Variant report

Variant	nsv10541
Chromosome Location	chr4:103778446-103785639
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	CBX3	chr4:103780106-103780649	K562	blood:	n/a	n/a
2	CBX3	chr4:103780722-103781005	K562	blood:	n/a	n/a
3	CBX3	chr4:103780219-103780585	K562	blood:	n/a	n/a
4	CBX3	chr4:103780235-103780691	HCT-116	colon:	n/a	n/a
5	CCNT2	chr4:103782119-103782224	K562	blood:	n/a	n/a
6	CTCF	chr4:103781960-103782110	WERI-Rb-1	eye:	n/a	n/a
7	E2F6	chr4:103782194-103782326	K562	blood:	n/a	n/a
8	GATA1	chr4:103781676-103782280	PBDE	blood:	n/a	n/a
9	GATA3	chr4:103783607-103783786	SH-SY5Y	brain:	n/a	n/a
10	GTF2F1	chr4:103780288-103780473	H1-hESC	embryonic stem cell:	n/a	n/a
11	IRF1	chr4:103780229-103780494	K562	blood:	n/a	n/a
12	KAP1	chr4:103780140-103780854	HEK293	kidney:	n/a	n/a
13	KAP1	chr4:103779820-103780845	K562	blood:	n/a	n/a
14	KAP1	chr4:103780272-103780620	U2OS	brain:	n/a	n/a
15	POLR2A	chr4:103784290-103784321	MCF-7	breast:	n/a	n/a
16	POLR2A	chr4:103785286-103785360	GM12878	blood:	n/a	n/a
17	POLR2A	chr4:103781708-103781959	K562	blood:	n/a	n/a
18	SETDB1	chr4:103779940-103780960	U2OS	brain:	n/a	n/a
19	SPI1	chr4:103783061-103783616	HL-60	blood:	n/a	chr4:103783394-103783407 chr4:103783382-103783391 chr4:103783380-103783393 chr4:103783337-103783344 chr4:103783395-103783408 chr4:103783336-103783345 chr4:103783334-103783347 chr4:103783397-103783406
20	SPI1	chr4:103783264-103783417	K562	blood:	n/a	chr4:103783394-103783407 chr4:103783382-103783391 chr4:103783380-103783393 chr4:103783337-103783344 chr4:103783395-103783408 chr4:103783336-103783345 chr4:103783334-103783347 chr4:103783397-103783406
21	SPI1	chr4:103783093-103783535	HL-60	blood:	n/a	chr4:103783394-103783407 chr4:103783382-103783391 chr4:103783380-103783393 chr4:103783337-103783344 chr4:103783395-103783408 chr4:103783336-103783345 chr4:103783334-103783347 chr4:103783397-103783406
22	STAT3	chr4:103780431-103780615	MCF10A-Er-Src	breast:	n/a	n/a
23	TRIM28	chr4:103780221-103780651	K562	blood:	n/a	n/a
24	TRIM28	chr4:103780264-103780545	K562	blood:	n/a	n/a
25	ZNF143	chr4:103780265-103780609	GM12878	blood:	n/a	n/a
26	ZNF143	chr4:103780279-103780586	K562	blood:	n/a	n/a
27	ZNF143	chr4:103780292-103780600	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:103775754..103778384-chr4:103782833..103785617,2	MCF-7	breast:
2	chr4:103775426..103778667-chr4:103788378..103789993,3	MCF-7	breast:
3	chr4:103781973..103785521-chr4:103788128..103792048,4	MCF-7	breast:
4	chr4:103782734..103784847-chr4:103785870..103787705,2	MCF-7	breast:
5	chr4:103767414..103770049-chr4:103783423..103785065,2	MCF-7	breast:
6	chr4:103741330..103752134-chr4:103778393..103796398,92	K562	blood:
7	chr4:103757925..103760228-chr4:103782951..103785960,3	K562	blood:
8	chr4:103776066..103778071-chr4:103784776..103786781,2	K562	blood:
9	chr4:103747316..103751264-chr4:103783852..103786816,4	MCF-7	breast:
10	chr4:103746438..103750337-chr4:103782400..103786138,6	MCF-7	breast:
11	chr4:103782723..103785636-chr4:103787155..103789919,2	MCF-7	breast:
12	chr4:103736995..103756245-chr4:103778393..103800311,117	K562	blood:

Variant related genes	Relation type
CISD2	TF binding region
ENSG00000238948	TF binding region
ENSG00000109332	chromatin interactions
ENSG00000246560	chromatin interactions
ENSG00000252739	chromatin interactions
ENSG00000145354	chromatin interactions

Extended variants
information (count: 259 )
Associated
traits (count: 78 )

Variant overlapped rSNPs/rCNVs (count:259 , 50 per page) page: 1 2 3 4 5 6

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs566202007	chr4:103778502-103778503	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs182476162	chr4:103778504-103778505	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs186400256	chr4:103778566-103778567	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs576397172	chr4:103778603-103778604	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs191159767	chr4:103778704-103778705	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs555513809	chr4:103778738-103778739	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs183330570	chr4:103778742-103778743	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs188540779	chr4:103778760-103778761	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs541234582	chr4:103778767-103778768	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs532095165	chr4:103778783-103778784	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs146327847	chr4:103778818-103778819	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs577321964	chr4:103778890-103778891	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs59884692	chr4:103778921-103778922	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs544563363	chr4:103778922-103778923	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs138965140	chr4:103778944-103778945	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs532011729	chr4:103778952-103778953	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs556282993	chr4:103778960-103778961	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs571402046	chr4:103778968-103778969	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs539246478	chr4:103778984-103778985	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs554054476	chr4:103778988-103778989	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs223348	chr4:103779007-103779008	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	mRNA abundance
22	rs191628547	chr4:103779008-103779009	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs562421788	chr4:103779040-103779041	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs542971850	chr4:103779056-103779057	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs555253220	chr4:103779063-103779064	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs576115789	chr4:103779066-103779067	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs543432476	chr4:103779073-103779074	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs565002222	chr4:103779079-103779080	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs532093541	chr4:103779085-103779086	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs566140414	chr4:103779095-103779096	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs539981434	chr4:103779100-103779101	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs551794231	chr4:103779113-103779114	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs569977811	chr4:103779114-103779115	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs556542890	chr4:103779128-103779129	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs183083125	chr4:103779144-103779145	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs573901389	chr4:103779178-103779179	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs534464851	chr4:103779190-103779191	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs113293812	chr4:103779218-103779219	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs74793270	chr4:103779300-103779301	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs565292832	chr4:103779310-103779311	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs544733079	chr4:103779331-103779332	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs74661152	chr4:103779413-103779414	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs575097243	chr4:103779414-103779415	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs542629942	chr4:103779417-103779418	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs551704016	chr4:103779488-103779489	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs559306936	chr4:103779503-103779504	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs150350765	chr4:103779514-103779515	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs529602992	chr4:103779526-103779527	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs377744333	chr4:103779547-103779548	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs138012460	chr4:103779548-103779549	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:78)

Disease	PMID	Source
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Medulloblastoma	21979893	CNVD
Neuroblastoma	18923191	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21858162	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Gastric cancer	21586687	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Melanoma	18172304	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Breast cancer	17603634	CNVD
Hepatocellular carcinoma	16750200	CNVD
Myxofibrosarcoma	16751306	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Breast cancer	16272173	CNVD
Colorectal cancer	19359472	CNVD
Malignant mesothelioma	18160781	CNVD
Medulloblastoma	18056178	CNVD
Multiple myeloma	17077331	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Oral squamous cell carcinoma	17134496	CNVD
4q-syndrome	17576883	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Colorectal cancer	20709793	CNVD
Muscular dystrophy	21149563	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Liposarcoma	21253554	CNVD
Oligodendroglial tumors	17285580	CNVD
Cervical cancer	21062161	CNVD
Metanephric adenoma	20802469	CNVD
Breast cancer	16608533	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Lung cancer	19208797	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	21785460	CNVD
Myelodysplastic syndrome	21251322	CNVD
Lung cancer	18438408	CNVD
Cancer	22429812	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Cancer	21183584	CNVD
primary effusion lymphomas	17116491	CNVD
small cell lung cancer	20016488	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17133270	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Colorectal cancer	20459617	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Congenital anomalies of the kidney and urinary tract	20505237	CNVD
Breast cancer	17393978	CNVD
Ovarian cancer	21720365	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Esophageal cancer	21851588	CNVD
Prostate cancer	16573809	CNVD
Multiple myeloma	16616336	CNVD
Melanoma	20688739	CNVD
Breast cancer	16397240	CNVD
Acute myeloid leukemia	18000384	CNVD
Cutaneous T-cell lymphoma	21881587	CNVD
Myelofibrosis	22110671	CNVD
myeloid cancer	21057493	CNVD
Cancer	20164919	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103750800-103788000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr4:103751600-103780200	Weak transcription	Dnd41	blood
3	chr4:103761600-103779800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:103765000-103783600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:103765200-103780000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr4:103765400-103788800	Weak transcription	Left Ventricle	heart
7	chr4:103768600-103781800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr4:103776600-103780000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr4:103779000-103787600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr4:103780000-103781000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr4:103780000-103781000	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:103780000-103782000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
13	chr4:103780000-103788000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:103780200-103780800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
15	chr4:103780200-103782200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:103780200-103782800	ZNF genes & repeats	Dnd41	blood
17	chr4:103780200-103789200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr4:103780400-103781000	ZNF genes & repeats	Primary T cells from cord blood	blood
19	chr4:103780400-103788800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr4:103780600-103781400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr4:103780800-103788000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr4:103781000-103783000	Weak transcription	Brain Angular Gyrus	brain
23	chr4:103781000-103785000	Weak transcription	Primary T cells from cord blood	blood
24	chr4:103781000-103788800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr4:103781000-103789400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr4:103781200-103785800	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr4:103781200-103788600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr4:103781400-103781800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr4:103781400-103782200	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr4:103781400-103782400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
31	chr4:103781400-103782600	ZNF genes & repeats	Fetal Stomach	stomach
32	chr4:103781600-103781800	Active TSS	Fetal Brain Male	brain
33	chr4:103781600-103782200	ZNF genes & repeats	Liver	Liver
34	chr4:103781600-103782200	ZNF genes & repeats	Fetal Thymus	thymus
35	chr4:103781600-103782400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
36	chr4:103781600-103782400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr4:103781600-103782400	ZNF genes & repeats	Fetal Intestine Small	intestine
38	chr4:103781600-103782400	ZNF genes & repeats	GM12878-XiMat	blood
39	chr4:103781600-103783400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr4:103781800-103782000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr4:103781800-103782200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr4:103781800-103782200	ZNF genes & repeats	Aorta	Aorta
43	chr4:103781800-103782200	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
44	chr4:103781800-103782200	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
45	chr4:103781800-103782400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr4:103781800-103782400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
47	chr4:103781800-103782400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr4:103781800-103782400	ZNF genes & repeats	Fetal Muscle Leg	muscle
49	chr4:103781800-103782600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr4:103781800-103783400	Enhancers	Primary monocytes fromperipheralblood	blood

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