chr3:195949996-195949997	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
14	rs533990478	chr3:195950000-195950001	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
15	rs147722295	chr3:195950069-195950070	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
16	rs142502876	chr3:195950080-195950081	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
17	rs146910433	chr3:195950097-195950098	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
18	rs555278367	chr3:195950137-195950138	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
19	rs74475893	chr3:195950164-195950165	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
20	rs569125206	chr3:195950176-195950177	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:83)

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
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	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
Basal cell lymphoma	21115979	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Breast cancer	16608533	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21785460	CNVD
Breast cancer	17133270	CNVD
Cancer	16751803	CNVD
abnormal development	18461090	CNVD
Autism	19653912	CNVD
small cell lung cancer	20016488	CNVD
Cancer	20164920	CNVD
Prostate cancer	18632612	CNVD
Cervical cancer	21062161	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Austim spectrum disorder	21302340	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	16397240	CNVD
Epilepsy	20736978	CNVD
Mental retardation	20736978	CNVD
speech impairment	20736978	CNVD
Intracranial aneurysm	16715129	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Mental retardation	17124404	CNVD
Congenital anomalies of the kidney and urinary tract	20299530	CNVD
Developmental delay	21147756	CNVD
Breast cancer	21509527	CNVD
Cancer	21129771	CNVD
Myelofibrosis	22110671	CNVD
Neurodevelopmental disorder	16760732	CNVD
Schizophrenia	22118685	CNVD
Schizophrenia	22958593	CNVD
Schizophrenia	21285140	CNVD
Schizophrenia	20970697	CNVD
Mental retardation	19951919	CNVD
Autism	20970697	CNVD
Developmental delay	18471269	CNVD
Intellectual disability	22045946	CNVD
Breast cancer	21045282	CNVD
Primary central nervous system lymphoma	21088137	CNVD
Ovarian cancer	20844748	CNVD
Adenocarcinoma	19607727	CNVD
Squamous cell cancer	19607727	CNVD
Uveal melanoma	20484589	CNVD
3q29 microdeletion syndrome	20500065	CNVD
Biliary cancer	20453639	CNVD
3q29 microdeletion syndrome	22283845	CNVD
3q29 microdeletion syndrome	21626679	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Ovarian cancer	21720365	CNVD
Breast cancer	21364760	CNVD
Urothelial carcinoma	21177765	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195944000-195950000	Weak transcription	Gastric	stomach
2	chr3:195944200-195950000	Weak transcription	Pancreas	Pancrea
3	chr3:195944200-195964000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:195945000-195968400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:195946600-195950000	Weak transcription	K562	blood
6	chr3:195946600-195950200	Weak transcription	Fetal Kidney	kidney
7	chr3:195946600-195954200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:195946600-195955000	Weak transcription	Right Atrium	heart
9	chr3:195946600-195965600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:195946800-195950200	Weak transcription	HSMM	muscle
11	chr3:195946800-195954200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:195946800-195962600	Weak transcription	Primary T cells from cord blood	blood
13	chr3:195946800-195964200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:195946800-195967400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr3:195947000-195949800	Weak transcription	HSMMtube	muscle
16	chr3:195947000-195950000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:195947000-195950200	Weak transcription	Duodenum Mucosa	Duodenum
18	chr3:195947000-195954200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:195947000-195954200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr3:195947000-195954400	Weak transcription	Fetal Brain Female	brain
21	chr3:195947000-195954600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:195947000-195959000	Weak transcription	Dnd41	blood
23	chr3:195947000-195960800	Weak transcription	Fetal Intestine Large	intestine
24	chr3:195947000-195963800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr3:195947000-195964000	Weak transcription	Colonic Mucosa	Colon
26	chr3:195947200-195950000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr3:195947200-195951800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr3:195947200-195952200	Weak transcription	HepG2	liver
29	chr3:195947200-195954000	Weak transcription	Fetal Muscle Leg	muscle
30	chr3:195947200-195962000	Weak transcription	Fetal Brain Male	brain
31	chr3:195947200-195962600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:195947200-195962600	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:195947400-195950200	Weak transcription	Placenta	Placenta
34	chr3:195947400-195958800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr3:195948000-195970400	Strong transcription	Liver	Liver
36	chr3:195948600-195950600	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr3:195948600-195951400	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr3:195949000-195953800	Weak transcription	Fetal Intestine Small	intestine
39	chr3:195949800-195950600	Enhancers	HSMMtube	muscle
40	chr3:195950000-195950200	Enhancers	Gastric	stomach
41	chr3:195950000-195950400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
42	chr3:195950000-195950600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr3:195950000-195950600	Enhancers	Pancreas	Pancrea
44	chr3:195950000-195952600	Enhancers	K562	blood

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