Variant report

Variant	nsv1061112
Chromosome Location	chr21:28738028-28775601
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	BACH1	chr21:28749194-28749197	H1-hESC	embryonic stem cell:	n/a	n/a
2	BHLHE40	chr21:28758540-28758541	HepG2	liver:	n/a	n/a
3	CEBPB	chr21:28752716-28752953	Hela-S3	cervix:	n/a	n/a
4	CEBPB	chr21:28744334-28745001	Hela-S3	cervix:	n/a	n/a
5	CEBPB	chr21:28748519-28748876	Hela-S3	cervix:	n/a	chr21:28748698-28748711
6	CEBPB	chr21:28759712-28760052	K562	blood:	n/a	n/a
7	CEBPB	chr21:28764507-28764611	IMR90	lung:	n/a	n/a
8	CEBPB	chr21:28766076-28766713	IMR90	lung:	n/a	n/a
9	CEBPB	chr21:28744347-28744754	IMR90	lung:	n/a	n/a
10	CTCF	chr21:28754660-28754810	HMF	breast:	n/a	chr21:28754717-28754726 chr21:28754717-28754730
11	CTCF	chr21:28765699-28765882	K562	blood:	n/a	n/a
12	CTCF	chr21:28753242-28753271	GM13976	blood:	n/a	n/a
13	CTCF	chr21:28765542-28765617	Lung_OC	lung:	n/a	n/a
14	E2F4	chr21:28758533-28758612	MCF10A-Er-Src	breast:	n/a	n/a
15	EP300	chr21:28744091-28744647	Hela-S3	cervix:	n/a	chr21:28744526-28744540
16	EP300	chr21:28748593-28748826	Hela-S3	cervix:	n/a	chr21:28748800-28748809
17	FOS	chr21:28754690-28755201	HUVEC	blood vessel:	n/a	chr21:28754938-28754945
18	FOS	chr21:28761223-28761461	MCF10A-Er-Src	breast:	n/a	n/a
19	FOS	chr21:28761283-28761460	MCF10A-Er-Src	breast:	n/a	n/a
20	FOS	chr21:28744300-28744645	HUVEC	blood vessel:	n/a	chr21:28744521-28744528 chr21:28744518-28744529 chr21:28744520-28744528 chr21:28744351-28744360
21	FOS	chr21:28742455-28742933	HUVEC	blood vessel:	n/a	n/a
22	FOSL2	chr21:28765706-28765888	HepG2	liver:	n/a	n/a
23	FOXA2	chr21:28765627-28765922	A549	lung:	n/a	n/a
24	FOXA2	chr21:28765631-28765942	A549	lung:	n/a	n/a
25	FOXP2	chr21:28766101-28766323	SK-N-MC	brain:	n/a	n/a
26	GATA2	chr21:28742435-28742888	HUVEC	blood vessel:	n/a	n/a
27	GATA2	chr21:28744240-28744639	HUVEC	blood vessel:	n/a	chr21:28744411-28744421 chr21:28744407-28744421 chr21:28744350-28744360 chr21:28744408-28744424 chr21:28744483-28744492 chr21:28744483-28744490
28	GATA2	chr21:28762771-28763114	HUVEC	blood vessel:	n/a	chr21:28763093-28763100
29	GATA3	chr21:28743585-28745082	SK-N-SH	brain:	n/a	chr21:28743806-28743813 chr21:28744411-28744421 chr21:28743650-28743671 chr21:28744350-28744360 chr21:28744100-28744121 chr21:28744408-28744424 chr21:28743806-28743813 chr21:28743799-28743820 chr21:28744483-28744492 chr21:28743804-28743813 chr21:28743806-28743813 chr21:28744483-28744490 chr21:28744107-28744116
30	GATA3	chr21:28737539-28738241	SK-N-SH	brain:	n/a	chr21:28737814-28737826 chr21:28737812-28737823
31	GATA3	chr21:28748427-28748615	SH-SY5Y	brain:	n/a	n/a
32	GATA3	chr21:28743847-28745083	SK-N-SH	brain:	n/a	chr21:28744411-28744421 chr21:28744350-28744360 chr21:28744100-28744121 chr21:28744408-28744424 chr21:28744483-28744492 chr21:28744483-28744490 chr21:28744107-28744116
33	GATA3	chr21:28737620-28738237	SK-N-SH	brain:	n/a	chr21:28737814-28737826 chr21:28737812-28737823
34	GATA3	chr21:28744351-28744462	SH-SY5Y	brain:	n/a	chr21:28744411-28744421 chr21:28744408-28744424
35	GTF2F1	chr21:28754720-28754761	H1-hESC	embryonic stem cell:	n/a	n/a
36	JUN	chr21:28769966-28770213	HepG2	liver:	n/a	chr21:28770096-28770109
37	JUND	chr21:28769921-28770272	HepG2	liver:	n/a	n/a
38	MAFF	chr21:28764261-28764508	HepG2	liver:	n/a	n/a
39	MAFK	chr21:28764257-28764570	IMR90	lung:	n/a	n/a
40	MAFK	chr21:28743342-28743525	Hela-S3	cervix:	n/a	n/a
41	MAFK	chr21:28743386-28743717	IMR90	lung:	n/a	chr21:28743640-28743655
42	MAFK	chr21:28743486-28743544	HepG2	liver:	n/a	n/a
43	MAFK	chr21:28764246-28764509	HepG2	liver:	n/a	n/a
44	MAFK	chr21:28764242-28764591	HepG2	liver:	n/a	n/a
45	MAFK	chr21:28773324-28773544	HepG2	liver:	n/a	n/a
46	MYC	chr21:28761347-28761348	MCF10A-Er-Src	breast:	n/a	n/a
47	NFYA	chr21:28749446-28749626	Hela-S3	cervix:	n/a	n/a
48	PBX3	chr21:28744283-28744775	SK-N-SH	brain:	n/a	n/a
49	PBX3	chr21:28765760-28765857	GM12878	blood:	n/a	n/a
50	POLR2A	chr21:28765801-28765865	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:28745546..28748022-chr21:28748168..28750966,2	K562	blood:
2	chr21:28745546..28748022-chr21:28748168..28750966,2	K562	blood:
3	chr21:28743113..28745036-chr21:28748011..28750615,2	K562	blood:
4	chr21:28743113..28745036-chr21:28748011..28750615,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ADAMTS5-5	chr21:28738741-28739001	NONHSAT081570
2	lnc-GABPA-7	chr21:28767900-28768106	ENSG00000236332
3	lnc-ADAMTS5-1	chr21:28770799-28770884	ENSG00000231236.2
4	lnc-ADAMTS5-5	chr21:28733502-28739560	l_2188_chr21:28733501-28920917_placenta
5	lnc-GABPA-7	chr21:28759786-28759979	ENSG00000236332
6	lnc-ADAMTS5-5	chr21:28739620-28740664	l_2188_chr21:28733501-28920917_placenta
7	lnc-GABPA-7	chr21:28763709-28763870	ENSG00000236332
8	lnc-ADAMTS5-5	chr21:28738741-28739001	NONHSAT081571
9	lnc-ADAMTS5-5	chr21:28740482-28740664	NONHSAT081571
10	lnc-ADAMTS5-5	chr21:28740482-28740664	NONHSAT081570
11	lnc-ADAMTS5-1	chr21:28771851-28771893	ENSG00000231236.2

Variant related genes	Relation type
EIF4A1P1	TF binding region

Extended variants
information (count: 1394 )
Associated
traits (count: 65 )

Variant overlapped rSNPs/rCNVs (count:1394 , 50 per page) page: 1 2 3 4 5 6 7 ... 28

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1452097	chr21:28738028-28738029	Enhancers Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs1452096	chr21:28738059-28738060	Enhancers Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
3	rs534120349	chr21:28738100-28738101	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
4	rs188317410	chr21:28738108-28738109	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
5	rs562559622	chr21:28738131-28738132	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
6	rs754017	chr21:28738152-28738153	Enhancers Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs558796700	chr21:28738173-28738174	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
8	rs56902278	chr21:28738208-28738209	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs544199254	chr21:28738246-28738247	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
10	rs2218931	chr21:28738286-28738287	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
11	rs192769943	chr21:28738390-28738391	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
12	rs543623804	chr21:28738426-28738427	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
13	rs568205980	chr21:28738464-28738465	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
14	rs34260662	chr21:28738500-28738501	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
15	rs540599990	chr21:28738521-28738522	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
16	rs57379385	chr21:28738552-28738553	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs532613102	chr21:28738579-28738580	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
18	rs535386647	chr21:28738581-28738582	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
19	rs145937756	chr21:28738605-28738606	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
20	rs751951	chr21:28738653-28738654	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs751950	chr21:28738661-28738662	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs73901219	chr21:28738707-28738708	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs373418346	chr21:28738744-28738745	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
24	rs534057156	chr21:28738762-28738763	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
25	rs547394914	chr21:28738765-28738766	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
26	rs570589511	chr21:28738866-28738867	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
27	rs539263771	chr21:28738870-28738871	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
28	rs8130161	chr21:28738899-28738900	Enhancers Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs139879971	chr21:28738908-28738909	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
30	rs537985237	chr21:28738936-28738937	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
31	rs527261503	chr21:28738948-28738949	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
32	rs552176864	chr21:28738951-28738952	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
33	rs554523235	chr21:28738953-28738954	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
34	rs574515285	chr21:28738957-28738958	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
35	rs371550555	chr21:28739021-28739022	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
36	rs1893579	chr21:28739022-28739023	Enhancers Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs577321416	chr21:28739052-28739053	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
38	rs182738364	chr21:28739064-28739065	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
39	rs563115220	chr21:28739088-28739089	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
40	rs531417083	chr21:28739095-28739096	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
41	rs548331944	chr21:28739100-28739101	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
42	rs141194798	chr21:28739107-28739108	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
43	rs527301444	chr21:28739134-28739135	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
44	rs1893580	chr21:28739190-28739191	Enhancers Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs186967969	chr21:28739204-28739205	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
46	rs74739783	chr21:28739206-28739207	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
47	rs1893581	chr21:28739215-28739216	Enhancers Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
48	rs569545141	chr21:28739219-28739220	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
49	rs192488623	chr21:28739222-28739223	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
50	rs5843277	chr21:28739225-28739226	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:65)

Disease	PMID	Source
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
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
small cell lung cancer	20016488	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
lymphocytic leukemia	21291569	CNVD
Hodgkin''s lymphoma	18641027	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
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
Acute myeloid leukemia	21251322	CNVD
Developmental delay	21147756	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
Ewing''s sarcoma	17952124	CNVD
Myelofibrosis	22110671	CNVD
Ovarian cancer	22174824	CNVD
Renal cell carcinoma	18765545	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Gastric cancer	18160780	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:28736600-28739600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr21:28737400-28738600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr21:28737600-28738200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr21:28737600-28738200	Enhancers	Muscle Satellite Cultured Cells	--
5	chr21:28737600-28738200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr21:28737600-28738400	Enhancers	HMEC	breast
7	chr21:28737600-28738400	Enhancers	NHEK	skin
8	chr21:28737800-28738200	Enhancers	HSMM	muscle
9	chr21:28738000-28738200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr21:28738000-28738400	Enhancers	HSMMtube	muscle
11	chr21:28738000-28740000	Enhancers	Fetal Intestine Large	intestine
12	chr21:28738000-28740200	Enhancers	Fetal Intestine Small	intestine
13	chr21:28738000-28742600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr21:28738000-28743400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr21:28738400-28742600	Weak transcription	HSMMtube	muscle
16	chr21:28738600-28741600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr21:28738800-28739600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr21:28738800-28740000	Enhancers	Ovary	ovary
19	chr21:28739200-28739800	Enhancers	Duodenum Mucosa	Duodenum
20	chr21:28739200-28741600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr21:28739600-28741200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr21:28739600-28743400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr21:28740000-28741600	Weak transcription	Ovary	ovary
24	chr21:28740200-28742600	Weak transcription	Fetal Intestine Small	intestine
25	chr21:28741200-28743200	Enhancers	Right Atrium	heart
26	chr21:28741200-28745600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr21:28741400-28741800	Enhancers	Fetal Heart	heart
28	chr21:28741400-28744800	Enhancers	Dnd41	blood
29	chr21:28741600-28741800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr21:28741600-28741800	Enhancers	H9 Cell Line	embryonic stem cell
31	chr21:28741600-28741800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr21:28741600-28742200	Enhancers	Left Ventricle	heart
33	chr21:28741600-28743200	Enhancers	Ovary	ovary
34	chr21:28741600-28744400	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr21:28741800-28742200	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr21:28741800-28742400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr21:28741800-28742400	Weak transcription	Fetal Heart	heart
38	chr21:28741800-28745200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr21:28742000-28743600	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr21:28742200-28742600	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr21:28742200-28743200	Enhancers	H9 Cell Line	embryonic stem cell
42	chr21:28742200-28743400	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr21:28742200-28743400	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr21:28742200-28744400	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr21:28742200-28763600	Weak transcription	Left Ventricle	heart
46	chr21:28742400-28743000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr21:28742400-28745200	Enhancers	Fetal Heart	heart
48	chr21:28742400-28745800	Enhancers	Fetal Lung	lung
49	chr21:28742600-28743000	Enhancers	H1 Cell Line	embryonic stem cell
50	chr21:28742600-28743000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links