Variant report

Variant	nsv579620
Chromosome Location	chr19:42400791-42401313
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:6)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:42401055-42401255	K562	blood:	n/a	n/a
2	POLR2A	chr19:42400799-42400823	K562	blood:	n/a	n/a
3	POLR2A	chr19:42401240-42401734	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:42398848..42401100-chr19:42409902..42411983,2	MCF-7	breast:
2	chr19:42399993..42402789-chr19:42426992..42429764,2	MCF-7	breast:
3	chr19:42399244..42402499-chr19:42406088..42408738,6	MCF-7	breast:
4	chr19:42385849..42388501-chr19:42399623..42401678,2	K562	blood:
5	chr19:42400409..42404033-chr19:42410840..42416491,6	K562	blood:
6	chr19:42387549..42389204-chr19:42401111..42402879,2	MCF-7	breast:
7	chr19:42400726..42402812-chr19:42407325..42408926,2	K562	blood:
8	chr19:42399554..42401550-chr19:42461897..42463730,2	MCF-7	breast:
9	chr19:42400938..42403112-chr19:42412847..42414847,2	MCF-7	breast:

(count:6 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LYPD4-2	chr19:42400972-42402807	NONHSAT066497
2	lnc-LYPD4-2	chr19:42400176-42400914	NONHSAT066497
3	lnc-LYPD4-2	chr19:42400853-42400876	NONHSAT066499
4	lnc-LYPD4-2	chr19:42400449-42400876	NONHSAT066498
5	lnc-LYPD4-2	chr19:42401027-42401182	NONHSAT066498
6	lnc-LYPD4-2	chr19:42400991-42402843	NONHSAT066499

No data

Variant related genes	Relation type
ARHGEF1	TF binding region
ENSG00000105404	chromatin interactions
ENSG00000076928	chromatin interactions
ENSG00000268041	chromatin interactions

Extended variants
information (count: 32 )
Associated
traits (count: 62 )

Variant overlapped rSNPs/rCNVs (count:32 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs147215129	chr19:42400861-42400862	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
2	rs200018784	chr19:42400864-42400865	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
3	rs587756094	chr19:42400874-42400875	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
4	rs116682533	chr19:42400883-42400884	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
5	rs587684956	chr19:42400884-42400885	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
6	rs373474997	chr19:42400887-42400888	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
7	rs138101783	chr19:42400903-42400904	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
8	rs140536035	chr19:42400906-42400907	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
9	rs185955886	chr19:42400917-42400918	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
10	rs111522017	chr19:42400920-42400921	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
11	rs547687925	chr19:42400963-42400964	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
12	rs550314718	chr19:42400970-42400971	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
13	rs571781430	chr19:42400973-42400974	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
14	rs566322398	chr19:42400977-42400978	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
15	rs539464375	chr19:42400979-42400980	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
16	rs553893745	chr19:42400989-42400990	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
17	rs572096231	chr19:42400992-42400993	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
18	rs114173339	chr19:42401012-42401013	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
19	rs536202068	chr19:42401021-42401022	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
20	rs554543753	chr19:42401025-42401026	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
21	rs192313544	chr19:42401033-42401034	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
22	rs543370287	chr19:42401056-42401057	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
23	rs565077122	chr19:42401070-42401071	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
24	rs576993609	chr19:42401078-42401079	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
25	rs541125156	chr19:42401082-42401083	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
26	rs559532077	chr19:42401090-42401091	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
27	rs529823832	chr19:42401138-42401139	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
28	rs181758974	chr19:42401163-42401164	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
29	rs78194969	chr19:42401179-42401180	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
30	rs548161122	chr19:42401226-42401227	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
31	rs563153434	chr19:42401272-42401273	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
32	rs140396923	chr19:42401281-42401282	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:62)

Disease	PMID	Source
Myelodysplastic syndrome	17634407	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chordoma	21602918	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Cancer	21637783	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Ovarian cancer	21720365	CNVD
Cancer	20164919	CNVD
Thoracic aortic aneurysm	21092924	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Prostate cancer	18632612	CNVD
Autism	22495311	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Ductal carcinoma	22052326	CNVD
Congenital nephrotic syndrome	18421352	CNVD
Astrocytoma	17934521	CNVD
Leukemia	17361228	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Breast cancer	21858162	CNVD
Breast cancer	17603634	CNVD
Glioma	21971842	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Endometrial cancer	22040021	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Oligodendroglial tumors	17285580	CNVD
renal disease	20603712	CNVD
Salivary gland adenoid cystic carcinoma	17545515	CNVD
Ovarian cancer	22174824	CNVD
Breast cancer	16608533	CNVD
Neuroblastoma	18923191	CNVD
Breast cancer	21364760	CNVD
Invasive pancreatic ductal carcinoma	18765526	CNVD
Rhabdomyosarcoma	16790082	CNVD
Chordoma	18071362	CNVD
Urothelial carcinoma	21177765	CNVD
small cell lung cancer	20016488	CNVD
Wilms tumour	21544195	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Ovarian neoplasms	16753589	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Metanephric adenoma	20802469	CNVD
Acute myeloid leukemia	16864856	CNVD
Bladder cancer	21909424	CNVD
Medulloblastoma	16783165	CNVD
Gastric cancer	18160780	CNVD
Hepatocellular carcinoma	16750200	CNVD
Basal cell lymphoma	19029149	CNVD
Breast cancer	20409316	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Multiple myeloma	16616336	CNVD
Renal cell carcinoma	18765545	CNVD
Acute myeloid leukemia	20729466	CNVD
Lung cancer	18438408	CNVD
Genital abnormality	22378287	CNVD
Hypospadia	22378287	CNVD
Ovarian clear cell carcinoma	19293255	CNVD
Astrocytoma	22246337	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:145 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42389200-42407200	Weak transcription	Fetal Kidney	kidney
2	chr19:42389200-42429200	Weak transcription	Right Atrium	heart
3	chr19:42389400-42402000	Weak transcription	Psoas Muscle	Psoas
4	chr19:42389400-42406000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:42389400-42411400	Weak transcription	Fetal Brain Male	brain
6	chr19:42389800-42409000	Strong transcription	Fetal Stomach	stomach
7	chr19:42390800-42411200	Weak transcription	Hela-S3	cervix
8	chr19:42391400-42407400	Weak transcription	K562	blood
9	chr19:42391600-42404600	Weak transcription	HSMM	muscle
10	chr19:42392000-42404000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr19:42392000-42412600	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr19:42392000-42412600	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr19:42392000-42412600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr19:42392200-42400800	Strong transcription	Skeletal Muscle Male	skeletal muscle
15	chr19:42392200-42401400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr19:42392200-42407600	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr19:42392200-42408400	Strong transcription	Liver	Liver
18	chr19:42392200-42412400	Strong transcription	Fetal Muscle Leg	muscle
19	chr19:42392200-42412800	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr19:42392400-42401800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr19:42392400-42407600	Strong transcription	Fetal Intestine Small	intestine
22	chr19:42392400-42410200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr19:42392400-42412400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr19:42392400-42413200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr19:42392600-42402200	Strong transcription	Adipose Nuclei	Adipose
26	chr19:42392600-42406200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr19:42392600-42407400	Strong transcription	Colonic Mucosa	Colon
28	chr19:42392600-42411800	Strong transcription	Placenta	Placenta
29	chr19:42392600-42413600	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr19:42392800-42400800	Strong transcription	Brain Inferior Temporal Lobe	brain
31	chr19:42392800-42401000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr19:42392800-42402400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr19:42392800-42407800	Strong transcription	Fetal Intestine Large	intestine
34	chr19:42393000-42403600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
35	chr19:42393400-42400800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr19:42393400-42400800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr19:42393400-42404600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
38	chr19:42393400-42413600	Strong transcription	Thymus	Thymus
39	chr19:42393800-42401800	Weak transcription	NH-A	brain
40	chr19:42393800-42402200	Genic enhancers	Primary T cells from cord blood	blood
41	chr19:42393800-42404400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr19:42393800-42413000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr19:42394000-42403400	Genic enhancers	Primary T cells fromperipheralblood	blood
44	chr19:42394000-42413000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr19:42394200-42401000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr19:42394800-42405000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr19:42395200-42400800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr19:42395600-42400800	Strong transcription	Brain Cingulate Gyrus	brain
49	chr19:42395600-42401000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr19:42395600-42412400	Strong transcription	Right Ventricle	heart

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