Variant report

Variant	nsv1008070
Chromosome Location	chr1:189957274-190059876
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	chr1:190016214-190016230	K562	blood:	n/a	n/a
2	ATF1	chr1:190051157-190051215	K562	blood:	n/a	n/a
3	ATF1	chr1:190051988-190052145	K562	blood:	n/a	n/a
4	BATF	chr1:190036725-190037097	GM12878	blood:	n/a	n/a
5	BATF	chr1:189991830-189992153	GM12878	blood:	n/a	chr1:189992041-189992052 chr1:189992005-189992016
6	BATF	chr1:189991842-189992164	GM12878	blood:	n/a	chr1:189992041-189992052 chr1:189992005-189992016
7	BCL11A	chr1:190047886-190048042	H1-hESC	embryonic stem cell:	n/a	n/a
8	BCL3	chr1:189988838-189989301	A549	lung:	n/a	n/a
9	BCL3	chr1:189969460-189970122	A549	lung:	n/a	chr1:189969632-189969641 chr1:189969514-189969523
10	BHLHE40	chr1:190036771-190037053	GM12878	blood:	n/a	n/a
11	CBX3	chr1:189991798-189992237	HCT-116	colon:	n/a	n/a
12	CCNT2	chr1:190031477-190031677	K562	blood:	n/a	n/a
13	CEBPB	chr1:189969426-189970047	A549	lung:	n/a	n/a
14	CEBPB	chr1:189966553-189966843	A549	lung:	n/a	chr1:189966685-189966696
15	CEBPB	chr1:189966532-189966826	HepG2	liver:	n/a	chr1:189966685-189966696
16	CEBPB	chr1:189969579-189969895	A549	lung:	n/a	n/a
17	CEBPB	chr1:190022786-190023087	A549	lung:	n/a	chr1:190022908-190022919 chr1:190022910-190022921
18	CEBPB	chr1:190022731-190023097	HepG2	liver:	n/a	chr1:190022908-190022919 chr1:190022910-190022921
19	CEBPB	chr1:189966602-189966802	K562	blood:	n/a	chr1:189966685-189966696
20	CEBPB	chr1:189966558-189966824	H1-hESC	embryonic stem cell:	n/a	chr1:189966685-189966696
21	CEBPB	chr1:190022770-190023091	Hela-S3	cervix:	n/a	chr1:190022908-190022919 chr1:190022910-190022921
22	CEBPB	chr1:189984024-189984217	IMR90	lung:	n/a	n/a
23	CEBPB	chr1:190018701-190018975	HepG2	liver:	n/a	chr1:190018868-190018879
24	CEBPB	chr1:189966592-189966813	MCF-7	breast:	n/a	chr1:189966685-189966696
25	CEBPB	chr1:189966523-189966870	IMR90	lung:	n/a	chr1:189966685-189966696
26	CEBPB	chr1:190030719-190030908	HepG2	liver:	n/a	n/a
27	CEBPB	chr1:190022738-190023096	IMR90	lung:	n/a	chr1:190022908-190022919 chr1:190022910-190022921
28	CEBPB	chr1:190022753-190023086	K562	blood:	n/a	chr1:190022908-190022919 chr1:190022910-190022921
29	CEBPB	chr1:190036611-190037203	IMR90	lung:	n/a	n/a
30	CEBPB	chr1:190022698-190023110	A549	lung:	n/a	chr1:190022908-190022919 chr1:190022910-190022921
31	CEBPB	chr1:190018699-190018999	A549	lung:	n/a	chr1:190018868-190018879
32	CEBPB	chr1:189969527-189969898	IMR90	lung:	n/a	n/a
33	CEBPB	chr1:190001836-190002036	A549	lung:	n/a	n/a
34	CEBPB	chr1:189988895-189989826	A549	lung:	n/a	chr1:189989433-189989445 chr1:189989431-189989448
35	CREB1	chr1:189988905-189989150	A549	lung:	n/a	n/a
36	CREB1	chr1:189988862-189989160	A549	lung:	n/a	n/a
37	CTCF	chr1:190053736-190053973	MCF-7	breast:	n/a	n/a
38	CTCF	chr1:190053720-190053870	GM12869	blood:	n/a	n/a
39	CTCF	chr1:190053800-190053950	GM12867	blood:	n/a	n/a
40	CTCF	chr1:190054160-190054310	GM12864	blood:	n/a	n/a
41	CTCF	chr1:190053720-190053870	HCPEpiC	choroid plexus:	n/a	n/a
42	CTCF	chr1:190049157-190049186	MCF-7	breast:	n/a	n/a
43	CTCF	chr1:190053612-190053990	MCF-7	breast:	n/a	n/a
44	CTCF	chr1:190053783-190053948	HUVEC	blood vessel:	n/a	n/a
45	CTCF	chr1:190053840-190053990	HRE	kidney:	n/a	n/a
46	CTCF	chr1:189978420-189978570	WI-38	lung:	n/a	n/a
47	CTCF	chr1:190053709-190054012	HepG2	liver:	n/a	n/a
48	CTCF	chr1:190048987-190049309	MCF-7	breast:	n/a	chr1:190049145-190049166 chr1:190049143-190049161 chr1:190049144-190049160 chr1:190049147-190049154
49	CTCF	chr1:190053744-190053986	GM12878	blood:	n/a	n/a
50	CTCF	chr1:189999434-189999499	Medullo	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:190055531..190057704-chr1:190069392..190071855,2	MCF-7	breast:
2	chr1:189677502..189678569-chr1:190053452..190054228,3	MCF-7	breast:
3	chr1:190017220..190019071-chr1:190031921..190033627,2	MCF-7	breast:
4	chr1:189955705..189957975-chr1:189976972..189978590,2	K562	blood:
5	chr1:189955705..189957975-chr1:189976972..189978590,2	K562	blood:
6	chr1:190017220..190019071-chr1:190031921..190033627,2	MCF-7	breast:
7	chr1:190011663..190013449-chr1:190017469..190019523,2	K562	blood:
8	chr1:189897967..189900169-chr1:190054489..190056512,2	MCF-7	breast:
9	chr1:190011663..190013449-chr1:190017469..190019523,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM5C-5	chr1:189958700-189962227	NONHSAT008489

Variant related genes	Relation type
ENSG00000230987	TF binding region

Extended variants
information (count: 1498 )
Associated
traits (count: 87 )

Variant overlapped rSNPs/rCNVs (count:1498 , 50 per page) page: 1 2 3 4 5 6 7 ... 30

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs16829300	chr1:189958756-189958757	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs568294189	chr1:189958775-189958776	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
3	rs16829304	chr1:189958783-189958784	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs150784030	chr1:189958792-189958793	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
5	rs576716505	chr1:189958795-189958796	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
6	rs545018508	chr1:189958818-189958819	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
7	rs545793895	chr1:189958850-189958851	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
8	rs1730734	chr1:189958874-189958875	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
9	rs74128405	chr1:189958919-189958920	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs542150858	chr1:189958961-189958962	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
11	rs375062914	chr1:189958973-189958974	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
12	rs182924143	chr1:189958980-189958981	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
13	rs527925457	chr1:189958981-189958982	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
14	rs541077614	chr1:189959011-189959012	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
15	rs115914944	chr1:189959015-189959016	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
16	rs74128406	chr1:189959039-189959040	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs550168365	chr1:189959053-189959054	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
18	rs139641778	chr1:189959074-189959075	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
19	rs548546516	chr1:189959075-189959076	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
20	rs568259722	chr1:189959089-189959090	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
21	rs78356759	chr1:189959093-189959094	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
22	rs1711762	chr1:189959106-189959107	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
23	rs371531361	chr1:189959111-189959112	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
24	rs539035077	chr1:189959120-189959121	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
25	rs145198456	chr1:189959121-189959122	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
26	rs376882609	chr1:189959122-189959123	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
27	rs542112799	chr1:189959138-189959139	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
28	rs555641560	chr1:189959142-189959143	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
29	rs572263609	chr1:189959156-189959157	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
30	rs541239780	chr1:189959161-189959162	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
31	rs564393424	chr1:189959172-189959173	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
32	rs187928752	chr1:189959181-189959182	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
33	rs552226299	chr1:189959222-189959223	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
34	rs115548550	chr1:189959260-189959261	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
35	rs34976499	chr1:189959266-189959267	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
36	rs563693719	chr1:189959296-189959297	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
37	rs147647071	chr1:189959303-189959304	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
38	rs548458950	chr1:189959324-189959325	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
39	rs561974057	chr1:189959353-189959354	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
40	rs140560405	chr1:189959383-189959384	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
41	rs547592428	chr1:189959408-189959409	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
42	rs191812126	chr1:189959435-189959436	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
43	rs149668793	chr1:189959453-189959454	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
44	rs549655753	chr1:189959462-189959463	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
45	rs374273243	chr1:189959487-189959488	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
46	rs552642864	chr1:189959499-189959500	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
47	rs145454586	chr1:189959503-189959504	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
48	rs555604472	chr1:189959504-189959505	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
49	rs116052962	chr1:189959505-189959506	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
50	rs535010385	chr1:189959510-189959511	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:87)

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
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
Chronic lymphocytic leukemia	22228453	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:189968400-189969600	Enhancers	A549	lung
2	chr1:189969400-189970600	Enhancers	Muscle Satellite Cultured Cells	--
3	chr1:189969600-189969800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:189969600-189970600	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr1:189969600-189970600	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr1:189969600-189970600	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr1:189969600-189970600	Flanking Active TSS	A549	lung
8	chr1:189969800-189970400	Enhancers	Hela-S3	cervix
9	chr1:189970000-189970400	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr1:189970200-189971000	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr1:189970400-189970600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:189970600-189970800	Enhancers	A549	lung
13	chr1:189979000-189979400	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr1:189983000-189986200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:189985800-189986600	Enhancers	A549	lung
16	chr1:189986600-189989000	Weak transcription	A549	lung
17	chr1:189988400-189988800	Active TSS	Placenta	Placenta
18	chr1:189988800-189990000	Enhancers	Placenta	Placenta
19	chr1:189989000-189989200	Flanking Active TSS	A549	lung
20	chr1:189989200-189989600	Active TSS	A549	lung
21	chr1:189989600-189990400	Enhancers	A549	lung
22	chr1:189990400-189991400	Weak transcription	A549	lung
23	chr1:189991400-189992200	Enhancers	A549	lung
24	chr1:190006600-190007200	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr1:190006600-190007200	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr1:190007200-190020600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr1:190016000-190016800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:190016000-190016800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:190018600-190018800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:190018800-190021200	Enhancers	Muscle Satellite Cultured Cells	--
31	chr1:190019600-190019800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr1:190019800-190021400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr1:190020400-190021800	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr1:190020600-190021200	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr1:190021000-190021400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:190021400-190021800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:190036200-190036600	Enhancers	Fetal Intestine Large	intestine
38	chr1:190036200-190037000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:190036200-190037600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:190036600-190036800	Enhancers	Muscle Satellite Cultured Cells	--
41	chr1:190037400-190037600	Enhancers	Muscle Satellite Cultured Cells	--
42	chr1:190053600-190054200	Enhancers	Placenta	Placenta

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