Variant report

Variant	esv3419163
Chromosome Location	chr4:2898554-2904052
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:61)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr4:2902505-2902705	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr4:2902450-2902706	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr4:2902467-2902789	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr4:2902450-2902780	MCF10A-Er-Src	breast:	n/a	n/a
5	GATA3	chr4:2903737-2904077	SH-SY5Y	brain:	n/a	n/a
6	GATA3	chr4:2899766-2900168	MCF-7	breast:	n/a	n/a
7	JUND	chr4:2902619-2902675	HepG2	liver:	n/a	n/a
8	MAFK	chr4:2898788-2898895	HepG2	liver:	n/a	n/a
9	POLR2A	chr4:2903573-2903655	K562	blood:	n/a	n/a
10	POLR2A	chr4:2900976-2901215	HepG2	liver:	n/a	n/a
11	POLR2A	chr4:2902761-2902955	GM12878	blood:	n/a	n/a
12	POLR2A	chr4:2902815-2902965	GM12878	blood:	n/a	n/a
13	POLR2A	chr4:2900910-2902093	K562	blood:	n/a	n/a
14	POLR2A	chr4:2900100-2900477	K562	blood:	n/a	n/a
15	POLR2A	chr4:2901997-2902193	GM12878	blood:	n/a	n/a
16	POLR2A	chr4:2902387-2902943	K562	blood:	n/a	n/a
17	POLR2A	chr4:2903322-2903352	K562	blood:	n/a	n/a
18	POLR2A	chr4:2902785-2903086	K562	blood:	n/a	n/a
19	POLR2A	chr4:2900257-2900269	HepG2	liver:	n/a	n/a
20	POLR2A	chr4:2902072-2902172	HepG2	liver:	n/a	n/a
21	STAT3	chr4:2902526-2902661	MCF10A-Er-Src	breast:	n/a	n/a
22	ZNF263	chr4:2903577-2904155	HEK293-T-REx	kidney:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:2902126-2902176	U87	brain:	n/a
2	chr4:2902126-2902176	SK-N-MC	brain:	n/a
3	chr4:2902126-2902176	GM12878	blood:	n/a
4	chr4:2902126-2902176	HRCEpiC	kidney:	n/a
5	chr4:2902126-2902176	HUVEC	blood vessel:	n/a
6	chr4:2902126-2902176	AG09309	skin:	n/a
7	chr4:2902126-2902176	ovcar-3	ovarian:	n/a
8	chr4:2902126-2902176	SK-N-SH_RA	brain:	n/a
9	chr4:2902126-2902176	NT2-D1	testis:	n/a
10	chr4:2902126-2902176	GM12892	blood:	n/a
11	chr4:2902126-2902176	SAEC	small airway:	n/a
12	chr4:2902126-2902176	HCPEpiC	choroid plexus:	n/a
13	chr4:2902126-2902176	AG10803	skin:	n/a
14	chr4:2902126-2902176	HAEpiC	amniotic membrane:	n/a
15	chr4:2902126-2902176	HCT-116	colon:	n/a
16	chr4:2902126-2902176	NB4	blood:	n/a
17	chr4:2902126-2902176	AG04449	skin:	fetal
18	chr4:2902126-2902176	HPAEpiC	pulmonary alveolar:	n/a
19	chr4:2902126-2902176	GM12891	blood:	n/a
20	chr4:2902126-2902176	HL-60	blood:	n/a
21	chr4:2902126-2902176	GM19239	blood:	n/a
22	chr4:2902126-2902176	MCF-7	breast:	n/a
23	chr4:2902126-2902176	CMK	blood:	n/a
24	chr4:2902126-2902176	AoSMC	blood vessel:	n/a
25	chr4:2902126-2902176	SK-N-SH	brain:	n/a
26	chr4:2902126-2902176	H1-hESC	embryonic stem cell:	embryo
27	chr4:2902126-2902176	HEEpiC	esophagus:	n/a
28	chr4:2902126-2902176	HNPCEpiC	eye:	n/a
29	chr4:2902126-2902176	Hela-S3	cervix:	n/a
30	chr4:2902126-2902176	HIPEpiC	eye:	n/a
31	chr4:2902126-2902176	HRE	kidney:	n/a
32	chr4:2902126-2902176	AG09319	gingival:	n/a
33	chr4:2902126-2902176	MCF10A-Er-Src	breast:	n/a
34	chr4:2902126-2902176	NHBE	bronchial:	n/a
35	chr4:2902126-2902176	HRPEpiC	eye:	n/a
36	chr4:2902126-2902176	LNCaP	prostate:	n/a
37	chr4:2902126-2902176	BE2_C	brain:	n/a
38	chr4:2902126-2902176	IMR90	lung:	fetal
39	chr4:2902126-2902176	SKMC	muscle:	n/a
40	chr4:2902126-2902176	ECC-1	luminal epithelium:	n/a
41	chr4:2902126-2902176	NHDF-neo	bronchial:	n/a
42	chr4:2902126-2902176	HMEC	breast:	n/a
43	chr4:2902126-2902176	K562	blood:	n/a
44	chr4:2902126-2902176	RPTEC	kidney:	n/a
45	chr4:2902126-2902176	HCM	heart:	n/a
46	chr4:2902126-2902176	Hepatocyte	liver:	n/a
47	chr4:2902126-2902176	BJ	skin:	n/a
48	chr4:2902126-2902176	NH-A	brain:	n/a
49	chr4:2902126-2902176	PANC-1	pancreas:	n/a
50	chr4:2902126-2902176	T-47D	breast:	n/a

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:2903718..2915473-chr4:2930612..2941584,27	MCF-7	breast:
2	chr4:2898532..2900285-chr4:2936066..2937849,2	MCF-7	breast:
3	chr4:2892123..2895002-chr4:2897727..2899403,2	K562	blood:
4	chr4:2901620..2903390-chr4:2929996..2931803,2	MCF-7	breast:
5	chr4:2842830..2845663-chr4:2899333..2901190,2	K562	blood:
6	chr4:2900149..2902689-chr4:2931088..2933616,2	MCF-7	breast:
7	chr4:2897346..2900302-chr4:2903352..2905568,2	MCF-7	breast:
8	chr4:2898305..2901238-chr4:2907549..2909946,2	K562	blood:
9	chr4:2883697..2886623-chr4:2900900..2904831,4	MCF-7	breast:
10	chr4:2901261..2903208-chr4:2909740..2911464,2	MCF-7	breast:
11	chr4:2794368..2797381-chr4:2901324..2903887,3	MCF-7	breast:
12	chr4:2892098..2895386-chr4:2900898..2904479,3	K562	blood:

No data

Variant related genes	Relation type
ADD1	TF binding region
ADD1	CpG island
ENSG00000087266	chromatin interactions
ENSG00000109736	chromatin interactions
ENSG00000249673	chromatin interactions
ENSG00000087274	chromatin interactions

Extended variants
information (count: 229 )
Associated
traits (count: 63 )

Variant overlapped rSNPs/rCNVs (count:229 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs562652260	chr4:2898556-2898557	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
2	rs146067384	chr4:2898599-2898600	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
3	rs548430068	chr4:2898624-2898625	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
4	rs138925350	chr4:2898633-2898634	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
5	rs2857869	chr4:2898634-2898635	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
6	rs547604266	chr4:2898642-2898643	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
7	rs142935452	chr4:2898675-2898676	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
8	rs539490758	chr4:2898676-2898677	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
9	rs550107207	chr4:2898699-2898700	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
10	rs2857868	chr4:2898713-2898714	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs535719540	chr4:2898746-2898747	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
12	rs148306384	chr4:2898869-2898870	Weak transcription Strong transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
13	rs75179468	chr4:2898927-2898928	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
14	rs16843539	chr4:2898934-2898935	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs535196752	chr4:2899050-2899051	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
16	rs555725810	chr4:2899128-2899129	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
17	rs553630366	chr4:2899132-2899133	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
18	rs4690063	chr4:2899141-2899142	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
19	rs573001745	chr4:2899200-2899201	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
20	rs150855737	chr4:2899205-2899206	Strong transcription Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
21	rs545485977	chr4:2899212-2899213	Strong transcription Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
22	rs562479187	chr4:2899246-2899247	Strong transcription Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
23	rs34592055	chr4:2899269-2899270	Strong transcription Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
24	rs574447859	chr4:2899289-2899290	Strong transcription Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
25	rs59692453	chr4:2899292-2899293	Strong transcription Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
26	rs577348916	chr4:2899386-2899387	Strong transcription Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
27	rs542179349	chr4:2899423-2899424	Strong transcription Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
28	rs561941961	chr4:2899430-2899431	Strong transcription Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
29	rs76974547	chr4:2899438-2899439	Strong transcription Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
30	rs183227201	chr4:2899467-2899468	Strong transcription Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
31	rs188088572	chr4:2899469-2899470	Strong transcription Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
32	rs144405249	chr4:2899470-2899471	Strong transcription Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
33	rs569679359	chr4:2899489-2899490	Strong transcription Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
34	rs572093718	chr4:2899545-2899546	Strong transcription Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
35	rs549291677	chr4:2899601-2899602	Strong transcription Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
36	rs566028810	chr4:2899626-2899627	Strong transcription Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
37	rs111981818	chr4:2899648-2899649	Strong transcription Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
38	rs558286448	chr4:2899661-2899662	Strong transcription Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
39	rs570477762	chr4:2899664-2899665	Strong transcription Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
40	rs572610680	chr4:2899694-2899695	Strong transcription Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
41	rs370103094	chr4:2899708-2899709	Strong transcription Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
42	rs35966433	chr4:2899709-2899710	Strong transcription Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
43	rs146138001	chr4:2899736-2899737	Strong transcription Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
44	rs140178054	chr4:2899742-2899743	Strong transcription Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
45	rs149858627	chr4:2899754-2899755	Strong transcription Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
46	rs555740703	chr4:2899800-2899801	Strong transcription Weak transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
47	rs34086869	chr4:2899814-2899815	Strong transcription Weak transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
48	rs572329404	chr4:2899840-2899841	Strong transcription Weak transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
49	rs540870548	chr4:2899851-2899852	Strong transcription Weak transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
50	rs373602091	chr4:2899865-2899866	Strong transcription Weak transcription Enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:63)

Disease	PMID	Source
Myelofibrosis	22110671	CNVD
Wolf-Hirschhorn syndrome	21549014	CNVD
Breast cancer	21806811	CNVD
Wolf-Hirschhorn syndrome	22283845	CNVD
Wolf-Hirschhorn syndrome	16773131	CNVD
Mental retardation	16773131	CNVD
Wolf-Hirschhorn syndrome	22470819	CNVD
Wolf-Hirschhorn syndrome	18541967	CNVD
sporadic birth defects	19047251	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
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
Developmental delay	21147756	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
Facial dysmorphism	22438245	CNVD
Wolf-Hirschhorn syndrome	22438245	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:252 , 50 per page) page: 1 2 3 4 5 6

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2870200-2914000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:2871200-2900600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:2874200-2900000	Weak transcription	Hela-S3	cervix
4	chr4:2876600-2919200	Strong transcription	Primary B cells from peripheral blood	blood
5	chr4:2877200-2919400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:2880600-2915000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr4:2883600-2918600	Strong transcription	Fetal Stomach	stomach
8	chr4:2888200-2899200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr4:2888600-2899600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr4:2888600-2899800	Weak transcription	Fetal Brain Male	brain
11	chr4:2888800-2899400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:2889200-2899400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:2889600-2898600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr4:2889600-2900200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr4:2890000-2900400	Weak transcription	Psoas Muscle	Psoas
16	chr4:2890400-2918000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr4:2893000-2907800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr4:2893000-2919400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:2893200-2899000	Strong transcription	Brain Germinal Matrix	brain
20	chr4:2893200-2907600	Strong transcription	Primary T cells from cord blood	blood
21	chr4:2893200-2907600	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr4:2893200-2914000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr4:2893200-2918800	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr4:2893200-2918800	Strong transcription	Fetal Muscle Trunk	muscle
25	chr4:2893200-2919200	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr4:2893200-2932600	Strong transcription	Fetal Thymus	thymus
27	chr4:2893400-2915800	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr4:2893400-2918800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr4:2893400-2919000	Strong transcription	Fetal Muscle Leg	muscle
30	chr4:2893800-2909200	Strong transcription	Lung	lung
31	chr4:2893800-2918600	Strong transcription	Thymus	Thymus
32	chr4:2893800-2919000	Strong transcription	Duodenum Mucosa	Duodenum
33	chr4:2894000-2902600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr4:2894000-2903800	Strong transcription	Fetal Intestine Small	intestine
35	chr4:2894000-2923000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:2894400-2907600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr4:2894600-2907600	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr4:2894800-2919800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr4:2895000-2903200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr4:2895000-2903200	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr4:2895000-2903200	Strong transcription	Osteobl	bone
42	chr4:2895000-2907600	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr4:2895000-2917800	Strong transcription	Dnd41	blood
44	chr4:2895200-2901600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr4:2895200-2903200	Strong transcription	Colonic Mucosa	Colon
46	chr4:2895200-2903200	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr4:2895200-2907800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr4:2895200-2915000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr4:2895200-2919000	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr4:2895400-2898800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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