Variant report

Variant	esv2755103
Chromosome Location	chr21:40847196-40877805
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	chr21:40855824-40856205	K562	blood:	n/a	n/a
2	ATF1	chr21:40855897-40856232	K562	blood:	n/a	n/a
3	CCNT2	chr21:40855949-40856278	K562	blood:	n/a	n/a
4	CEBPB	chr21:40854429-40854467	HepG2	liver:	n/a	n/a
5	CEBPB	chr21:40854366-40854487	K562	blood:	n/a	n/a
6	CEBPB	chr21:40849772-40850000	IMR90	lung:	n/a	n/a
7	CEBPB	chr21:40855884-40856247	MCF-7	breast:	n/a	n/a
8	CEBPB	chr21:40852102-40852236	HepG2	liver:	n/a	chr21:40852187-40852198
9	CEBPB	chr21:40852153-40852237	A549	lung:	n/a	chr21:40852187-40852198
10	CEBPB	chr21:40855967-40856284	Hela-S3	cervix:	n/a	n/a
11	CTCF	chr21:40858827-40858870	Kidney_OC	kidney:	n/a	n/a
12	CTCF	chr21:40851379-40851424	GM19239	blood:	n/a	n/a
13	CTCF	chr21:40851164-40851351	MCF-7	breast:	n/a	n/a
14	CTCF	chr21:40851277-40851340	Fibrobl	skin:	n/a	n/a
15	CTCF	chr21:40875123-40875158	GM20000	blood:	n/a	n/a
16	CTCF	chr21:40864996-40865026	GM20000	blood:	n/a	n/a
17	CTCF	chr21:40848600-40848750	HEK293	kidney:	n/a	chr21:40848723-40848732 chr21:40848722-40848743
18	CTCF	chr21:40872652-40872678	Kidney_OC	kidney:	n/a	n/a
19	CUX1	chr21:40852474-40852611	K562	blood:	n/a	n/a
20	E2F6	chr21:40874391-40874667	H1-hESC	embryonic stem cell:	n/a	n/a
21	E2F6	chr21:40874296-40874737	H1-hESC	embryonic stem cell:	n/a	n/a
22	EBF1	chr21:40861505-40861772	GM12878	blood:	n/a	chr21:40861601-40861612
23	EBF1	chr21:40861503-40861712	GM12878	blood:	n/a	chr21:40861601-40861612
24	EP300	chr21:40856823-40857367	SK-N-SH	brain:	n/a	n/a
25	EP300	chr21:40855871-40856268	K562	blood:	n/a	n/a
26	EP300	chr21:40855851-40856238	SK-N-SH_RA	brain:	n/a	n/a
27	EP300	chr21:40856900-40857328	SK-N-SH_RA	brain:	n/a	n/a
28	EP300	chr21:40855790-40856297	SK-N-SH_RA	brain:	n/a	n/a
29	EP300	chr21:40855964-40856194	Hela-S3	cervix:	n/a	n/a
30	EP300	chr21:40856838-40857309	T-47D	breast:	n/a	n/a
31	EP300	chr21:40856923-40857248	SK-N-SH_RA	brain:	n/a	n/a
32	EP300	chr21:40873430-40873576	K562	blood:	n/a	n/a
33	ESR1	chr21:40864859-40865275	T-47D	breast:	n/a	n/a
34	ESR1	chr21:40856902-40857329	T-47D	breast:	n/a	n/a
35	ESR1	chr21:40856877-40857406	T-47D	breast:	n/a	n/a
36	ESR1	chr21:40856938-40857386	T-47D	breast:	n/a	n/a
37	ESR1	chr21:40856931-40857396	T-47D	breast:	n/a	n/a
38	FOS	chr21:40855995-40856171	MCF10A-Er-Src	breast:	n/a	n/a
39	FOSL2	chr21:40855828-40856395	SK-N-SH	brain:	n/a	n/a
40	FOSL2	chr21:40855861-40856379	MCF-7	breast:	n/a	n/a
41	FOXA1	chr21:40856916-40857300	T-47D	breast:	n/a	n/a
42	FOXA1	chr21:40856930-40857349	T-47D	breast:	n/a	n/a
43	FOXA1	chr21:40864876-40865235	T-47D	breast:	n/a	n/a
44	FOXA1	chr21:40864902-40865218	T-47D	breast:	n/a	n/a
45	GABPA	chr21:40874940-40875486	HL-60	blood:	n/a	n/a
46	GABPA	chr21:40874960-40875452	HL-60	blood:	n/a	n/a
47	GATA1	chr21:40854994-40856502	K562	blood:	n/a	chr21:40856430-40856437 chr21:40855985-40855992 chr21:40856423-40856444 chr21:40855983-40855993 chr21:40856148-40856155 chr21:40856426-40856442 chr21:40855985-40855992 chr21:40856148-40856155 chr21:40856430-40856437 chr21:40856117-40856126 chr21:40855978-40855999 chr21:40856430-40856437 chr21:40855981-40855994 chr21:40855985-40855992 chr21:40856148-40856155 chr21:40855983-40855992
48	GATA2	chr21:40855978-40856297	SH-SY5Y	brain:	n/a	chr21:40855985-40855992 chr21:40855983-40855993 chr21:40856148-40856155 chr21:40855985-40855992 chr21:40856148-40856155 chr21:40856117-40856126 chr21:40855978-40855999 chr21:40855981-40855994 chr21:40855985-40855992 chr21:40856148-40856155 chr21:40855983-40855992
49	GATA3	chr21:40856823-40857408	T-47D	breast:	n/a	n/a
50	GATA3	chr21:40855987-40856326	MCF-7	breast:	n/a	chr21:40856148-40856155 chr21:40856148-40856155 chr21:40856117-40856126 chr21:40856148-40856155

No.	Distal block	Cell Line	Cell type
1	chr21:40856524..40858264-chr21:41041120..41043051,2	MCF-7	breast:
2	chr21:40855062..40856739-chr21:40872543..40874201,2	K562	blood:
3	chr21:40866413..40867950-chr21:40879488..40881131,2	K562	blood:
4	chr21:40842346..40845248-chr21:40847999..40850536,2	K562	blood:
5	chr21:40870583..40873437-chr21:40873635..40876593,2	K562	blood:
6	chr21:40845066..40847673-chr21:40849022..40851771,3	MCF-7	breast:
7	chr21:40877342..40880312-chr21:40887456..40889959,2	MCF-7	breast:
8	chr21:40873636..40875613-chr21:40877130..40879236,2	K562	blood:
9	chr21:40854953..40857406-chr21:40860627..40862371,2	MCF-7	breast:
10	chr21:40845066..40847673-chr21:40849022..40851771,3	MCF-7	breast:
11	chr21:40868881..40871731-chr21:40873960..40875993,2	MCF-7	breast:
12	chr21:40817030..40819753-chr21:40851641..40854167,2	MCF-7	breast:
13	chr21:40825465..40827848-chr21:40854649..40856447,2	K562	blood:
14	chr21:40855062..40856739-chr21:40872543..40874201,2	K562	blood:
15	chr21:40873636..40875613-chr21:40877130..40879236,2	K562	blood:
16	chr21:40868881..40871731-chr21:40873960..40875993,2	MCF-7	breast:
17	chr21:40854953..40857406-chr21:40860627..40862371,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LCA5L-1	chr21:40863470-40863824	NONHSAT082197
2	lnc-WRB-4	chr21:40860253-40860686	NONHSAT082196

Variant related genes	Relation type
RPS26P4	TF binding region
MYL6P2	TF binding region
SH3BGR	TF binding region
ENSG00000185437	chromatin interactions
ENSG00000157578	chromatin interactions

Extended variants
information (count: 1125 )
Associated
traits (count: 71 )

Variant overlapped rSNPs/rCNVs (count:1125 , 50 per page) page: 1 2 3 4 5 6 7 ... 23

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs940625	chr21:40847196-40847197	Weak transcription Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs144648200	chr21:40847206-40847207	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs62222761	chr21:40847210-40847211	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs537004834	chr21:40847219-40847220	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs186326424	chr21:40847231-40847232	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs190041564	chr21:40847247-40847248	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs760284	chr21:40847249-40847250	Weak transcription Active TSS Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs564056350	chr21:40847261-40847262	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs181300731	chr21:40847264-40847265	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs185936084	chr21:40847276-40847277	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs147849831	chr21:40847291-40847292	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs555591577	chr21:40847317-40847318	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs575448315	chr21:40847329-40847330	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs189927234	chr21:40847356-40847357	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs181844024	chr21:40847365-40847366	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs139775499	chr21:40847387-40847388	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs7281516	chr21:40847391-40847392	Weak transcription Active TSS Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs559436962	chr21:40847398-40847399	Weak transcription Active TSS Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs528622132	chr21:40847400-40847401	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
20	rs79186558	chr21:40847435-40847436	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs145186453	chr21:40847454-40847455	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs190593467	chr21:40847536-40847537	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs183846872	chr21:40847543-40847544	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs188386090	chr21:40847549-40847550	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs570328641	chr21:40847554-40847555	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
26	rs539459096	chr21:40847580-40847581	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
27	rs2837042	chr21:40847614-40847615	Weak transcription Strong transcription Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
28	rs545356200	chr21:40847674-40847675	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
29	rs566578670	chr21:40847745-40847746	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
30	rs561679189	chr21:40847761-40847762	Weak transcription Strong transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
31	rs114129299	chr21:40847902-40847903	Weak transcription Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
32	rs150989513	chr21:40847949-40847950	Weak transcription Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
33	rs537728543	chr21:40847961-40847962	Weak transcription Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
34	rs535271708	chr21:40847967-40847968	Weak transcription Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
35	rs558055481	chr21:40848008-40848009	Weak transcription Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
36	rs76438424	chr21:40848041-40848042	Weak transcription Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
37	rs545803026	chr21:40848079-40848080	Weak transcription Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
38	rs529159894	chr21:40848082-40848083	Weak transcription Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
39	rs559374291	chr21:40848131-40848132	Weak transcription Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
40	rs572997126	chr21:40848143-40848144	Weak transcription Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
41	rs1735137	chr21:40848174-40848175	Weak transcription Strong transcription Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs572254894	chr21:40848194-40848195	Weak transcription Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
43	rs562126316	chr21:40848215-40848216	Enhancers Weak transcription Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
44	rs531161767	chr21:40848283-40848284	Enhancers Weak transcription Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
45	rs191265207	chr21:40848307-40848308	Enhancers Weak transcription Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
46	rs183067655	chr21:40848342-40848343	Enhancers Weak transcription Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
47	rs532913975	chr21:40848350-40848351	Enhancers Weak transcription Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs369937898	chr21:40848354-40848355	Enhancers Weak transcription Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs548481754	chr21:40848365-40848366	Enhancers Weak transcription Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs566515998	chr21:40848373-40848374	Enhancers Weak transcription Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:71)

Disease	PMID	Source
Glioblastoma multiforme	21080181	CNVD
Cancer	16751803	CNVD
Medulloblastoma	21979893	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
Down syndrome	17412756	CNVD
Down syndrome	17576883	CNVD
Acute promyelocytic leukemia	19109227	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute myeloid leukemia	20729466	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Astrocytoma	17387387	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	17387387	CNVD
Renal cell carcinoma	19461508	CNVD
Seminomas	18059402	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Prostate cancer	19156837	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
small cell lung cancer	20016488	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
lymphocytic leukemia	21291569	CNVD
Melanoma	18172304	CNVD
Autism	22958593	CNVD
Schizophrenia	22958593	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Wilms tumour	21544195	CNVD
Ewing''s sarcoma	17952124	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Acute myeloid leukemia	16864856	CNVD
Mental retardation	21031080	CNVD
Polymicrogyria	21031080	CNVD
periventricular nodular heterotopia	21031080	CNVD
Myelodysplastic syndrome	21606161	CNVD
Chronic lymphocytic leukemia	18922857	CNVD
Autism	18414403	CNVD
Gastrointestinal stromal cancer	19259404	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Breast cancer	21858162	CNVD
Neuroblastoma	18923191	CNVD
Breast cancer	17899364	CNVD
Down syndrome	20877625	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21364760	CNVD
Cancer	20164920	CNVD
Myelofibrosis	22110671	CNVD
Hirschsprung''s Disease	21712996	CNVD
Prostate cancer	21147910	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Prostate cancer	17245344	CNVD
Prostate cancer	20473283	CNVD
Chordoma	18071362	CNVD
Breast cancer	22522925	CNVD
T-cell lymphomas	22341440	CNVD
Pancreatic cancer	17952125	CNVD
Cancer	20164919	CNVD

Chromatin state (count:177 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40824000-40852400	Weak transcription	Pancreas	Pancrea
2	chr21:40825000-40847800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr21:40826600-40849800	Weak transcription	HSMMtube	muscle
4	chr21:40827400-40879800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr21:40828600-40847400	Weak transcription	Brain Substantia Nigra	brain
6	chr21:40828800-40847600	Weak transcription	Brain Angular Gyrus	brain
7	chr21:40828800-40847600	Weak transcription	Brain Anterior Caudate	brain
8	chr21:40829800-40856200	Weak transcription	Aorta	Aorta
9	chr21:40830200-40849800	Weak transcription	Primary T cells from cord blood	blood
10	chr21:40833000-40847200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr21:40835600-40851000	Weak transcription	Ovary	ovary
12	chr21:40835800-40847800	Weak transcription	Left Ventricle	heart
13	chr21:40836200-40851000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr21:40836200-40852200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr21:40836400-40851400	Weak transcription	Brain Hippocampus Middle	brain
16	chr21:40836400-40894800	Weak transcription	Right Ventricle	heart
17	chr21:40838800-40849800	Weak transcription	Liver	Liver
18	chr21:40840600-40847600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr21:40840600-40847800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr21:40844600-40848400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr21:40844800-40847200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr21:40844800-40855800	Weak transcription	Adipose Nuclei	Adipose
23	chr21:40845000-40851200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr21:40845000-40856600	Weak transcription	Colon Smooth Muscle	Colon
25	chr21:40846800-40854600	Weak transcription	Psoas Muscle	Psoas
26	chr21:40846800-40862800	Weak transcription	Gastric	stomach
27	chr21:40847000-40847200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
28	chr21:40847000-40850200	Weak transcription	Fetal Heart	heart
29	chr21:40847200-40847800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr21:40847200-40848000	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr21:40847200-40848200	Strong transcription	Stomach Smooth Muscle	stomach
32	chr21:40847400-40848400	Strong transcription	Brain Substantia Nigra	brain
33	chr21:40847600-40848200	Strong transcription	Brain Angular Gyrus	brain
34	chr21:40847600-40848200	Strong transcription	Brain Anterior Caudate	brain
35	chr21:40847600-40848200	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr21:40847800-40848400	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr21:40847800-40848400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
38	chr21:40847800-40848400	Strong transcription	Left Ventricle	heart
39	chr21:40847800-40850400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr21:40848000-40851000	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr21:40848200-40848600	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr21:40848200-40848600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
43	chr21:40848200-40851600	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr21:40848200-40852200	Weak transcription	Brain Angular Gyrus	brain
45	chr21:40848200-40852400	Weak transcription	Brain Anterior Caudate	brain
46	chr21:40848200-40895600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr21:40848400-40848800	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr21:40848400-40851400	Weak transcription	Brain Substantia Nigra	brain
49	chr21:40848400-40853800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr21:40848400-40863600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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