Variant report

Variant	esv2757015
Chromosome Location	chr3:145615852-145661771
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	chr3:145617884-145618161	GM12878	blood:	n/a	chr3:145617976-145617987
2	BATF	chr3:145661502-145661720	GM12878	blood:	n/a	chr3:145661650-145661660 chr3:145661649-145661660
3	BATF	chr3:145617078-145617323	GM12878	blood:	n/a	chr3:145617167-145617178
4	BATF	chr3:145617922-145618098	GM12878	blood:	n/a	chr3:145617976-145617987
5	BATF	chr3:145617031-145617299	GM12878	blood:	n/a	chr3:145617167-145617178
6	BCL11A	chr3:145617839-145618177	GM12878	blood:	n/a	chr3:145617979-145617988 chr3:145617980-145617989
7	BCL11A	chr3:145617942-145618090	GM12878	blood:	n/a	chr3:145617979-145617988 chr3:145617980-145617989
8	BHLHE40	chr3:145617829-145618365	GM12878	blood:	n/a	n/a
9	BHLHE40	chr3:145616343-145617288	GM12878	blood:	n/a	n/a
10	CEBPB	chr3:145627345-145627605	IMR90	lung:	n/a	chr3:145627469-145627480
11	CEBPB	chr3:145654814-145655116	IMR90	lung:	n/a	chr3:145654981-145654992 chr3:145654981-145654990
12	CEBPB	chr3:145654854-145655147	HepG2	liver:	n/a	chr3:145654981-145654992 chr3:145654981-145654990
13	CEBPB	chr3:145643113-145643361	A549	lung:	n/a	chr3:145643198-145643209 chr3:145643269-145643282 chr3:145643200-145643211 chr3:145643216-145643227
14	CEBPB	chr3:145643100-145643364	HepG2	liver:	n/a	chr3:145643198-145643209 chr3:145643269-145643282 chr3:145643200-145643211 chr3:145643216-145643227
15	CEBPB	chr3:145617031-145617489	IMR90	lung:	n/a	chr3:145617318-145617329
16	CEBPB	chr3:145627344-145627617	Hela-S3	cervix:	n/a	chr3:145627469-145627480
17	CEBPB	chr3:145616337-145617569	Hela-S3	cervix:	n/a	chr3:145617318-145617329
18	CEBPB	chr3:145627381-145627633	A549	lung:	n/a	chr3:145627469-145627480
19	CEBPB	chr3:145617147-145617472	A549	lung:	n/a	chr3:145617318-145617329
20	CEBPB	chr3:145627345-145627654	HepG2	liver:	n/a	chr3:145627469-145627480
21	CEBPB	chr3:145617170-145617502	HepG2	liver:	n/a	chr3:145617318-145617329
22	CEBPB	chr3:145654848-145655110	A549	lung:	n/a	chr3:145654981-145654992 chr3:145654981-145654990
23	CHD1	chr3:145618779-145618801	GM12878	blood:	n/a	n/a
24	CHD2	chr3:145617860-145618182	GM12878	blood:	n/a	n/a
25	CHD2	chr3:145657978-145657991	HepG2	liver:	n/a	n/a
26	CTCF	chr3:145633720-145633870	GM12875	blood:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
27	CTCF	chr3:145633680-145633830	GM12873	blood:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
28	CTCF	chr3:145633700-145633850	HCPEpiC	choroid plexus:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
29	CTCF	chr3:145633760-145633910	HFF	foreskin:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
30	CTCF	chr3:145633680-145633930	GM12872	blood:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
31	CTCF	chr3:145633660-145633810	RPTEC	kidney:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
32	CTCF	chr3:145633639-145633942	GM12878	blood:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
33	CTCF	chr3:145633740-145633890	GM12867	blood:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
34	CTCF	chr3:145633640-145633790	GM12872	blood:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
35	CTCF	chr3:145633597-145634009	MCF-7	breast:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
36	CTCF	chr3:145633620-145633770	BE2_C	brain:	n/a	n/a
37	CTCF	chr3:145633660-145633810	HMF	breast:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
38	CTCF	chr3:145633620-145633770	HMEC	breast:	n/a	n/a
39	CTCF	chr3:145633660-145633810	HEK293	kidney:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
40	CTCF	chr3:145633710-145633889	MCF-7	breast:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
41	CTCF	chr3:145635708-145635840	GM20000	blood:	n/a	n/a
42	CTCF	chr3:145633689-145633849	HepG2	liver:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
43	CTCF	chr3:145633680-145633830	MCF-7	breast:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
44	CTCF	chr3:145633740-145633890	HCT-116	colon:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
45	CTCF	chr3:145633704-145633867	Hela-S3	cervix:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
46	CTCF	chr3:145633860-145634010	A549	lung:	n/a	n/a
47	CTCF	chr3:145633751-145633795	GM12878	blood:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
48	CTCF	chr3:145633660-145633810	Caco-2	colon:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
49	CTCF	chr3:145633700-145633850	HepG2	liver:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784
50	CTCF	chr3:145633700-145633850	WERI-Rb-1	eye:	n/a	chr3:145633771-145633784 chr3:145633769-145633787 chr3:145633770-145633786 chr3:145633775-145633784

No.	Distal block	Cell Line	Cell type
1	chr3:145621110..145623041-chr3:145624593..145626157,2	K562	blood:
2	chr3:145621110..145623041-chr3:145624593..145626157,2	K562	blood:
3	chr3:145604775..145606383-chr3:145616815..145618517,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC107021.1-3	chr3:145657755-145657941	XLOC_002852
2	lnc-AC107021.1-3	chr3:145657699-145657941	XLOC_002852

Variant related genes	Relation type
ENSG00000244358	TF binding region
TWSG1	miRNA target sites

Extended variants
information (count: 756 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:756 , 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	rs1849514	chr3:145615852-145615853	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs562508862	chr3:145615862-145615863	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
3	rs529920337	chr3:145615941-145615942	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
4	rs149297549	chr3:145615958-145615959	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
5	rs566570061	chr3:145615960-145615961	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
6	rs545389236	chr3:145615963-145615964	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
7	rs183172269	chr3:145615984-145615985	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs563962742	chr3:145616008-145616009	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs3914311	chr3:145616107-145616108	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs368441762	chr3:145616132-145616133	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
11	rs35010900	chr3:145616137-145616138	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
12	rs5853245	chr3:145616149-145616150	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
13	rs397744469	chr3:145616159-145616160	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs78703182	chr3:145616160-145616161	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs201081924	chr3:145616161-145616162	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs112391176	chr3:145616172-145616173	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
17	rs570487500	chr3:145616174-145616175	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs539307024	chr3:145616192-145616193	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
19	rs1718315	chr3:145616204-145616205	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs373964054	chr3:145616236-145616237	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs144523861	chr3:145616248-145616249	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs3914310	chr3:145616281-145616282	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs554906598	chr3:145616283-145616284	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs148063397	chr3:145616284-145616285	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs1708436	chr3:145616313-145616314	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs374232941	chr3:145616442-145616443	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
27	rs141767978	chr3:145616448-145616449	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
28	rs544149237	chr3:145616449-145616450	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
29	rs7652032	chr3:145616506-145616507	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs529807943	chr3:145616524-145616525	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
31	rs541996652	chr3:145616526-145616527	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
32	rs147250748	chr3:145616593-145616594	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
33	rs533512138	chr3:145616628-145616629	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
34	rs527356949	chr3:145616630-145616631	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
35	rs552319539	chr3:145616835-145616836	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
36	rs76693863	chr3:145616860-145616861	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
37	rs4318523	chr3:145616862-145616863	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
38	rs531342813	chr3:145616871-145616872	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
39	rs74532389	chr3:145616879-145616880	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
40	rs140688952	chr3:145616972-145616973	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
41	rs536590978	chr3:145617074-145617075	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs78691972	chr3:145617078-145617079	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs115130776	chr3:145617082-145617083	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs4365596	chr3:145617087-145617088	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs533995776	chr3:145617121-145617122	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs549512096	chr3:145617147-145617148	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs558647337	chr3:145617163-145617164	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs367716389	chr3:145617185-145617186	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs80195847	chr3:145617201-145617202	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs576779266	chr3:145617211-145617212	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:57)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Basal cell lymphoma	21115979	CNVD
Colorectal cancer	18645599	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Hepatocellular carcinoma	16750200	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Blepharophimosis-ptosis-epicanthus inversus syndrome	22067867	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
abnormal development	18461090	CNVD
Breast cancer	21364760	CNVD
Mental retardation	17847001	CNVD
Basal cell lymphoma	17170743	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Autism	18923514	CNVD
Autism	22241247	CNVD
Myelofibrosis	22110671	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Autism	21956041	CNVD
Ovarian clear cell carcinoma	19293255	CNVD
Breast cancer	16608533	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	21509527	CNVD
Bipolar disorder	19114987	CNVD
Schizophrenia	23813976	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:130 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145611200-145616000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr3:145613200-145616200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:145615000-145621000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:145615600-145616000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:145615600-145616400	Enhancers	Colon Smooth Muscle	Colon
6	chr3:145615800-145616000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:145615800-145616000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:145615800-145616000	Enhancers	Osteobl	bone
9	chr3:145615800-145616200	Enhancers	Brain Hippocampus Middle	brain
10	chr3:145615800-145616600	Active TSS	Aorta	Aorta
11	chr3:145615800-145616600	Enhancers	Rectal Smooth Muscle	rectum
12	chr3:145615800-145617000	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr3:145615800-145617000	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr3:145615800-145617200	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr3:145615800-145617400	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr3:145615800-145617400	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr3:145616000-145616200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:145616000-145616200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:145616000-145616200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:145616000-145616200	Enhancers	Hela-S3	cervix
21	chr3:145616000-145616600	Active TSS	A549	lung
22	chr3:145616000-145616800	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr3:145616000-145616800	Flanking Active TSS	Osteobl	bone
24	chr3:145616000-145617000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:145616000-145617600	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr3:145616200-145616400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:145616200-145616400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:145616200-145616400	Active TSS	Brain Cingulate Gyrus	brain
29	chr3:145616200-145616400	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr3:145616200-145616400	Active TSS	NH-A	brain
31	chr3:145616200-145616600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:145616200-145616600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:145616200-145616600	Active TSS	Brain Anterior Caudate	brain
34	chr3:145616200-145616600	Active TSS	Brain Inferior Temporal Lobe	brain
35	chr3:145616200-145616600	Active TSS	Ovary	ovary
36	chr3:145616200-145616600	Active TSS	Right Atrium	heart
37	chr3:145616200-145616600	Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr3:145616200-145616600	Active TSS	NHDF-Ad	bronchial
39	chr3:145616200-145616600	Active TSS	NHLF	lung
40	chr3:145616200-145616800	Active TSS	Brain Hippocampus Middle	brain
41	chr3:145616200-145617000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr3:145616200-145617000	Enhancers	Adipose Nuclei	Adipose
43	chr3:145616200-145617000	Active TSS	Stomach Smooth Muscle	stomach
44	chr3:145616200-145617000	Flanking Active TSS	Hela-S3	cervix
45	chr3:145616400-145616600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:145616400-145616600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr3:145616400-145616600	Flanking Active TSS	Brain Cingulate Gyrus	brain
48	chr3:145616400-145616600	Flanking Active TSS	NH-A	brain
49	chr3:145616400-145616800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:145616400-145616800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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