Variant report

Variant	nsv548543
Chromosome Location	chr1:189785833-189841516
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:311)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:311 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr1:189821289-189821443	GM12878	blood:	n/a	n/a
2	CBX3	chr1:189828579-189828874	K562	blood:	n/a	n/a
3	CBX3	chr1:189828545-189828884	K562	blood:	n/a	n/a
4	CEBPB	chr1:189818371-189818983	HepG2	liver:	n/a	chr1:189818808-189818821
5	CEBPB	chr1:189818364-189818608	A549	lung:	n/a	n/a
6	CEBPB	chr1:189837043-189837350	A549	lung:	n/a	n/a
7	CHD2	chr1:189828659-189828858	GM12878	blood:	n/a	n/a
8	CTCF	chr1:189828640-189828790	AG09319	gingival:	n/a	n/a
9	CTCF	chr1:189828600-189828750	HCPEpiC	choroid plexus:	n/a	n/a
10	CTCF	chr1:189828888-189828892	GM19238	blood:	n/a	n/a
11	CTCF	chr1:189828620-189828770	GM12875	blood:	n/a	n/a
12	CTCF	chr1:189828580-189828730	HCM	heart:	n/a	n/a
13	CTCF	chr1:189828640-189828790	HCPEpiC	choroid plexus:	n/a	n/a
14	CTCF	chr1:189828547-189828793	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr1:189828600-189828750	HBMEC	blood vessel:	n/a	n/a
16	CTCF	chr1:189828620-189828770	GM12869	blood:	n/a	n/a
17	CTCF	chr1:189828660-189828810	GM12872	blood:	n/a	n/a
18	CTCF	chr1:189828609-189828838	GM20000	blood:	n/a	n/a
19	CTCF	chr1:189828580-189828730	GM12867	blood:	n/a	n/a
20	CTCF	chr1:189828640-189828790	SAEC	small airway:	n/a	n/a
21	CTCF	chr1:189790367-189790393	Kidney_OC	kidney:	n/a	n/a
22	CTCF	chr1:189828580-189828730	NHDF-neo	bronchial:	n/a	n/a
23	CTCF	chr1:189828640-189828790	HepG2	liver:	n/a	n/a
24	CTCF	chr1:189828620-189828770	WERI-Rb-1	eye:	n/a	n/a
25	CTCF	chr1:189828620-189828770	BE2_C	brain:	n/a	n/a
26	CTCF	chr1:189828620-189828770	GM12873	blood:	n/a	n/a
27	CTCF	chr1:189828660-189828810	RPTEC	kidney:	n/a	n/a
28	CTCF	chr1:189828750-189828755	Kidney_OC	kidney:	n/a	n/a
29	CTCF	chr1:189828660-189828810	HMEC	breast:	n/a	n/a
30	CTCF	chr1:189828640-189828790	GM12864	blood:	n/a	n/a
31	CTCF	chr1:189828572-189828883	GM19238	blood:	n/a	n/a
32	CTCF	chr1:189828581-189828866	LNCaP	prostate:	n/a	n/a
33	CTCF	chr1:189828576-189828844	MCF-7	breast:	n/a	n/a
34	CTCF	chr1:189828591-189828863	GM19239	blood:	n/a	n/a
35	CTCF	chr1:189828640-189828790	HMF	breast:	n/a	n/a
36	CTCF	chr1:189828640-189828790	SK-N-SH_RA	brain:	n/a	n/a
37	CTCF	chr1:189828640-189828790	HEEpiC	esophagus:	n/a	n/a
38	CTCF	chr1:189828600-189828750	AG09319	gingival:	n/a	n/a
39	CTCF	chr1:189828700-189828850	A549	lung:	n/a	n/a
40	CTCF	chr1:189828620-189828770	Hela-S3	cervix:	n/a	n/a
41	CTCF	chr1:189828680-189828830	HRE	kidney:	n/a	n/a
42	CTCF	chr1:189828661-189828747	Kidney_OC	kidney:	n/a	n/a
43	CTCF	chr1:189828620-189828770	GM12871	blood:	n/a	n/a
44	CTCF	chr1:189828540-189828690	HA-sp	spinal cord:	n/a	n/a
45	CTCF	chr1:189828897-189828966	GM19238	blood:	n/a	n/a
46	CTCF	chr1:189828600-189828750	HEEpiC	esophagus:	n/a	n/a
47	CTCF	chr1:189828530-189828779	HepG2	liver:	n/a	n/a
48	CTCF	chr1:189828640-189828790	Hela-S3	cervix:	n/a	n/a
49	CTCF	chr1:189828620-189828770	GM12872	blood:	n/a	n/a
50	CTCF	chr1:189828620-189828770	GM12874	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:189778329..189781313-chr1:189784587..189786793,2	MCF-7	breast:
2	chr1:189828427..189829123-chr1:190093339..190093859,2	MCF-7	breast:
3	chr1:189790429..189793066-chr1:189800961..189802500,2	MCF-7	breast:
4	chr1:189790429..189793066-chr1:189800961..189802500,2	MCF-7	breast:
5	chr1:189813747..189815721-chr1:189850350..189852733,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM5C-1	chr1:189837457-189837658	XLOC_001130
2	lnc-FAM5C-1	chr1:189837131-189837342	XLOC_001130

No data

Variant related genes	Relation type
ENSG00000238270	TF binding region

Extended variants
information (count: 752 )
Associated
traits (count: 88 )

Variant overlapped rSNPs/rCNVs (count:752 , 50 per page) page: 1 2 3 4 5 6 7 ... 16

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs3931586	chr1:189785833-189785834	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs551621611	chr1:189785949-189785950	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs115437899	chr1:189785964-189785965	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs1517098	chr1:189785983-189785984	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
5	rs182103475	chr1:189785996-189785997	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs187650983	chr1:189786002-189786003	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs563712093	chr1:189786041-189786042	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs555219021	chr1:189786051-189786052	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs374812169	chr1:189786056-189786057	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs1517099	chr1:189786148-189786149	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs1517100	chr1:189786171-189786172	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs192003396	chr1:189786184-189786185	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs1517101	chr1:189786213-189786214	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs4845154	chr1:189786228-189786229	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs533472616	chr1:189786239-189786240	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs557607527	chr1:189786301-189786302	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs10919808	chr1:189786347-189786348	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs4845198	chr1:189786356-189786357	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs4845199	chr1:189786362-189786363	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs71637218	chr1:189786389-189786390	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs138084665	chr1:189786432-189786433	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs545385305	chr1:189786433-189786434	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs115676743	chr1:189786439-189786440	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs182630522	chr1:189786524-189786525	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs550632594	chr1:189786557-189786558	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs9427447	chr1:189786558-189786559	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
27	rs142276769	chr1:189786561-189786562	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs549049547	chr1:189786580-189786581	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs185389200	chr1:189786600-189786601	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs534568169	chr1:189786630-189786631	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs9427448	chr1:189786691-189786692	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs111342047	chr1:189786692-189786693	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs9427449	chr1:189786693-189786694	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs146070165	chr1:189786744-189786745	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs138689944	chr1:189786764-189786765	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs558258404	chr1:189786787-189786788	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs9427450	chr1:189786807-189786808	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs12027808	chr1:189786819-189786820	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs553242114	chr1:189786875-189786876	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs9427451	chr1:189786885-189786886	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs545342192	chr1:189786889-189786890	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs9427452	chr1:189786896-189786897	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs141147410	chr1:189786924-189786925	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs544333772	chr1:189786952-189786953	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs563570999	chr1:189786970-189786971	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs190094938	chr1:189786980-189786981	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs9427453	chr1:189786984-189786985	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs12027840	chr1:189786998-189786999	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs182793224	chr1:189787045-189787046	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs551361703	chr1:189787061-189787062	Weak transcription	n/a	n/a	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
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
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
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
Ewing''s sarcoma	17952124	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Lung cancer	18438408	CNVD
Breast cancer	21509527	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Metanephric adenoma	20802469	CNVD
Melanoma	20688739	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	21611746	CNVD
primary effusion lymphomas	17116491	CNVD
Breast cancer	17393978	CNVD
Hepatocellular carcinoma	16750200	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Breast cancer	17899364	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
Acute lymphoblastic leukemia	21390130	CNVD
Cutaneous T-cell lymphoma	21881587	CNVD
Lung adenocarcinoma	17086460	CNVD
Glioblastoma multiforme	22286061	CNVD
Pancreatic cancer	17952125	CNVD
Chronic lymphocytic leukemia	22228453	CNVD

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:189785400-189786000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr1:189785600-189786000	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr1:189785600-189786200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:189785600-189786200	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr1:189785600-189786200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr1:189785800-189786200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:189785800-189786200	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr1:189786200-189789400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:189786200-189789800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:189786200-189789800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:189786200-189790000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:189789000-189789200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:189789400-189790800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:189789400-189792800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:189789800-189790200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:189789800-189790200	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr1:189789800-189790600	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr1:189790000-189791600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:189790200-189791200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:189790800-189791600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:189791200-189791400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:189791600-189791800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:189801800-189804400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:189802000-189803200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:189803200-189804000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:189804000-189804200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:189806400-189806800	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr1:189819400-189819800	Enhancers	iPS-15b Cell Line	embryonic stem cell
29	chr1:189819600-189821400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:189820200-189821400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr1:189828600-189829200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
32	chr1:189828600-189830800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:189829200-189829800	ZNF genes & repeats	Pancreas	Pancrea
34	chr1:189837200-189837600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:189839800-189841000	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr1:189840000-189841000	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr1:189840000-189841200	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr1:189840400-189840600	Enhancers	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links