Variant report

Variant	esv2758984
Chromosome Location	chr1:189959106-189995212
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	BATF	chr1:189991842-189992164	GM12878	blood:	n/a	chr1:189992041-189992052 chr1:189992005-189992016
2	BATF	chr1:189991830-189992153	GM12878	blood:	n/a	chr1:189992041-189992052 chr1:189992005-189992016
3	BCL3	chr1:189969460-189970122	A549	lung:	n/a	chr1:189969632-189969641 chr1:189969514-189969523
4	BCL3	chr1:189988838-189989301	A549	lung:	n/a	n/a
5	CBX3	chr1:189991798-189992237	HCT-116	colon:	n/a	n/a
6	CEBPB	chr1:189966592-189966813	MCF-7	breast:	n/a	chr1:189966685-189966696
7	CEBPB	chr1:189966523-189966870	IMR90	lung:	n/a	chr1:189966685-189966696
8	CEBPB	chr1:189966553-189966843	A549	lung:	n/a	chr1:189966685-189966696
9	CEBPB	chr1:189969527-189969898	IMR90	lung:	n/a	n/a
10	CEBPB	chr1:189984024-189984217	IMR90	lung:	n/a	n/a
11	CEBPB	chr1:189969579-189969895	A549	lung:	n/a	n/a
12	CEBPB	chr1:189966532-189966826	HepG2	liver:	n/a	chr1:189966685-189966696
13	CEBPB	chr1:189969426-189970047	A549	lung:	n/a	n/a
14	CEBPB	chr1:189966558-189966824	H1-hESC	embryonic stem cell:	n/a	chr1:189966685-189966696
15	CEBPB	chr1:189988895-189989826	A549	lung:	n/a	chr1:189989433-189989445 chr1:189989431-189989448
16	CEBPB	chr1:189966602-189966802	K562	blood:	n/a	chr1:189966685-189966696
17	CREB1	chr1:189988905-189989150	A549	lung:	n/a	n/a
18	CREB1	chr1:189988862-189989160	A549	lung:	n/a	n/a
19	CTCF	chr1:189961249-189961379	K562	blood:	n/a	n/a
20	CTCF	chr1:189961252-189961345	K562	blood:	n/a	n/a
21	CTCF	chr1:189980816-189980870	GM10266	blood:	n/a	n/a
22	CTCF	chr1:189978420-189978570	WI-38	lung:	n/a	n/a
23	E2F4	chr1:189964669-189964792	MCF10A-Er-Src	breast:	n/a	n/a
24	E2F4	chr1:189972563-189972857	MCF10A-Er-Src	breast:	n/a	n/a
25	E2F4	chr1:189969566-189969780	MCF10A-Er-Src	breast:	n/a	n/a
26	E2F4	chr1:189991842-189992193	MCF10A-Er-Src	breast:	n/a	n/a
27	EBF1	chr1:189959644-189959721	GM12878	blood:	n/a	n/a
28	EP300	chr1:189969356-189969962	A549	lung:	n/a	chr1:189969731-189969741 chr1:189969482-189969492 chr1:189969631-189969640
29	EP300	chr1:189970388-189970597	SK-N-SH_RA	brain:	n/a	chr1:189970503-189970512
30	EP300	chr1:189969450-189970053	A549	lung:	n/a	chr1:189969731-189969741 chr1:189969482-189969492 chr1:189969631-189969640
31	EP300	chr1:189991748-189992107	SK-N-SH_RA	brain:	n/a	n/a
32	EP300	chr1:189988686-189989384	A549	lung:	n/a	n/a
33	EP300	chr1:189970336-189970684	SK-N-SH_RA	brain:	n/a	chr1:189970503-189970512
34	EP300	chr1:189988751-189989337	A549	lung:	n/a	n/a
35	EP300	chr1:189970236-189970897	SK-N-SH	brain:	n/a	chr1:189970503-189970512
36	ESR1	chr1:189975314-189975671	ECC-1	luminal epithelium:	n/a	n/a
37	ESR1	chr1:189975324-189975656	ECC-1	luminal epithelium:	n/a	n/a
38	ESR1	chr1:189975368-189975792	ECC-1	luminal epithelium:	n/a	n/a
39	ESR1	chr1:189975302-189975707	ECC-1	luminal epithelium:	n/a	n/a
40	ESR1	chr1:189975353-189975639	ECC-1	luminal epithelium:	n/a	n/a
41	FAM48A	chr1:189993921-189994117	GM12878	blood:	n/a	n/a
42	FOS	chr1:189991768-189992245	MCF10A-Er-Src	breast:	n/a	chr1:189992043-189992054 chr1:189992007-189992018
43	FOS	chr1:189969468-189969904	MCF10A-Er-Src	breast:	n/a	chr1:189969689-189969696 chr1:189969631-189969641 chr1:189969688-189969696 chr1:189969631-189969641 chr1:189969687-189969697 chr1:189969633-189969640 chr1:189969631-189969640 chr1:189969630-189969641
44	FOS	chr1:189970344-189970635	MCF10A-Er-Src	breast:	n/a	chr1:189970501-189970513 chr1:189970503-189970511 chr1:189970502-189970512 chr1:189970503-189970510 chr1:189970503-189970511
45	FOS	chr1:189970336-189970696	MCF10A-Er-Src	breast:	n/a	chr1:189970501-189970513 chr1:189970503-189970511 chr1:189970502-189970512 chr1:189970503-189970510 chr1:189970503-189970511
46	FOS	chr1:189991823-189992259	MCF10A-Er-Src	breast:	n/a	chr1:189992043-189992054 chr1:189992007-189992018
47	FOS	chr1:189969441-189969881	HUVEC	blood vessel:	n/a	chr1:189969689-189969696 chr1:189969631-189969641 chr1:189969688-189969696 chr1:189969631-189969641 chr1:189969687-189969697 chr1:189969633-189969640 chr1:189969631-189969640 chr1:189969630-189969641
48	FOS	chr1:189988911-189989144	MCF10A-Er-Src	breast:	n/a	n/a
49	FOS	chr1:189966590-189966750	MCF10A-Er-Src	breast:	n/a	n/a
50	FOS	chr1:189991830-189992249	HUVEC	blood vessel:	n/a	chr1:189992043-189992054 chr1:189992007-189992018

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:189955705..189957975-chr1:189976972..189978590,2	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: 791 )
Associated
traits (count: 86 )

Variant overlapped rSNPs/rCNVs (count:791 , 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	rs1711762	chr1:189959106-189959107	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs371531361	chr1:189959111-189959112	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
3	rs539035077	chr1:189959120-189959121	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
4	rs145198456	chr1:189959121-189959122	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
5	rs376882609	chr1:189959122-189959123	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
6	rs542112799	chr1:189959138-189959139	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
7	rs555641560	chr1:189959142-189959143	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
8	rs572263609	chr1:189959156-189959157	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
9	rs541239780	chr1:189959161-189959162	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
10	rs564393424	chr1:189959172-189959173	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
11	rs187928752	chr1:189959181-189959182	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
12	rs552226299	chr1:189959222-189959223	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
13	rs115548550	chr1:189959260-189959261	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
14	rs34976499	chr1:189959266-189959267	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
15	rs563693719	chr1:189959296-189959297	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
16	rs147647071	chr1:189959303-189959304	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
17	rs548458950	chr1:189959324-189959325	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
18	rs561974057	chr1:189959353-189959354	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
19	rs140560405	chr1:189959383-189959384	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
20	rs547592428	chr1:189959408-189959409	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
21	rs191812126	chr1:189959435-189959436	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
22	rs149668793	chr1:189959453-189959454	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
23	rs549655753	chr1:189959462-189959463	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
24	rs374273243	chr1:189959487-189959488	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
25	rs552642864	chr1:189959499-189959500	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
26	rs145454586	chr1:189959503-189959504	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
27	rs555604472	chr1:189959504-189959505	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
28	rs116052962	chr1:189959505-189959506	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
29	rs535010385	chr1:189959510-189959511	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
30	rs558317224	chr1:189959519-189959520	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
31	rs578141822	chr1:189959524-189959525	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
32	rs377639500	chr1:189959553-189959554	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
33	rs184291625	chr1:189959618-189959619	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
34	rs574044419	chr1:189959622-189959623	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
35	rs187224669	chr1:189959629-189959630	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
36	rs34905823	chr1:189959648-189959649	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
37	rs148862196	chr1:189959661-189959662	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
38	rs527562891	chr1:189959669-189959670	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
39	rs143485334	chr1:189959692-189959693	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
40	rs564301989	chr1:189959699-189959700	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
41	rs145302935	chr1:189959713-189959714	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
42	rs532985056	chr1:189959735-189959736	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
43	rs192098749	chr1:189959785-189959786	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
44	rs373842868	chr1:189959810-189959811	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
45	rs569426078	chr1:189959825-189959826	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
46	rs112444765	chr1:189959836-189959837	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
47	rs539386415	chr1:189959838-189959839	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
48	rs535053003	chr1:189959889-189959890	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
49	rs114817354	chr1:189959898-189959899	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
50	rs573006290	chr1:189959899-189959900	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:86)

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

Chromatin state (count:23 , 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

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