Variant report

Variant	esv3322779
Chromosome Location	chr1:228743675-228746630
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	BHLHE40	chr1:228745511-228745711	HepG2	liver:	n/a	chr1:228745571-228745587 chr1:228745576-228745592
2	CBX3	chr1:228746295-228748726	K562	blood:	n/a	n/a
3	CBX3	chr1:228746546-228747624	K562	blood:	n/a	n/a
4	CBX3	chr1:228744333-228746248	K562	blood:	n/a	n/a
5	CBX3	chr1:228745450-228746485	K562	blood:	n/a	n/a
6	CBX3	chr1:228744029-228745432	K562	blood:	n/a	n/a
7	CEBPB	chr1:228745768-228746337	GM12878	blood:	n/a	n/a
8	CREB1	chr1:228743297-228743744	HepG2	liver:	n/a	n/a
9	CTCF	chr1:228744110-228745197	K562	blood:	n/a	chr1:228744444-228744457 chr1:228744447-228744456 chr1:228745037-228745050
10	CTCF	chr1:228746048-228746418	K562	blood:	n/a	n/a
11	CTCF	chr1:228745512-228745967	K562	blood:	n/a	n/a
12	CTCF	chr1:228744518-228745229	K562	blood:	n/a	chr1:228745037-228745050
13	CTCF	chr1:228745254-228745650	K562	blood:	n/a	n/a
14	CTCF	chr1:228744638-228745020	K562	blood:	n/a	n/a
15	EP300	chr1:228745503-228745711	GM12878	blood:	n/a	n/a
16	FOSL2	chr1:228745423-228745703	HepG2	liver:	n/a	chr1:228745487-228745496
17	FOXA2	chr1:228743895-228782766	A549	lung:	n/a	n/a
18	FOXM1	chr1:228745852-228746269	GM12878	blood:	n/a	n/a
19	FOXM1	chr1:228745834-228746340	GM12878	blood:	n/a	n/a
20	FOXP2	chr1:228746594-228746942	SK-N-MC	brain:	n/a	n/a
21	FOXP2	chr1:228744552-228744978	SK-N-MC	brain:	n/a	n/a
22	FOXP2	chr1:228746029-228746797	PFSK-1	brain:	n/a	n/a
23	FOXP2	chr1:228745882-228746313	SK-N-MC	brain:	n/a	n/a
24	FOXP2	chr1:228744445-228744645	PFSK-1	brain:	n/a	n/a
25	FOXP2	chr1:228745285-228745496	PFSK-1	brain:	n/a	n/a
26	GABPA	chr1:228745454-228745674	Hela-S3	cervix:	n/a	n/a
27	GABPA	chr1:228745433-228745704	Hela-S3	cervix:	n/a	n/a
28	GTF3C2	chr1:228743328-228743740	K562	blood:	n/a	n/a
29	GTF3C2	chr1:228743389-228743767	Hela-S3	cervix:	n/a	n/a
30	HEY1	chr1:228745413-228745715	HepG2	liver:	n/a	chr1:228745572-228745587 chr1:228745466-228745481 chr1:228745575-228745590
31	HEY1	chr1:228745430-228745699	K562	blood:	n/a	chr1:228745572-228745587 chr1:228745466-228745481 chr1:228745575-228745590
32	HEY1	chr1:228744834-228744982	K562	blood:	n/a	n/a
33	HEY1	chr1:228745509-228745710	K562	blood:	n/a	chr1:228745572-228745587 chr1:228745575-228745590
34	HEY1	chr1:228744816-228745001	HepG2	liver:	n/a	n/a
35	JUND	chr1:228745451-228745677	HepG2	liver:	n/a	chr1:228745487-228745496
36	JUND	chr1:228744099-228759006	A549	lung:	n/a	chr1:228748791-228748805 chr1:228747728-228747737 chr1:228753273-228753287 chr1:228744309-228744323 chr1:228746550-228746564 chr1:228745487-228745496 chr1:228755514-228755528 chr1:228751032-228751046 chr1:228758886-228758895 chr1:228749969-228749978 chr1:228752210-228752219 chr1:228754451-228754460 chr1:228757729-228757743
37	JUND	chr1:228745453-228745693	HepG2	liver:	n/a	chr1:228745487-228745496
38	MYBL2	chr1:228745620-228747502	HepG2	liver:	n/a	n/a
39	MYBL2	chr1:228744274-228747606	HepG2	liver:	n/a	n/a
40	NFIC	chr1:228744315-228744938	GM12878	blood:	n/a	n/a
41	NR2F2	chr1:228745879-228746172	K562	blood:	n/a	n/a
42	PAX5	chr1:228745508-228745703	GM12878	blood:	n/a	n/a
43	PAX5	chr1:228745392-228745747	GM12878	blood:	n/a	n/a
44	PAX5	chr1:228744841-228744975	GM12878	blood:	n/a	n/a
45	PAX5	chr1:228745436-228745693	GM12878	blood:	n/a	n/a
46	PBX3	chr1:228745459-228745677	GM12878	blood:	n/a	n/a
47	POLR2A	chr1:228745758-228752131	SK-N-MC	brain:	n/a	n/a
48	POLR2A	chr1:228745735-228746424	HepG2	liver:	n/a	n/a
49	POLR2A	chr1:228745689-228746509	SK-N-MC	brain:	n/a	n/a
50	POLR2A	chr1:228745422-228745707	Hela-S3	cervix:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:228744111-228744161	HIPEpiC	eye:	n/a
2	chr1:228744111-228744161	IMR90	lung:	fetal
3	chr1:228744111-228744161	SK-N-SH_RA	brain:	n/a
4	chr1:228744111-228744161	HL-60	blood:	n/a
5	chr1:228744111-228744161	PrEC	prostate:	n/a
6	chr1:228744111-228744161	HRE	kidney:	n/a
7	chr1:228744111-228744161	SK-N-MC	brain:	n/a
8	chr1:228744111-228744161	NH-A	brain:	n/a
9	chr1:228744111-228744161	HEK293	kidney:	embryo
10	chr1:228744111-228744161	HNPCEpiC	eye:	n/a
11	chr1:228744111-228744161	GM12891	blood:	n/a
12	chr1:228744111-228744161	MCF10A-Er-Src	breast:	n/a
13	chr1:228744111-228744161	SAEC	small airway:	n/a
14	chr1:228744111-228744161	A549	lung:	n/a
15	chr1:228744111-228744161	AoSMC	blood vessel:	n/a
16	chr1:228744111-228744161	BE2_C	brain:	n/a
17	chr1:228744111-228744161	GM19239	blood:	n/a
18	chr1:228744111-228744161	Hela-S3	cervix:	n/a
19	chr1:228744111-228744161	H1-hESC	embryonic stem cell:	embryo
20	chr1:228744111-228744161	HCT-116	colon:	n/a
21	chr1:228744111-228744161	GM12878	blood:	n/a
22	chr1:228744111-228744161	HRCEpiC	kidney:	n/a
23	chr1:228744111-228744161	PFSK-1	brain:	n/a
24	chr1:228744111-228744161	HUVEC	blood vessel:	n/a
25	chr1:228744111-228744161	HCF	heart:	n/a
26	chr1:228744111-228744161	HMEC	breast:	n/a
27	chr1:228744111-228744161	HCM	heart:	n/a
28	chr1:228744111-228744161	Jurkat	blood:	n/a
29	chr1:228744111-228744161	U87	brain:	n/a
30	chr1:228744111-228744161	MCF-7	breast:	n/a
31	chr1:228744111-228744161	BJ	skin:	n/a
32	chr1:228744111-228744161	NHBE	bronchial:	n/a
33	chr1:228744111-228744161	Caco-2	colon:	n/a
34	chr1:228744111-228744161	ECC-1	luminal epithelium:	n/a
35	chr1:228744111-228744161	T-47D	breast:	n/a
36	chr1:228744111-228744161	K562	blood:	n/a
37	chr1:228744111-228744161	AG09319	gingival:	n/a
38	chr1:228744111-228744161	HEEpiC	esophagus:	n/a
39	chr1:228744111-228744161	AG09309	skin:	n/a
40	chr1:228744111-228744161	HCPEpiC	choroid plexus:	n/a
41	chr1:228744111-228744161	ProgFib	skin:	n/a
42	chr1:228744111-228744161	GM06990	blood:	n/a
43	chr1:228744111-228744161	AG04449	skin:	fetal
44	chr1:228744111-228744161	HRPEpiC	eye:	n/a
45	chr1:228744111-228744161	CMK	blood:	n/a
46	chr1:228744111-228744161	HepG2	liver:	n/a
47	chr1:228744111-228744161	AG04450	lung:	fetal
48	chr1:228744111-228744161	SKMC	muscle:	n/a
49	chr1:228744111-228744161	NT2-D1	testis:	n/a
50	chr1:228744111-228744161	Hepatocyte	liver:	n/a

Variant related genes	Relation type
DUSP5P1	TF binding region
RNA5S1	TF binding region
DUSP5P1	CpG island
RNA5S1	CpG island

Extended variants
information (count: 88 )
Associated
traits (count: 90 )

Variant overlapped rSNPs/rCNVs (count:88 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs531447947	chr1:228743685-228743686	Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs551599367	chr1:228743687-228743688	Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs12028536	chr1:228743706-228743707	Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs374840368	chr1:228743711-228743712	Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs141196307	chr1:228743729-228743730	Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs371939412	chr1:228743743-228743744	Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs547834160	chr1:228743747-228743748	Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs181661376	chr1:228743757-228743758	Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs567616681	chr1:228743759-228743760	Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs536758108	chr1:228743763-228743764	Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs145054226	chr1:228743766-228743767	Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs570128906	chr1:228743770-228743771	Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs538893067	chr1:228743780-228743781	Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs190243498	chr1:228743786-228743787	Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs28593474	chr1:228743793-228743794	Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs78918231	chr1:228743795-228743796	Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
17	rs553356292	chr1:228743799-228743800	Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
18	rs573517734	chr1:228743810-228743811	Bivalent Enhancer Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
19	rs80018489	chr1:228743822-228743823	Bivalent Enhancer Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
20	rs182871318	chr1:228743838-228743839	Bivalent Enhancer Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs562490524	chr1:228743839-228743840	Bivalent Enhancer Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs531419589	chr1:228743861-228743862	Bivalent Enhancer Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs370150372	chr1:228743870-228743871	Bivalent Enhancer Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs187469629	chr1:228743874-228743875	Bivalent Enhancer Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs140299453	chr1:228743882-228743883	Bivalent Enhancer Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
26	rs565043913	chr1:228743901-228743902	Bivalent Enhancer Bivalent/Poised TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs150339411	chr1:228743909-228743910	Bivalent Enhancer Bivalent/Poised TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs527585545	chr1:228743926-228743927	Bivalent Enhancer Bivalent/Poised TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs531527989	chr1:228743965-228743966	Bivalent Enhancer Bivalent/Poised TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs114961372	chr1:228743966-228743967	Bivalent Enhancer Bivalent/Poised TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs370023376	chr1:228743969-228743970	Bivalent Enhancer Bivalent/Poised TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs575981049	chr1:228743978-228743979	Bivalent Enhancer Bivalent/Poised TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs146068274	chr1:228743992-228743993	Bivalent Enhancer Bivalent/Poised TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs369837442	chr1:228743995-228743996	Bivalent Enhancer Bivalent/Poised TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs570088691	chr1:228743999-228744000	Bivalent Enhancer Bivalent/Poised TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs538715185	chr1:228744011-228744012	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs558750226	chr1:228744013-228744014	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs565890447	chr1:228744035-228744036	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs534996463	chr1:228744041-228744042	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs138804100	chr1:228744046-228744047	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs374655978	chr1:228744048-228744049	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs115831821	chr1:228744058-228744059	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs542286509	chr1:228744063-228744064	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs556089595	chr1:228744064-228744065	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs576077941	chr1:228744066-228744067	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs60733763	chr1:228744070-228744071	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs56709082	chr1:228744073-228744074	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs572309065	chr1:228744074-228744075	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs6682928	chr1:228744092-228744093	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs74141305	chr1:228744096-228744097	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:90)

Disease	PMID	Source
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Autism	22495311	CNVD
Melanoma	18172304	CNVD
Rett syndrome	21593744	CNVD
Medulloblastoma	21979893	CNVD
Cancer	20164919	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	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
Liposarcoma	21253554	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
Breast cancer	17603634	CNVD
Neuroblastoma	21899760	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
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
Breast cancer	21509527	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Urothelial carcinoma	21177765	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Chordoma	18071362	CNVD
T-cell lymphomas	19863542	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hepatocellular carcinoma	18803288	CNVD
Urothelial tumor	18831757	CNVD
Lung cancer	18438408	CNVD
Medulloblastoma	16783165	CNVD
Basal cell lymphoma	17170743	CNVD
Mental retardation	19951919	CNVD
Non-syndromic sensorineural hearing loss	17873649	CNVD
Basal cell lymphoma	17053054	CNVD
Autism	14699429	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Fumarase deficiency	21572526	CNVD
Autism	17483303	CNVD
Kartagener syndrome	16639409	CNVD
Congenital abnormalities	21549014	CNVD
Developmental delay	21549014	CNVD
Mental retardation	21549014	CNVD
small cell lung cancer	20016488	CNVD
Glioblastoma multiforme	21138945	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Cancer	20164920	CNVD
Cancer	17060936	CNVD
Myelofibrosis	22110671	CNVD
abnormal development	18461090	CNVD
Breast cancer	21364760	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Melanoma	17363583	CNVD

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228743000-228744000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:228743200-228744000	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:228743400-228743800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:228743800-228744000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin

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