Variant report

Variant	esv2594574
Chromosome Location	chr2:234475591-234477600
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	ARID3A	chr2:234475017-234475641	HepG2	liver:	n/a	n/a
2	ARID3A	chr2:234475265-234475676	K562	blood:	n/a	n/a
3	ATF3	chr2:234475068-234475632	A549	lung:	n/a	n/a
4	BCL3	chr2:234474395-234475621	A549	lung:	n/a	chr2:234475543-234475556 chr2:234474817-234474826 chr2:234475463-234475476
5	BCL3	chr2:234474862-234475661	A549	lung:	n/a	chr2:234475543-234475556 chr2:234475463-234475476
6	BCLAF1	chr2:234475180-234475695	GM12878	blood:	n/a	chr2:234475543-234475556 chr2:234475463-234475476
7	BHLHE40	chr2:234475109-234475603	HepG2	liver:	n/a	n/a
8	BHLHE40	chr2:234474978-234475601	K562	blood:	n/a	n/a
9	CBX3	chr2:234475002-234475717	HCT-116	colon:	n/a	n/a
10	CBX3	chr2:234475220-234475608	K562	blood:	n/a	n/a
11	CEBPB	chr2:234475193-234475666	ECC-1	luminal epithelium:	n/a	n/a
12	CEBPD	chr2:234475114-234475658	HepG2	liver:	n/a	n/a
13	CHD2	chr2:234474605-234475617	GM12878	blood:	n/a	n/a
14	CHD2	chr2:234475194-234475640	H1-hESC	embryonic stem cell:	n/a	n/a
15	CHD2	chr2:234474405-234475666	Hela-S3	cervix:	n/a	n/a
16	CREB1	chr2:234475086-234475670	H1-hESC	embryonic stem cell:	n/a	n/a
17	CREB1	chr2:234474666-234475695	HepG2	liver:	n/a	n/a
18	CREB1	chr2:234475048-234475664	A549	lung:	n/a	n/a
19	CTCF	chr2:234477247-234477295	GM20000	blood:	n/a	n/a
20	CTCF	chr2:234475480-234475630	AG10803	skin:	n/a	n/a
21	CTCF	chr2:234475460-234475610	HMEC	breast:	n/a	n/a
22	CUX1	chr2:234475408-234475592	K562	blood:	n/a	n/a
23	E2F4	chr2:234475295-234475736	MCF10A-Er-Src	breast:	n/a	chr2:234475310-234475320
24	E2F6	chr2:234474638-234475672	A549	lung:	n/a	chr2:234475310-234475320 chr2:234474823-234474835
25	EGR1	chr2:234475078-234475638	ECC-1	luminal epithelium:	n/a	chr2:234475488-234475512 chr2:234475444-234475468
26	ELF1	chr2:234474985-234475602	HepG2	liver:	n/a	n/a
27	ELF1	chr2:234474823-234475657	GM12878	blood:	n/a	n/a
28	ELF1	chr2:234475170-234475631	HepG2	liver:	n/a	n/a
29	ELK1	chr2:234475233-234475632	Hela-S3	cervix:	n/a	n/a
30	EP300	chr2:234474805-234475678	A549	lung:	n/a	n/a
31	EP300	chr2:234475202-234475612	SK-N-SH_RA	brain:	n/a	n/a
32	EP300	chr2:234475138-234475661	SK-N-SH	brain:	n/a	n/a
33	EP300	chr2:234474968-234475661	ECC-1	luminal epithelium:	n/a	n/a
34	EP300	chr2:234475176-234475612	SK-N-SH_RA	brain:	n/a	n/a
35	EP300	chr2:234475308-234475612	K562	blood:	n/a	n/a
36	EP300	chr2:234475214-234475653	HepG2	liver:	n/a	n/a
37	EP300	chr2:234475254-234475592	GM12878	blood:	n/a	n/a
38	ESR1	chr2:234475210-234475619	ECC-1	luminal epithelium:	n/a	n/a
39	ETS1	chr2:234474857-234475712	A549	lung:	n/a	chr2:234475000-234475011
40	ETS1	chr2:234474877-234475630	GM12878	blood:	n/a	chr2:234475000-234475011
41	FOS	chr2:234475373-234475632	MCF10A-Er-Src	breast:	n/a	chr2:234475583-234475591
42	FOS	chr2:234475367-234475632	MCF10A-Er-Src	breast:	n/a	chr2:234475583-234475591
43	FOSL2	chr2:234474655-234475721	A549	lung:	n/a	chr2:234475583-234475591
44	FOXA1	chr2:234475110-234475641	HepG2	liver:	n/a	n/a
45	FOXA2	chr2:234475157-234475695	A549	lung:	n/a	n/a
46	FOXP2	chr2:234475273-234475605	SK-N-MC	brain:	n/a	n/a
47	GATA2	chr2:234475060-234475642	HUVEC	blood vessel:	n/a	n/a
48	GATA2	chr2:234475453-234475951	K562	blood:	n/a	n/a
49	GATA2	chr2:234475199-234475688	SH-SY5Y	brain:	n/a	n/a
50	GATA3	chr2:234477406-234477556	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:234475954..234478927-chr2:234479708..234482579,2	MCF-7	breast:
2	chr2:234474046..234476375-chr2:234618981..234621894,3	MCF-7	breast:
3	chr2:234472037..234477650-chr2:234599067..234602356,8	MCF-7	breast:
4	chr2:234400872..234402381-chr2:234473582..234476254,2	MCF-7	breast:
5	chr2:234389092..234391362-chr2:234473035..234476486,3	MCF-7	breast:
6	chr2:234473282..234477495-chr2:234598048..234603332,9	MCF-7	breast:
7	chr2:234393753..234400835-chr2:234472864..234476478,8	MCF-7	breast:
8	chr2:234472403..234474529-chr2:234475981..234478934,2	MCF-7	breast:
9	chr2:234473931..234475939-chr2:234762064..234763860,2	K562	blood:

Variant related genes	Relation type
USP40	TF binding region
ENSG00000240224	chromatin interactions
ENSG00000167165	chromatin interactions
ENSG00000085982	chromatin interactions
ENSG00000123485	chromatin interactions

Extended variants
information (count: 54 )
Associated
traits (count: 59 )

Variant overlapped rSNPs/rCNVs (count:54 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs542932313	chr2:234475596-234475597	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
2	rs559713330	chr2:234475606-234475607	Active TSS Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
3	rs557068522	chr2:234475642-234475643	Active TSS Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
4	rs186935219	chr2:234475650-234475651	Active TSS Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
5	rs542792250	chr2:234475684-234475685	Active TSS Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
6	rs71058564	chr2:234475708-234475709	Active TSS Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
7	rs66727805	chr2:234475735-234475736	Active TSS Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
8	rs71359949	chr2:234475851-234475852	Weak transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
9	rs71359948	chr2:234475877-234475878	Weak transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
10	rs372538075	chr2:234475903-234475904	Weak transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
11	rs545267675	chr2:234475929-234475930	Weak transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
12	rs141112333	chr2:234475955-234475956	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
13	rs567400315	chr2:234475961-234475962	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
14	rs191567223	chr2:234475990-234475991	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
15	rs550760900	chr2:234475992-234475993	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
16	rs184946919	chr2:234475995-234475996	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
17	rs111215084	chr2:234476232-234476233	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
18	rs530067676	chr2:234476286-234476287	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
19	rs546956985	chr2:234476312-234476313	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
20	rs111214906	chr2:234476330-234476331	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
21	rs566864360	chr2:234476333-234476334	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
22	rs189834870	chr2:234476408-234476409	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs374496721	chr2:234476414-234476415	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs569069628	chr2:234476430-234476431	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs181935809	chr2:234476458-234476459	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs556755323	chr2:234476476-234476477	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs573659973	chr2:234476484-234476485	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs35576313	chr2:234476903-234476904	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs145099760	chr2:234477131-234477132	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
30	rs185513250	chr2:234477144-234477145	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
31	rs13404501	chr2:234477148-234477149	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs550477771	chr2:234477196-234477197	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
33	rs112932661	chr2:234477198-234477199	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
34	rs189594900	chr2:234477202-234477203	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs180783996	chr2:234477203-234477204	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs142452936	chr2:234477228-234477229	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs373138331	chr2:234477229-234477230	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs530201244	chr2:234477255-234477256	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
39	rs145957129	chr2:234477276-234477277	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
40	rs13389374	chr2:234477284-234477285	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs532675682	chr2:234477295-234477296	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
42	rs545289083	chr2:234477312-234477313	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs185201629	chr2:234477384-234477385	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs569457383	chr2:234477388-234477389	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs531841396	chr2:234477397-234477398	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs548750024	chr2:234477410-234477411	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
47	rs567293092	chr2:234477446-234477447	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
48	rs13401703	chr2:234477460-234477461	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs189899890	chr2:234477461-234477462	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
50	rs116160762	chr2:234477463-234477464	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:59)

Disease	PMID	Source
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Medulloblastoma	21979893	CNVD
Ependymoma	16718352	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	17603634	CNVD
Breast cancer	16272173	CNVD
Ewing''s sarcoma	17952124	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Embryonal rhabdomyosarcoma	16790082	CNVD
Autism	16446308	CNVD
Autism	19401682	CNVD
Colorectal cancer	16272173	CNVD
Lung cancer	18438408	CNVD
Acute myeloid leukemia	20729466	CNVD
small cell lung cancer	20016488	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
Urothelial carcinoma	21177765	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Cervical cancer	21062161	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Chordoma	18071362	CNVD
Developmental delay	21147756	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Cancer	22429812	CNVD
Bladder cancer	21909424	CNVD
Renal cell carcinoma	21668985	CNVD
Breast cancer	21785460	CNVD
Prostate cancer	18632612	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Wilms tumour	21544195	CNVD
Esophageal adenocarcinoma	18519675	CNVD
prenatal diagnosis	22389664	CNVD
Myelofibrosis	22110671	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Mental retardation	20152051	CNVD
Cancer	21183584	CNVD
Albright''s disease	22277900	CNVD
Brachydactyly-Mental Retardation Syndrome	22470819	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Colorectal cancer	19359472	CNVD
Autism	18414403	CNVD
Chronic myeloid leukemia	21384125	CNVD

Chromatin state (count:132 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234474000-234475600	Active TSS	Fetal Brain Male	brain
2	chr2:234474000-234475800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:234474000-234475800	Active TSS	Right Atrium	heart
4	chr2:234474000-234475800	Active TSS	Stomach Smooth Muscle	stomach
5	chr2:234474200-234475600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:234474200-234475600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:234474200-234475800	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr2:234474200-234475800	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr2:234474200-234475800	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr2:234474200-234475800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:234474200-234475800	Active TSS	Fetal Intestine Small	intestine
12	chr2:234474200-234475800	Active TSS	Psoas Muscle	Psoas
13	chr2:234474200-234475800	Active TSS	Thymus	Thymus
14	chr2:234474400-234475600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:234474400-234475600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr2:234474400-234475600	Active TSS	Colon Smooth Muscle	Colon
17	chr2:234474400-234475600	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr2:234474400-234475600	Active TSS	Lung	lung
19	chr2:234474400-234475600	Active TSS	Ovary	ovary
20	chr2:234474400-234475600	Active TSS	Placenta Amnion	Placenta Amnion
21	chr2:234474400-234475600	Active TSS	Sigmoid Colon	Sigmoid Colon
22	chr2:234474400-234475600	Active TSS	GM12878-XiMat	blood
23	chr2:234474400-234475600	Active TSS	HSMMtube	muscle
24	chr2:234474400-234475800	Active TSS	H1 Cell Line	embryonic stem cell
25	chr2:234474400-234475800	Active TSS	H9 Cell Line	embryonic stem cell
26	chr2:234474400-234475800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:234474400-234475800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:234474400-234475800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:234474400-234475800	Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr2:234474400-234475800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:234474400-234475800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:234474400-234475800	Active TSS	Colonic Mucosa	Colon
33	chr2:234474400-234475800	Active TSS	Fetal Intestine Large	intestine
34	chr2:234474400-234475800	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr2:234474400-234475800	Active TSS	Fetal Muscle Trunk	muscle
36	chr2:234474400-234475800	Active TSS	Fetal Muscle Leg	muscle
37	chr2:234474400-234475800	Active TSS	Fetal Stomach	stomach
38	chr2:234474400-234475800	Active TSS	Rectal Smooth Muscle	rectum
39	chr2:234474400-234475800	Active TSS	Right Ventricle	heart
40	chr2:234474400-234475800	Active TSS	HSMM	muscle
41	chr2:234474400-234475800	Active TSS	K562	blood
42	chr2:234474600-234475600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr2:234474600-234475600	Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr2:234474600-234475600	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr2:234474600-234475600	Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr2:234474600-234475600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
47	chr2:234474600-234475600	Active TSS	Primary T killer memory cells from peripheral blood	blood
48	chr2:234474600-234475600	Active TSS	Brain Angular Gyrus	brain
49	chr2:234474600-234475600	Active TSS	Brain Anterior Caudate	brain
50	chr2:234474600-234475600	Active TSS	Brain Hippocampus Middle	brain

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