Variant report

Variant	esv3359336
Chromosome Location	chr1:180956329-180959227
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr1:180957649-180957941	HepG2	liver:	n/a	n/a
2	BHLHE40	chr1:180957647-180957883	K562	blood:	n/a	n/a
3	CEBPB	chr1:180957748-180958040	HepG2	liver:	n/a	n/a
4	CTCF	chr1:180957660-180957810	BE2_C	brain:	n/a	n/a
5	EP300	chr1:180957354-180958096	ECC-1	luminal epithelium:	n/a	n/a
6	ESR1	chr1:180957586-180957918	ECC-1	luminal epithelium:	n/a	n/a
7	FOXA1	chr1:180957803-180958211	HepG2	liver:	n/a	n/a
8	MAX	chr1:180957491-180957968	ECC-1	luminal epithelium:	n/a	n/a
9	MAX	chr1:180957526-180958019	ECC-1	luminal epithelium:	n/a	n/a
10	NFIC	chr1:180957283-180958120	ECC-1	luminal epithelium:	n/a	n/a
11	NFIC	chr1:180957334-180958019	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr1:180956261-180956561	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr1:180956262-180956359	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr1:180956379-180956414	HUVEC	blood vessel:	n/a	n/a
15	TBL1XR1	chr1:180957689-180957695	K562	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:180949324..180951935-chr1:180953444..180956382,3	K562	blood:
2	chr1:180959006..180960996-chr1:180963576..180966150,2	K562	blood:
3	chr1:180956077..180957992-chr1:181055022..181057950,3	K562	blood:
4	chr1:180955392..180957217-chr1:181057603..181059955,2	K562	blood:
5	chr1:180958996..180961747-chr1:180978821..180982179,3	K562	blood:
6	chr1:180959006..180960525-chr1:180963986..180966150,2	K562	blood:
7	chr1:180954145..180958035-chr1:180958971..180961801,3	MCF-7	breast:
8	chr1:180955050..180957807-chr1:181056708..181059227,4	MCF-7	breast:
9	chr1:180954965..180956478-chr1:181056393..181059194,2	MCF-7	breast:
10	chr1:180949324..180952994-chr1:180953444..180956382,4	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACBD6-7	chr1:180956861-180957231	NONHSAT008280
2	lnc-ACBD6-7	chr1:180957375-180957437	NONHSAT008280

No data

Variant related genes	Relation type
STX6	TF binding region
ENSG00000162783	chromatin interactions
ENSG00000135823	chromatin interactions

Extended variants
information (count: 131 )
Associated
traits (count: 88 )

Variant overlapped rSNPs/rCNVs (count:131 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs538117290	chr1:180956336-180956337	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs556821724	chr1:180956367-180956368	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs57728541	chr1:180956388-180956389	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs542625921	chr1:180956391-180956392	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs574268116	chr1:180956394-180956395	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs35435290	chr1:180956436-180956437	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs186173255	chr1:180956459-180956460	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs573019072	chr1:180956482-180956483	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs540416912	chr1:180956545-180956546	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs565030923	chr1:180956564-180956565	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs532337318	chr1:180956633-180956634	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs544150830	chr1:180956688-180956689	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs373734000	chr1:180956695-180956696	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs188293299	chr1:180956696-180956697	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs151018696	chr1:180956812-180956813	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs180725803	chr1:180956843-180956844	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs6425657	chr1:180956905-180956906	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs373950684	chr1:180956929-180956930	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
19	rs536037871	chr1:180956930-180956931	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
20	rs527822157	chr1:180956931-180956932	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
21	rs199524329	chr1:180956935-180956936	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
22	rs76560665	chr1:180956936-180956937	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
23	rs570911325	chr1:180956937-180956938	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
24	rs77480805	chr1:180956946-180956947	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
25	rs6425658	chr1:180956985-180956986	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
26	rs538206994	chr1:180956990-180956991	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
27	rs556517737	chr1:180956998-180956999	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
28	rs536248017	chr1:180957079-180957080	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
29	rs111823736	chr1:180957091-180957092	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
30	rs554643555	chr1:180957101-180957102	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
31	rs375644858	chr1:180957112-180957113	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
32	rs7528255	chr1:180957130-180957131	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs372474551	chr1:180957176-180957177	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
34	rs186466956	chr1:180957185-180957186	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
35	rs199640560	chr1:180957209-180957210	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
36	rs544429555	chr1:180957276-180957277	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs562619523	chr1:180957308-180957309	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs191248022	chr1:180957314-180957315	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs139556759	chr1:180957330-180957331	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs369399759	chr1:180957351-180957352	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs560076744	chr1:180957352-180957353	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs372942522	chr1:180957359-180957360	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs377395854	chr1:180957369-180957370	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs368981492	chr1:180957372-180957373	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs148101006	chr1:180957405-180957406	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
46	rs55788824	chr1:180957408-180957409	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
47	rs140743270	chr1:180957427-180957428	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
48	rs374326247	chr1:180957430-180957431	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
49	rs201572667	chr1:180957461-180957462	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs144912513	chr1:180957475-180957476	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:88)

Disease	PMID	Source
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Autism	22495311	CNVD
Hepatocellular carcinoma	16750200	CNVD
Liposarcoma	21253554	CNVD
Burkitt''s lymphoma	18698080	CNVD
Melanoma	18172304	CNVD
Cancer	21183584	CNVD
Multiple myeloma	16461302	CNVD
Rett syndrome	21593744	CNVD
Cancer	20164919	CNVD
Medulloblastoma	21979893	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	CNVD
Non-small cell lung cancer	21829676	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
Bladder cancer	19088036	CNVD
Ovarian neoplasms	16753589	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
Urothelial carcinoma	21177765	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
Trisomy 5 syndrome	21098271	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Neuroblastoma	18923191	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Ewing''s sarcoma	17952124	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Breast cancer	21509527	CNVD
Glioblastoma multiforme	17369134	CNVD
Cancer	17440070	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	21611746	CNVD
Breast cancer	16397240	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	23248035	CNVD
Metanephric adenoma	20802469	CNVD
Renal cell carcinoma	18765545	CNVD
Nephroblastoma	17189400	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Ovarian clear cell carcinoma	21343371	CNVD

Chromatin state (count:206 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180923600-180958800	Weak transcription	Small Intestine	intestine
2	chr1:180933400-180974600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:180939200-180965600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:180940400-180988400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:180943000-180957400	Weak transcription	Fetal Heart	heart
6	chr1:180943600-180972000	Weak transcription	Psoas Muscle	Psoas
7	chr1:180943600-180979800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:180944400-180962600	Strong transcription	Osteobl	bone
9	chr1:180944600-180957600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:180944800-180970800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:180945400-180975000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr1:180945600-180974800	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr1:180948200-180959400	Weak transcription	Stomach Mucosa	stomach
14	chr1:180948600-180961400	Strong transcription	Fetal Intestine Large	intestine
15	chr1:180948800-180959800	Strong transcription	Left Ventricle	heart
16	chr1:180948800-180961000	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr1:180949000-180962400	Strong transcription	Fetal Muscle Trunk	muscle
18	chr1:180949000-180962600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:180949400-180957400	Strong transcription	Fetal Muscle Leg	muscle
20	chr1:180949400-180963800	Strong transcription	Liver	Liver
21	chr1:180949800-180962600	Strong transcription	Adipose Nuclei	Adipose
22	chr1:180949800-180962600	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr1:180949800-180963800	Strong transcription	Duodenum Mucosa	Duodenum
24	chr1:180949800-180966200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:180950000-180962600	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr1:180950000-180964600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:180950000-180965200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:180950000-180966400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr1:180950000-180968200	Strong transcription	HMEC	breast
30	chr1:180950600-180962400	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr1:180950800-180962400	Strong transcription	Placenta	Placenta
32	chr1:180951000-180957400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:180951400-180960200	Strong transcription	Colon Smooth Muscle	Colon
34	chr1:180951400-180966200	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr1:180951600-180963800	Strong transcription	Fetal Lung	lung
36	chr1:180951600-180964800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr1:180951600-180966400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:180951800-180963600	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr1:180952000-180963000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:180952000-180963200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr1:180952000-180963800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:180952000-180965200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:180952000-180966000	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr1:180952000-180966200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr1:180952200-180957200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:180952200-180961200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:180952200-180962200	Strong transcription	GM12878-XiMat	blood
48	chr1:180952200-180964000	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr1:180952200-180974800	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr1:180952400-180963800	Strong transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links