Variant report

Variant	nsv593456
Chromosome Location	chr4:3427400-3429856
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	EBF1	chr4:3428395-3428652	GM12878	blood:	n/a	chr4:3428501-3428511 chr4:3428500-3428511 chr4:3428502-3428511 chr4:3428502-3428511 chr4:3428500-3428513
2	EBF1	chr4:3428394-3428594	GM12878	blood:	n/a	chr4:3428501-3428511 chr4:3428500-3428511 chr4:3428502-3428511 chr4:3428502-3428511 chr4:3428500-3428513
3	EBF1	chr4:3428374-3428604	GM12878	blood:	n/a	chr4:3428501-3428511 chr4:3428500-3428511 chr4:3428502-3428511 chr4:3428502-3428511 chr4:3428500-3428513
4	JUND	chr4:3428664-3428708	K562	blood:	n/a	chr4:3428685-3428694
5	MYC	chr4:3427610-3427657	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr4:3427476-3427847	HepG2	liver:	n/a	n/a
7	SPI1	chr4:3428030-3428355	HL-60	blood:	n/a	n/a
8	UBTF	chr4:3428302-3428414	K562	blood:	n/a	n/a
9	YY1	chr4:3428120-3428250	K562	blood:	n/a	chr4:3428223-3428233 chr4:3428211-3428233

No.	Distal block	Cell Line	Cell type
1	chr4:3418487..3420284-chr4:3426920..3428463,2	K562	blood:
2	chr4:3428890..3430804-chr4:3441748..3443973,2	MCF-7	breast:
3	chr4:3422645..3425998-chr4:3426569..3431321,4	K562	blood:
4	chr4:3422937..3425880-chr4:3426569..3429789,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RGS12-1	chr4:3429816-3429896	NONHSAT094871

Variant related genes	Relation type
RGS12	TF binding region
ENSG00000109758	chromatin interactions
ENSG00000159788	chromatin interactions

Extended variants
information (count: 111 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:111 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs541743365	chr4:3427433-3427434	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs199643083	chr4:3427504-3427505	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs558502720	chr4:3427541-3427542	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs188101280	chr4:3427542-3427543	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs578048161	chr4:3427574-3427575	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs543839291	chr4:3427587-3427588	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs62644692	chr4:3427667-3427668	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs62636034	chr4:3427680-3427681	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs563729629	chr4:3427681-3427682	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs62644693	chr4:3427846-3427847	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs57627572	chr4:3427899-3427900	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs74201781	chr4:3427935-3427936	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs56758205	chr4:3427952-3427953	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs113642133	chr4:3428005-3428006	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs529428022	chr4:3428029-3428030	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs541657615	chr4:3428033-3428034	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs561949257	chr4:3428067-3428068	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs527577907	chr4:3428103-3428104	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs181640763	chr4:3428150-3428151	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs139755631	chr4:3428151-3428152	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs532720502	chr4:3428162-3428163	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs549375283	chr4:3428219-3428220	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs558592195	chr4:3428245-3428246	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs569642422	chr4:3428274-3428275	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs535563719	chr4:3428298-3428299	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs549294371	chr4:3428317-3428318	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs566229744	chr4:3428337-3428338	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs377155606	chr4:3428356-3428357	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs558439377	chr4:3428357-3428358	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs369504557	chr4:3428371-3428372	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs578251795	chr4:3428383-3428384	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs373517257	chr4:3428392-3428393	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs117596165	chr4:3428395-3428396	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs369801479	chr4:3428409-3428410	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs113219369	chr4:3428420-3428421	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs543144819	chr4:3428449-3428450	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs186701188	chr4:3428454-3428455	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs572178328	chr4:3428486-3428487	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs540830316	chr4:3428492-3428493	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs191236825	chr4:3428546-3428547	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs533099528	chr4:3428548-3428549	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs181165811	chr4:3428584-3428585	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs553321156	chr4:3428599-3428600	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs373075372	chr4:3428633-3428634	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs563328978	chr4:3428702-3428703	Weak transcription Genic enhancers Strong transcription Enhancers	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs139465880	chr4:3428733-3428734	Weak transcription Genic enhancers Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs149686018	chr4:3428765-3428766	Weak transcription Genic enhancers Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs145521787	chr4:3428831-3428832	Weak transcription Genic enhancers Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs185102761	chr4:3428862-3428863	Weak transcription Genic enhancers Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs113546466	chr4:3428871-3428872	Weak transcription Genic enhancers Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:57)

Disease	PMID	Source
Retinitis pigmentosa	18421352	CNVD
Wolf-Hirschhorn syndrome	19259404	CNVD
Bladder cancer	19242612	CNVD
Breast cancer	19242612	CNVD
Congenital anomalies of the kidney and urinary tract	19242612	CNVD
abnormal development	18461090	CNVD
Olfactory neuroblastoma	18408657	CNVD
Wilms tumour	21544195	CNVD
Melanoma	20688739	CNVD
Colorectal cancer	16272173	CNVD
Non-syndromic sensorineural hearing loss	20606397	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17603634	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	17533364	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Cancer	21637783	CNVD
Melanoma	21693616	CNVD
Squamous cell cancer	21044232	CNVD
Colorectal cancer	20709793	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Non-small cell lung cancer	21044232	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	17387387	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Cervical cancer	21062161	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Neuroblastoma	18923191	CNVD
small cell lung cancer	20016488	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Urothelial carcinoma	21177765	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Lung cancer	18438408	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
Schizophrenia	21399695	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	21509527	CNVD
Ependymoma	20639864	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3399200-3432200	Weak transcription	Right Atrium	heart
2	chr4:3408800-3436600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr4:3411000-3436400	Strong transcription	Fetal Intestine Small	intestine
4	chr4:3411200-3436400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr4:3411200-3436600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr4:3413600-3437000	Strong transcription	Esophagus	oesophagus
7	chr4:3415000-3435600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:3415000-3436400	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr4:3415400-3437000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr4:3415600-3433600	Weak transcription	Fetal Kidney	kidney
11	chr4:3415800-3436400	Strong transcription	Lung	lung
12	chr4:3416400-3436200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr4:3416400-3436800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr4:3416600-3428200	Weak transcription	Primary B cells from peripheral blood	blood
15	chr4:3416600-3435600	Strong transcription	Skeletal Muscle Male	skeletal muscle
16	chr4:3416600-3437800	Weak transcription	Stomach Mucosa	stomach
17	chr4:3416800-3432000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:3416800-3436600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr4:3416800-3438400	Weak transcription	NHDF-Ad	bronchial
20	chr4:3417200-3433400	Strong transcription	Stomach Smooth Muscle	stomach
21	chr4:3417200-3435600	Strong transcription	Fetal Intestine Large	intestine
22	chr4:3417200-3444800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr4:3417400-3431000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr4:3417800-3427400	Strong transcription	Primary T cells from cord blood	blood
25	chr4:3417800-3427400	Strong transcription	Brain Hippocampus Middle	brain
26	chr4:3417800-3432800	Weak transcription	Small Intestine	intestine
27	chr4:3417800-3435200	Strong transcription	Adipose Nuclei	Adipose
28	chr4:3417800-3435200	Strong transcription	Fetal Brain Female	brain
29	chr4:3418200-3436600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr4:3418200-3438000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr4:3418200-3438000	Weak transcription	A549	lung
32	chr4:3418600-3428200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr4:3419000-3434600	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr4:3419200-3444600	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr4:3419400-3438400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr4:3419600-3435600	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr4:3419600-3438400	Weak transcription	NH-A	brain
38	chr4:3419800-3435200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr4:3419800-3438800	Weak transcription	NHLF	lung
40	chr4:3420000-3437000	Strong transcription	Brain Germinal Matrix	brain
41	chr4:3420200-3438400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr4:3420400-3435200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr4:3420400-3436000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr4:3420400-3436600	Weak transcription	Fetal Brain Male	brain
45	chr4:3420400-3438200	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr4:3420400-3438600	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr4:3420600-3430800	Weak transcription	HSMMtube	muscle
48	chr4:3420600-3435600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr4:3420600-3436400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr4:3421800-3427400	Strong transcription	NHEK	skin

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