Variant report

Variant	nsv946566
Chromosome Location	chr1:197659060-197661728
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	ATF1	chr1:197659216-197659501	K562	blood:	n/a	n/a
2	ATF3	chr1:197659190-197659476	K562	blood:	n/a	n/a
3	CBX3	chr1:197659156-197659567	K562	blood:	n/a	n/a
4	CTCF	chr1:197659644-197659695	GM20000	blood:	n/a	n/a
5	E2F4	chr1:197661586-197661683	MCF10A-Er-Src	breast:	n/a	n/a
6	FOSL1	chr1:197659150-197659608	K562	blood:	n/a	n/a
7	HNF4A	chr1:197660898-197661298	HepG2	liver:	n/a	chr1:197661121-197661136
8	HNF4A	chr1:197660905-197661217	HepG2	liver:	n/a	chr1:197661121-197661136
9	JUN	chr1:197659344-197659544	K562	blood:	n/a	n/a
10	JUND	chr1:197659213-197659583	K562	blood:	n/a	chr1:197659378-197659389
11	JUND	chr1:197659279-197659479	HepG2	liver:	n/a	chr1:197659378-197659389
12	NFYB	chr1:197659280-197659524	K562	blood:	n/a	n/a
13	NFYB	chr1:197659289-197659493	GM12878	blood:	n/a	n/a
14	POLR2A	chr1:197659339-197659376	Gliobla	brain:	n/a	n/a
15	POLR2A	chr1:197659226-197659465	ProgFib	skin:	n/a	n/a
16	POLR2A	chr1:197661320-197661555	MCF10A-Er-Src	breast:	n/a	n/a
17	RFX5	chr1:197661070-197661148	K562	blood:	n/a	n/a
18	STAT3	chr1:197660964-197661371	MCF10A-Er-Src	breast:	n/a	n/a
19	USF1	chr1:197659224-197659578	K562	blood:	n/a	n/a
20	USF1	chr1:197659171-197659560	K562	blood:	n/a	n/a
21	USF2	chr1:197659277-197659523	Hela-S3	cervix:	n/a	n/a
22	USF2	chr1:197659283-197659481	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:197650384..197656370-chr1:197660434..197666309,6	K562	blood:
2	chr1:197652165..197657690-chr1:197657725..197663370,6	K562	blood:

Variant related genes	Relation type
ENSG00000207139	TF binding region
ENSG00000207139	chromatin interactions

Extended variants
information (count: 78 )
Associated
traits (count: 94 )

Variant overlapped rSNPs/rCNVs (count:78 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs564072043	chr1:197659085-197659086	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs576803794	chr1:197659122-197659123	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs541073218	chr1:197659164-197659165	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs16841881	chr1:197659215-197659216	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs6691216	chr1:197659263-197659264	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
6	rs548665898	chr1:197659281-197659282	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs563704258	chr1:197659341-197659342	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs531151715	chr1:197659349-197659350	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs552889436	chr1:197659384-197659385	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs367596522	chr1:197659401-197659402	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs139889850	chr1:197659485-197659486	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs185454501	chr1:197659490-197659491	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs1891497	chr1:197659555-197659556	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs568062502	chr1:197659582-197659583	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs535169966	chr1:197659595-197659596	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs557043265	chr1:197659600-197659601	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs149838812	chr1:197659619-197659620	Weak transcription Strong transcription Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs79214532	chr1:197659632-197659633	Weak transcription Strong transcription Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs557622552	chr1:197659770-197659771	Weak transcription Strong transcription Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs190169910	chr1:197659803-197659804	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs36120921	chr1:197659822-197659823	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs540139842	chr1:197659902-197659903	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs569042821	chr1:197659918-197659919	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs199861293	chr1:197660009-197660010	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs398074548	chr1:197660016-197660017	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs574792067	chr1:197660050-197660051	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs149034937	chr1:197660059-197660060	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs182762279	chr1:197660085-197660086	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs76914805	chr1:197660122-197660123	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs530995663	chr1:197660138-197660139	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs2477076	chr1:197660143-197660144	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs564764687	chr1:197660164-197660165	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs188239930	chr1:197660174-197660175	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs540987714	chr1:197660187-197660188	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs35506280	chr1:197660391-197660392	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs567937356	chr1:197660409-197660410	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs528913876	chr1:197660493-197660494	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs144862841	chr1:197660503-197660504	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs148399301	chr1:197660530-197660531	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs191913778	chr1:197660546-197660547	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs183652176	chr1:197660669-197660670	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs145059429	chr1:197660754-197660755	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs371963719	chr1:197660772-197660773	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs533801448	chr1:197660799-197660800	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs551659335	chr1:197660839-197660840	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs376576969	chr1:197660884-197660885	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs555263640	chr1:197660886-197660887	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs574718302	chr1:197660974-197660975	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs147568820	chr1:197660991-197660992	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs557163712	chr1:197661097-197661098	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:94)

Disease	PMID	Source
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Autism	22495311	CNVD
Liposarcoma	21253554	CNVD
Burkitt''s lymphoma	18698080	CNVD
Melanoma	18172304	CNVD
Rett syndrome	21593744	CNVD
Cancer	20164919	CNVD
Medulloblastoma	21979893	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Non-small cell lung cancer	21044232	CNVD
Cervical cancer	21063398	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	20632083	CNVD
Endometrial cancer	22040021	CNVD
Ewing''s sarcoma	21437220	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Medulloblastoma	21292688	CNVD
Phyllodes tumor	17334353	CNVD
Breast cancer	21264507	CNVD
Multiple myeloma	21628407	CNVD
Cancer	16751803	CNVD
Prostate cancer	16705090	CNVD
Neuroblastoma	19435921	CNVD
Breast cancer	17850661	CNVD
Breast cancer	16461572	CNVD
Intracranial tumor	16823260	CNVD
Medulloblastoma	18056178	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Colorectal cancer	16272173	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Neuroblastoma	21899760	CNVD
Glioblastoma multiforme	17002787	CNVD
Breast cancer	21858162	CNVD
Non-small cell lung cancer	21385341	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	16608533	CNVD
Ewing''s sarcoma	22429812	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Hepatocellular carcinoma	18803288	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Acute myeloid leukemia	21251322	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Testicular germ cell tumor	18059402	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Breast cancer	21509527	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Lung cancer	18438408	CNVD
Metanephric adenoma	20802469	CNVD
Breast cancer	21611746	CNVD
Breast cancer	17393978	CNVD
Hepatocellular carcinoma	16750200	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Non-small cell lung cancer	19010865	CNVD
Mental retardation	17847001	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Trisomy 5 syndrome	21098271	CNVD
Urothelial carcinoma	21177765	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Chordoma	18071362	CNVD
small cell lung cancer	20016488	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Urothelial cell carcinoma	18451213	CNVD
Glioblastoma multiforme	19435819	CNVD
Glioblastoma multiforme	22291905	CNVD
Lung adenocarcinoma	21935476	CNVD
Myelofibrosis	22110671	CNVD
Glioblastoma multiforme	20472715	CNVD
Multiple myeloma	16461302	CNVD
Leukoplakia	24403051	CNVD
Macular degeneration	22558131	CNVD
Alzheimer''s disease	21403675	CNVD
van der Woude syndrome	22470819	CNVD
van der Woude syndrome	20818247	CNVD
T-cell lymphomas	19863542	CNVD

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197645200-197661000	Weak transcription	Esophagus	oesophagus
2	chr1:197653000-197665200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:197653000-197665400	Weak transcription	Osteobl	bone
4	chr1:197653200-197659400	Weak transcription	Left Ventricle	heart
5	chr1:197653200-197660600	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr1:197653400-197662000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:197653600-197660600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:197653600-197660800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr1:197654600-197662200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr1:197656000-197662000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:197656200-197659600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:197656200-197663600	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr1:197656400-197660400	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr1:197657000-197677000	Weak transcription	Ovary	ovary
15	chr1:197657600-197659200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
16	chr1:197657600-197659200	ZNF genes & repeats	Dnd41	blood
17	chr1:197657800-197663400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:197658000-197659600	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr1:197658000-197661000	Weak transcription	Liver	Liver
20	chr1:197658000-197661000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr1:197658000-197665200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:197658200-197659400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr1:197658200-197659400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:197658200-197659400	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr1:197658200-197659600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:197658200-197660400	Weak transcription	Fetal Lung	lung
27	chr1:197658200-197660600	Weak transcription	Colonic Mucosa	Colon
28	chr1:197658200-197662000	Weak transcription	Thymus	Thymus
29	chr1:197658200-197662800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:197658200-197668200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr1:197658400-197659400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:197658400-197659600	Strong transcription	Duodenum Mucosa	Duodenum
33	chr1:197658400-197659800	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
34	chr1:197658400-197665000	Weak transcription	NHEK	skin
35	chr1:197658600-197659600	ZNF genes & repeats	Primary T cells from cord blood	blood
36	chr1:197658600-197662000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:197658800-197659600	Strong transcription	Primary B cells from cord blood	blood
38	chr1:197658800-197659600	Genic enhancers	K562	blood
39	chr1:197658800-197659800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr1:197658800-197659800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr1:197659000-197659200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
42	chr1:197659000-197659400	Strong transcription	Fetal Thymus	thymus
43	chr1:197659000-197659600	Strong transcription	Fetal Intestine Large	intestine
44	chr1:197659000-197659600	Strong transcription	Gastric	stomach
45	chr1:197659000-197659600	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr1:197659200-197659800	Strong transcription	Primary hematopoietic stem cells	blood
47	chr1:197659200-197659800	Strong transcription	Dnd41	blood
48	chr1:197659400-197659800	Enhancers	Left Ventricle	heart
49	chr1:197659400-197659800	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr1:197659400-197661000	Weak transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links