Variant report

Variant	esv3438547
Chromosome Location	chr3:195720855-195726353
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:235)
CpG islands
(count:183)
Chromatin interactive
region (count:1)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:235 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BCL11A	chr3:195723014-195723259	GM12878	blood:	n/a	chr3:195723080-195723089
2	BCL11A	chr3:195722372-195722606	GM12878	blood:	n/a	n/a
3	CBX3	chr3:195721219-195721517	K562	blood:	n/a	n/a
4	CBX3	chr3:195721166-195721620	K562	blood:	n/a	n/a
5	CTCF	chr3:195721205-195721655	K562	blood:	n/a	n/a
6	CTCF	chr3:195721356-195721525	Hela-S3	cervix:	n/a	n/a
7	CTCF	chr3:195721260-195721410	WI-38	lung:	n/a	n/a
8	CTCF	chr3:195721760-195721910	AoAF	blood vessel:	n/a	n/a
9	CTCF	chr3:195721250-195721595	GM12878	blood:	n/a	n/a
10	CTCF	chr3:195721260-195721410	AG09319	gingival:	n/a	n/a
11	CTCF	chr3:195721260-195721410	WERI-Rb-1	eye:	n/a	n/a
12	CTCF	chr3:195721345-195721557	GM19238	blood:	n/a	n/a
13	CTCF	chr3:195721260-195721410	GM12874	blood:	n/a	n/a
14	CTCF	chr3:195721340-195721490	GM12867	blood:	n/a	n/a
15	CTCF	chr3:195721260-195721410	HRE	kidney:	n/a	n/a
16	CTCF	chr3:195721720-195721870	HCPEpiC	choroid plexus:	n/a	n/a
17	CTCF	chr3:195721275-195721547	A549	lung:	n/a	n/a
18	CTCF	chr3:195722140-195722290	GM12866	blood:	n/a	n/a
19	CTCF	chr3:195721330-195721519	GM10248	blood:	n/a	n/a
20	CTCF	chr3:195722080-195722230	HMF	breast:	n/a	n/a
21	CTCF	chr3:195721340-195721490	BE2_C	brain:	n/a	n/a
22	CTCF	chr3:195721280-195721430	GM12872	blood:	n/a	n/a
23	CTCF	chr3:195721720-195721870	WI-38	lung:	n/a	n/a
24	CTCF	chr3:195721340-195721490	GM12868	blood:	n/a	n/a
25	CTCF	chr3:195721300-195721450	HFF-Myc	foreskin:	n/a	n/a
26	CTCF	chr3:195721313-195721565	A549	lung:	n/a	n/a
27	CTCF	chr3:195721340-195721490	GM12869	blood:	n/a	n/a
28	CTCF	chr3:195721280-195721430	HRPEpiC	eye:	n/a	n/a
29	CTCF	chr3:195721364-195721549	MCF-7	breast:	n/a	n/a
30	CTCF	chr3:195721260-195721410	K562	blood:	n/a	n/a
31	CTCF	chr3:195721076-195721660	K562	blood:	n/a	n/a
32	CTCF	chr3:195721320-195721470	HPAF	blood vessel:	n/a	n/a
33	CTCF	chr3:195721382-195721522	MCF-7	breast:	n/a	n/a
34	CTCF	chr3:195721360-195721510	GM12871	blood:	n/a	n/a
35	CTCF	chr3:195721340-195721490	GM12865	blood:	n/a	n/a
36	CTCF	chr3:195721324-195721562	GM12878	blood:	n/a	n/a
37	CTCF	chr3:195721257-195721571	Gliobla	brain:	n/a	n/a
38	CTCF	chr3:195721280-195721430	HFF	foreskin:	n/a	n/a
39	CTCF	chr3:195721300-195721450	GM12871	blood:	n/a	n/a
40	CTCF	chr3:195721384-195721497	GM19239	blood:	n/a	n/a
41	CTCF	chr3:195721280-195721430	A549	lung:	n/a	n/a
42	CTCF	chr3:195721260-195721410	GM12864	blood:	n/a	n/a
43	CTCF	chr3:195721352-195721514	MCF-7	breast:	n/a	n/a
44	CTCF	chr3:195721260-195721410	AG10803	skin:	n/a	n/a
45	CTCF	chr3:195721300-195721450	HRPEpiC	eye:	n/a	n/a
46	CTCF	chr3:195722080-195722230	HCPEpiC	choroid plexus:	n/a	n/a
47	CTCF	chr3:195721320-195721470	HCPEpiC	choroid plexus:	n/a	n/a
48	CTCF	chr3:195721348-195721507	MCF-7	breast:	n/a	n/a
49	CTCF	chr3:195721320-195721470	GM12865	blood:	n/a	n/a
50	CTCF	chr3:195721340-195721490	MCF-7	breast:	n/a	n/a

(count:183 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:195724371-195724421	T-47D	breast:	n/a
2	chr3:195724371-195724421	AG04449	skin:	fetal
3	chr3:195723614-195723664	Caco-2	colon:	n/a
4	chr3:195723614-195723664	HRPEpiC	eye:	n/a
5	chr3:195723614-195723664	BE2_C	brain:	n/a
6	chr3:195723614-195723664	ProgFib	skin:	n/a
7	chr3:195724401-195724451	NHBE	bronchial:	n/a
8	chr3:195723614-195723664	HCPEpiC	choroid plexus:	n/a
9	chr3:195724401-195724451	Jurkat	blood:	n/a
10	chr3:195724371-195724421	H1-hESC	embryonic stem cell:	embryo
11	chr3:195724371-195724421	Hepatocyte	liver:	n/a
12	chr3:195723614-195723664	HAEpiC	amniotic membrane:	n/a
13	chr3:195724401-195724451	PrEC	prostate:	n/a
14	chr3:195724401-195724451	SK-N-SH_RA	brain:	n/a
15	chr3:195724401-195724451	AG10803	skin:	n/a
16	chr3:195723614-195723664	SK-N-SH	brain:	n/a
17	chr3:195723614-195723664	PANC-1	pancreas:	n/a
18	chr3:195724401-195724451	MCF10A-Er-Src	breast:	n/a
19	chr3:195724401-195724451	HCF	heart:	n/a
20	chr3:195724401-195724451	HCPEpiC	choroid plexus:	n/a
21	chr3:195724401-195724451	HCM	heart:	n/a
22	chr3:195724401-195724451	HUVEC	blood vessel:	n/a
23	chr3:195724401-195724451	HEEpiC	esophagus:	n/a
24	chr3:195724401-195724451	T-47D	breast:	n/a
25	chr3:195724401-195724451	ProgFib	skin:	n/a
26	chr3:195723614-195723664	PFSK-1	brain:	n/a
27	chr3:195723614-195723664	RPTEC	kidney:	n/a
28	chr3:195724371-195724421	PANC-1	pancreas:	n/a
29	chr3:195724401-195724451	CMK	blood:	n/a
30	chr3:195724371-195724421	NB4	blood:	n/a
31	chr3:195723614-195723664	K562	blood:	n/a
32	chr3:195724371-195724421	IMR90	lung:	fetal
33	chr3:195723614-195723664	PrEC	prostate:	n/a
34	chr3:195724401-195724451	GM12892	blood:	n/a
35	chr3:195723614-195723664	AG09319	gingival:	n/a
36	chr3:195724371-195724421	GM06990	blood:	n/a
37	chr3:195724371-195724421	HRE	kidney:	n/a
38	chr3:195724371-195724421	RPTEC	kidney:	n/a
39	chr3:195724401-195724451	Hepatocyte	liver:	n/a
40	chr3:195723614-195723664	MCF-7	breast:	n/a
41	chr3:195724371-195724421	SK-N-MC	brain:	n/a
42	chr3:195723614-195723664	H1-hESC	embryonic stem cell:	embryo
43	chr3:195724401-195724451	AG04450	lung:	fetal
44	chr3:195724371-195724421	GM12891	blood:	n/a
45	chr3:195724371-195724421	PFSK-1	brain:	n/a
46	chr3:195723614-195723664	HL-60	blood:	n/a
47	chr3:195723614-195723664	HPAEpiC	pulmonary alveolar:	n/a
48	chr3:195724401-195724451	HMEC	breast:	n/a
49	chr3:195723614-195723664	Hela-S3	cervix:	n/a
50	chr3:195723614-195723664	T-47D	breast:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:195586120..195586802-chr3:195721315..195721912,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TFRC-1	chr3:195726007-195726255	NONHSAT094273

No data

Variant related genes	Relation type
SDHAP1	TF binding region
ENSG00000231464	TF binding region
SDHAP1	CpG island
ENSG00000231464	CpG island

Extended variants
information (count: 292 )
Associated
traits (count: 81 )

Variant overlapped rSNPs/rCNVs (count:292 , 50 per page) page: 1 2 3 4 5 6

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs79368819	chr3:195720855-195720856	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs565741713	chr3:195720857-195720858	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs77007721	chr3:195720864-195720865	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs2343855	chr3:195720874-195720875	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs539661631	chr3:195720876-195720877	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs542902011	chr3:195720889-195720890	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs57653434	chr3:195720893-195720894	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs569893632	chr3:195720929-195720930	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs11712922	chr3:195720932-195720933	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs144598321	chr3:195720935-195720936	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs11711384	chr3:195720942-195720943	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs201302169	chr3:195720945-195720946	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs199686129	chr3:195720965-195720966	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs368553487	chr3:195720987-195720988	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs555633393	chr3:195721012-195721013	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs62283425	chr3:195721013-195721014	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs370202190	chr3:195721035-195721036	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs111979130	chr3:195721036-195721037	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs375932285	chr3:195721065-195721066	Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
20	rs371544413	chr3:195721163-195721164	Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
21	rs375345470	chr3:195721184-195721185	Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
22	rs573708553	chr3:195721206-195721207	Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
23	rs4639005	chr3:195721207-195721208	Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
24	rs377247286	chr3:195721228-195721229	Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
25	rs4374560	chr3:195721232-195721233	Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
26	rs534972473	chr3:195721236-195721237	Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
27	rs62283426	chr3:195721254-195721255	Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
28	rs79208480	chr3:195721269-195721270	Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
29	rs369729912	chr3:195721296-195721297	Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
30	rs200884480	chr3:195721297-195721298	Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
31	rs200926534	chr3:195721299-195721300	Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
32	rs73208036	chr3:195721300-195721301	Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
33	rs368302696	chr3:195721306-195721307	Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
34	rs545147490	chr3:195721307-195721308	Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
35	rs77128281	chr3:195721318-195721319	Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
36	rs564317125	chr3:195721321-195721322	Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
37	rs74360404	chr3:195721362-195721363	Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
38	rs543748941	chr3:195721373-195721374	Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
39	rs28802010	chr3:195721378-195721379	Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
40	rs372568770	chr3:195721387-195721388	Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
41	rs559070890	chr3:195721388-195721389	Weak transcription Enhancers	TF binding region	2 gene(s)	Overlapped CNVs	n/a
42	rs533076218	chr3:195721403-195721404	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
43	rs140664026	chr3:195721404-195721405	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
44	rs545308398	chr3:195721415-195721416	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
45	rs111383581	chr3:195721427-195721428	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
46	rs2638913	chr3:195721464-195721465	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
47	rs62283427	chr3:195721467-195721468	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
48	rs549271201	chr3:195721473-195721474	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
49	rs567912317	chr3:195721544-195721545	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
50	rs28852142	chr3:195721570-195721571	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:81)

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
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
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Breast cancer	16608533	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21785460	CNVD
Breast cancer	17133270	CNVD
Cancer	16751803	CNVD
abnormal development	18461090	CNVD
Autism	19653912	CNVD
small cell lung cancer	20016488	CNVD
Cancer	20164920	CNVD
Prostate cancer	18632612	CNVD
Cervical cancer	21062161	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Austim spectrum disorder	21302340	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	16397240	CNVD
Epilepsy	20736978	CNVD
Mental retardation	20736978	CNVD
speech impairment	20736978	CNVD
Intracranial aneurysm	16715129	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Mental retardation	17124404	CNVD
Congenital anomalies of the kidney and urinary tract	20299530	CNVD
Developmental delay	21147756	CNVD
Breast cancer	21509527	CNVD
Cancer	21129771	CNVD
Myelofibrosis	22110671	CNVD
Neurodevelopmental disorder	16760732	CNVD
Schizophrenia	22118685	CNVD
Schizophrenia	22958593	CNVD
Schizophrenia	21285140	CNVD
Schizophrenia	20970697	CNVD
Mental retardation	19951919	CNVD
Autism	20970697	CNVD
Developmental delay	18471269	CNVD
Intellectual disability	22045946	CNVD
Breast cancer	21045282	CNVD
Primary central nervous system lymphoma	21088137	CNVD
Ovarian cancer	20844748	CNVD
Adenocarcinoma	19607727	CNVD
Squamous cell cancer	19607727	CNVD
Uveal melanoma	20484589	CNVD
3q29 microdeletion syndrome	20500065	CNVD
Biliary cancer	20453639	CNVD
3q29 microdeletion syndrome	22283845	CNVD
3q29 microdeletion syndrome	21626679	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Ovarian cancer	21720365	CNVD
Breast cancer	21364760	CNVD
Urothelial carcinoma	21177765	CNVD

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195717800-195721200	Weak transcription	Fetal Muscle Leg	muscle
2	chr3:195718000-195721200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr3:195720400-195726200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:195721000-195721400	Enhancers	Primary T cells fromperipheralblood	blood
5	chr3:195721200-195721400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
6	chr3:195721200-195721400	Enhancers	Fetal Muscle Leg	muscle
7	chr3:195721400-195721800	Weak transcription	Fetal Muscle Leg	muscle
8	chr3:195721800-195722200	Enhancers	Fetal Muscle Leg	muscle
9	chr3:195726200-195726400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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