Variant report

Variant	nsv587049
Chromosome Location	chr21:15954103-15962331
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	chr21:15955288-15957571	K562	blood:	n/a	n/a
2	ARID3A	chr21:15954023-15954811	K562	blood:	n/a	n/a
3	ATF1	chr21:15957026-15957461	K562	blood:	n/a	n/a
4	ATF2	chr21:15962120-15962574	GM12878	blood:	n/a	n/a
5	ATF2	chr21:15962106-15962556	GM12878	blood:	n/a	n/a
6	BATF	chr21:15962199-15962469	GM12878	blood:	n/a	n/a
7	BCL11A	chr21:15962203-15962475	GM12878	blood:	n/a	n/a
8	BHLHE40	chr21:15962029-15962506	GM12878	blood:	n/a	n/a
9	CCNT2	chr21:15957137-15957477	K562	blood:	n/a	n/a
10	CCNT2	chr21:15956049-15956403	K562	blood:	n/a	n/a
11	CCNT2	chr21:15954161-15954740	K562	blood:	n/a	n/a
12	CEBPB	chr21:15957511-15957789	H1-hESC	embryonic stem cell:	n/a	chr21:15957622-15957633 chr21:15957624-15957633 chr21:15957622-15957635 chr21:15957624-15957635
13	CEBPB	chr21:15956744-15957817	K562	blood:	n/a	chr21:15956898-15956910 chr21:15957267-15957278 chr21:15957622-15957633 chr21:15957012-15957025 chr21:15957624-15957633 chr21:15957622-15957635 chr21:15957624-15957635 chr21:15956955-15956972
14	CEBPB	chr21:15957502-15957800	HepG2	liver:	n/a	chr21:15957622-15957633 chr21:15957624-15957633 chr21:15957622-15957635 chr21:15957624-15957635
15	CEBPB	chr21:15957499-15957789	IMR90	lung:	n/a	chr21:15957622-15957633 chr21:15957624-15957633 chr21:15957622-15957635 chr21:15957624-15957635
16	CEBPD	chr21:15954116-15954735	K562	blood:	n/a	n/a
17	CEBPD	chr21:15954148-15954694	K562	blood:	n/a	n/a
18	CHD2	chr21:15962257-15962500	GM12878	blood:	n/a	n/a
19	CREB1	chr21:15962069-15962610	GM12878	blood:	n/a	n/a
20	CUX1	chr21:15954096-15954815	K562	blood:	n/a	n/a
21	CUX1	chr21:15955332-15957848	K562	blood:	n/a	n/a
22	CUX1	chr21:15961918-15962462	GM12878	blood:	n/a	n/a
23	CUX1	chr21:15962322-15962397	K562	blood:	n/a	n/a
24	E2F4	chr21:15955854-15956127	MCF10A-Er-Src	breast:	n/a	n/a
25	EBF1	chr21:15962203-15962527	GM12878	blood:	n/a	n/a
26	ELF1	chr21:15954362-15954609	K562	blood:	n/a	n/a
27	ELK1	chr21:15957663-15957751	GM12878	blood:	n/a	n/a
28	EP300	chr21:15954335-15954742	GM12878	blood:	n/a	chr21:15954427-15954434
29	EP300	chr21:15955225-15956554	K562	blood:	n/a	chr21:15956378-15956387
30	EP300	chr21:15962082-15962645	GM12878	blood:	n/a	chr21:15962126-15962140
31	EP300	chr21:15956857-15957741	K562	blood:	n/a	chr21:15956954-15956968 chr21:15957623-15957637 chr21:15957493-15957503 chr21:15956959-15956967 chr21:15956868-15956882
32	EP300	chr21:15961923-15962589	GM12878	blood:	n/a	chr21:15962126-15962140 chr21:15961954-15961963 chr21:15961950-15961964
33	EP300	chr21:15956456-15956960	GM12878	blood:	n/a	chr21:15956542-15956556 chr21:15956868-15956882
34	EP300	chr21:15954130-15954885	K562	blood:	n/a	chr21:15954427-15954434
35	EP300	chr21:15955223-15956056	GM12878	blood:	n/a	n/a
36	EP300	chr21:15962190-15962749	GM12878	blood:	n/a	n/a
37	FOXM1	chr21:15962069-15962547	GM12878	blood:	n/a	n/a
38	GATA1	chr21:15956135-15957707	PBDE	blood:	n/a	chr21:15956379-15956388
39	GATA1	chr21:15954172-15955748	PBDE	blood:	n/a	chr21:15954420-15954427 chr21:15954420-15954427 chr21:15954420-15954427
40	GATA1	chr21:15953823-15957711	K562	blood:	n/a	chr21:15954420-15954427 chr21:15954420-15954427 chr21:15956379-15956388 chr21:15954420-15954427
41	GATA2	chr21:15954214-15954608	K562	blood:	n/a	chr21:15954420-15954427 chr21:15954420-15954427 chr21:15954420-15954427
42	GATA2	chr21:15954300-15954637	HUVEC	blood vessel:	n/a	chr21:15954420-15954427 chr21:15954420-15954427 chr21:15954420-15954427
43	GATA2	chr21:15954149-15954619	K562	blood:	n/a	chr21:15954420-15954427 chr21:15954420-15954427 chr21:15954420-15954427
44	GATA2	chr21:15954273-15954717	K562	blood:	n/a	chr21:15954420-15954427 chr21:15954420-15954427 chr21:15954420-15954427
45	GATA3	chr21:15961819-15962093	SH-SY5Y	brain:	n/a	chr21:15961952-15961962
46	GTF2B	chr21:15954425-15954669	K562	blood:	n/a	n/a
47	HEY1	chr21:15955561-15955867	K562	blood:	n/a	n/a
48	HEY1	chr21:15954310-15954782	K562	blood:	n/a	n/a
49	HMGN3	chr21:15954061-15954742	K562	blood:	n/a	chr21:15954419-15954426
50	IRF1	chr21:15961830-15962058	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:15916155..15918687-chr21:15956794..15958327,2	K562	blood:
2	chr21:15905941..15908063-chr21:15951429..15954293,3	K562	blood:
3	chr21:15913818..15915789-chr21:15955801..15958160,2	K562	blood:
4	chr21:15949855..15953983-chr21:15956777..15961120,5	K562	blood:
5	chr21:15956962..15958891-chr21:15974300..15976169,2	K562	blood:
6	chr21:15961455..15963973-chr21:15965969..15968617,3	K562	blood:
7	chr21:15955923..15958525-chr21:15986829..15988461,2	K562	blood:
8	chr21:15953103..15955709-chr21:15961850..15965268,4	K562	blood:
9	chr21:15916155..15921451-chr21:15952417..15958327,11	K562	blood:
10	chr21:15954130..15955883-chr21:15957190..15959546,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RBM11-3	chr21:15957683-15957859	ENSG00000223662.1
2	lnc-RBM11-3	chr21:15954523-15954612	ENSG00000223662.1

Variant related genes	Relation type
SAMSN1-AS1	TF binding region
SAMSN1	TF binding region
ENSG00000155307	chromatin interactions
ENSG00000223662	chromatin interactions
ENSG00000243440	chromatin interactions

Extended variants
information (count: 339 )
Associated
traits (count: 62 )

Variant overlapped rSNPs/rCNVs (count:339 , 50 per page) page: 1 2 3 4 5 6 7

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs2822784	chr21:15954103-15954104	Enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs376200341	chr21:15954108-15954109	Enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs530367573	chr21:15954117-15954118	Enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs535084242	chr21:15954125-15954126	Enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs113281132	chr21:15954201-15954202	Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs368109267	chr21:15954239-15954240	Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs575013996	chr21:15954283-15954284	Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs537648976	chr21:15954313-15954314	Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs557311328	chr21:15954379-15954380	Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs34865679	chr21:15954385-15954386	Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs549960012	chr21:15954439-15954440	Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs190362907	chr21:15954458-15954459	Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs569944717	chr21:15954487-15954488	Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs9636819	chr21:15954504-15954505	Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs546183526	chr21:15954509-15954510	Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs2822785	chr21:15954528-15954529	Enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
17	rs572521293	chr21:15954550-15954551	Enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
18	rs375632704	chr21:15954553-15954554	Enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
19	rs2822786	chr21:15954593-15954594	Enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
20	rs116256485	chr21:15954594-15954595	Enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
21	rs151160030	chr21:15954595-15954596	Enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
22	rs139465416	chr21:15954601-15954602	Enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
23	rs183385144	chr21:15954611-15954612	Enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
24	rs200030823	chr21:15954631-15954632	Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs546930039	chr21:15954639-15954640	Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs144978524	chr21:15954652-15954653	Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs2822787	chr21:15954660-15954661	Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
28	rs370821056	chr21:15954671-15954672	Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs202239654	chr21:15954681-15954682	Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs548648520	chr21:15954695-15954696	Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs6516894	chr21:15954789-15954790	Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs537157859	chr21:15954793-15954794	Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs147652215	chr21:15954845-15954846	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs2822788	chr21:15954849-15954850	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs34228133	chr21:15954862-15954863	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs201677006	chr21:15954866-15954867	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs377414544	chr21:15954898-15954899	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs142259108	chr21:15954948-15954949	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs146014614	chr21:15954955-15954956	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs145577553	chr21:15954979-15954980	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs577127309	chr21:15954981-15954982	Enhancers Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs570600692	chr21:15955014-15955015	Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs371230589	chr21:15955028-15955029	Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs575260858	chr21:15955034-15955035	Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs539672705	chr21:15955071-15955072	Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs543992941	chr21:15955076-15955077	Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs80109143	chr21:15955113-15955114	Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs76500087	chr21:15955115-15955116	Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs77357431	chr21:15955116-15955117	Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs74682993	chr21:15955117-15955118	Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:62)

Disease	PMID	Source
Ovarian cancer	21720365	CNVD
Wilms tumour	21544195	CNVD
Esophageal cancer	21851588	CNVD
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
Sudden cardiac death	19188705	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute myeloid leukemia	20729466	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell lymphomas	19863542	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
Acute lymphoblastic leukemia	21980252	CNVD
Metanephric adenoma	20802469	CNVD
Neuroblastoma	18923191	CNVD
Prostate cancer	19156837	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Cancer	20164919	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	20409316	CNVD
Autism	18414403	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
lymphocytic leukemia	21291569	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute myeloid leukemia	21251322	CNVD
abnormal development	18461090	CNVD
Breast cancer	21785460	CNVD
Breast cancer	21364760	CNVD
Multiple myeloma	17550852	CNVD
Myelofibrosis	22110671	CNVD
Alzheimer''s disease	18923514	CNVD
Alzheimer''s disease	20877625	CNVD
Follicular lymphoma	20505157	CNVD
Alzheimer''s disease	21956041	CNVD
Cancer	21183584	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Melanoma	18172304	CNVD
Autism	22958593	CNVD
Schizophrenia	22958593	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
XY gonadal dysgenesis	20685758	CNVD

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:15952800-15954200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr21:15953400-15954400	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr21:15953400-15954800	Enhancers	Dnd41	blood
4	chr21:15953600-15954400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr21:15953800-15954200	Active TSS	K562	blood
6	chr21:15954000-15954600	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr21:15954000-15954800	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr21:15954000-15955000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr21:15954200-15954600	Active TSS	Primary T cells fromperipheralblood	blood
10	chr21:15954200-15954600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
11	chr21:15954200-15954800	Enhancers	Primary T cells from cord blood	blood
12	chr21:15954200-15954800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr21:15954200-15954800	Flanking Active TSS	K562	blood
14	chr21:15954400-15954800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr21:15954400-15954800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
16	chr21:15954400-15954800	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr21:15954600-15954800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
18	chr21:15954800-15956400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr21:15954800-15957200	Active TSS	K562	blood
20	chr21:15954800-15961400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr21:15954800-15961800	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr21:15954800-15962000	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr21:15955000-15957400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr21:15956200-15957400	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr21:15956200-15957800	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr21:15956400-15956600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr21:15956400-15957800	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr21:15956600-15957000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr21:15956800-15957800	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr21:15957000-15957200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr21:15957000-15957400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr21:15957200-15957800	Flanking Active TSS	K562	blood
33	chr21:15957200-15961600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr21:15957400-15957800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr21:15957400-15957800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr21:15957800-15958000	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr21:15957800-15958800	Weak transcription	K562	blood
38	chr21:15957800-15962000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr21:15957800-15962400	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr21:15957800-15962600	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr21:15958000-15962000	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr21:15958800-15959400	Enhancers	K562	blood
43	chr21:15959400-15962000	Weak transcription	K562	blood
44	chr21:15961400-15965200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr21:15961600-15961800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr21:15961600-15961800	Enhancers	GM12878-XiMat	blood
47	chr21:15961600-15962400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr21:15961600-15962600	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr21:15961600-15962600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr21:15961800-15962400	Enhancers	Primary T helper cells fromperipheralblood	blood

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