Variant report

Variant	nsv979536
Chromosome Location	chr21:40499089-40500287
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:51)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:51 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr21:40499512-40499774	MCF-7	breast:	n/a	n/a
2	CTCF	chr21:40499600-40499750	K562	blood:	n/a	n/a
3	CTCF	chr21:40499500-40499650	K562	blood:	n/a	n/a
4	CTCF	chr21:40499560-40499710	HCM	heart:	n/a	n/a
5	CTCF	chr21:40499466-40499840	MCF-7	breast:	n/a	n/a
6	CTCF	chr21:40499520-40499670	GM12865	blood:	n/a	n/a
7	CTCF	chr21:40499456-40499778	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr21:40499520-40499670	AG09309	skin:	n/a	n/a
9	CTCF	chr21:40499540-40499690	HCPEpiC	choroid plexus:	n/a	n/a
10	CTCF	chr21:40499560-40499710	MCF-7	breast:	n/a	n/a
11	CTCF	chr21:40499540-40499690	HEK293	kidney:	n/a	n/a
12	CTCF	chr21:40499492-40499699	T-47D	breast:	n/a	n/a
13	CTCF	chr21:40499618-40499700	LNCaP	prostate:	n/a	n/a
14	CTCF	chr21:40499555-40499715	Gliobla	brain:	n/a	n/a
15	CTCF	chr21:40499565-40499736	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr21:40499600-40499750	Hela-S3	cervix:	n/a	n/a
17	CTCF	chr21:40499528-40499762	MCF-7	breast:	n/a	n/a
18	CTCF	chr21:40499560-40499710	RPTEC	kidney:	n/a	n/a
19	CTCF	chr21:40499523-40499762	K562	blood:	n/a	n/a
20	CTCF	chr21:40499540-40499690	HA-sp	spinal cord:	n/a	n/a
21	CTCF	chr21:40499545-40499753	MCF-7	breast:	n/a	n/a
22	CTCF	chr21:40499540-40499690	GM12867	blood:	n/a	n/a
23	CTCF	chr21:40499520-40499670	HBMEC	blood vessel:	n/a	n/a
24	CTCF	chr21:40499520-40499670	GM12873	blood:	n/a	n/a
25	CTCF	chr21:40499640-40499790	Caco-2	colon:	n/a	n/a
26	CTCF	chr21:40499600-40499750	GM12878	blood:	n/a	n/a
27	CTCF	chr21:40499428-40499884	MCF-7	breast:	n/a	n/a
28	CTCF	chr21:40499436-40499754	K562	blood:	n/a	n/a
29	CTCF	chr21:40499451-40499881	K562	blood:	n/a	n/a
30	CTCF	chr21:40499452-40499801	K562	blood:	n/a	n/a
31	CTCF	chr21:40499541-40499763	MCF-7	breast:	n/a	n/a
32	CTCF	chr21:40499620-40499649	Hela-S3	cervix:	n/a	n/a
33	CTCF	chr21:40499584-40499724	LNCaP	prostate:	n/a	n/a
34	CTCF	chr21:40499547-40499768	MCF-7	breast:	n/a	n/a
35	CTCF	chr21:40499600-40499750	GM12873	blood:	n/a	n/a
36	CTCF	chr21:40499513-40499815	H1-hESC	embryonic stem cell:	n/a	n/a
37	CTCF	chr21:40499620-40499770	Hela-S3	cervix:	n/a	n/a
38	CTCF	chr21:40499300-40499450	MCF-7	breast:	n/a	n/a
39	CTCF	chr21:40499600-40499750	HPAF	blood vessel:	n/a	n/a
40	CTCF	chr21:40499438-40499809	K562	blood:	n/a	n/a
41	CTCF	chr21:40499600-40499750	HCFaa	heart:	n/a	n/a
42	RAD21	chr21:40499607-40499631	Hela-S3	cervix:	n/a	n/a
43	RAD21	chr21:40499435-40499848	H1-hESC	embryonic stem cell:	n/a	n/a
44	RAD21	chr21:40499457-40499744	H1-hESC	embryonic stem cell:	n/a	n/a
45	RAD21	chr21:40499572-40499670	K562	blood:	n/a	n/a
46	RAD21	chr21:40499447-40499808	H1-hESC	embryonic stem cell:	n/a	n/a
47	RAD21	chr21:40499477-40499698	K562	blood:	n/a	n/a
48	RCOR1	chr21:40499610-40499613	K562	blood:	n/a	n/a
49	SMC3	chr21:40499582-40499779	Hela-S3	cervix:	n/a	n/a
50	SMC3	chr21:40499582-40499678	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr21:40488161..40490338-chr21:40496446..40499117,2	K562	blood:
2	chr21:40176416..40178956-chr21:40498284..40502065,4	MCF-7	breast:
3	chr21:40105498..40106623-chr21:40497124..40499103,7	MCF-7	breast:
4	chr17:6652834..6653337-chr21:40499511..40500077,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WRB-8	chr21:40499496-40499966	NONHSAT082150
2	lnc-WRB-8	chr21:40499494-40499966	NONHSAT082149

No data

Variant related genes	Relation type
RPL23AP12	TF binding region
ENSG00000262990	chromatin interactions
ENSG00000244283	chromatin interactions
ENSG00000157557	chromatin interactions

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

Variant overlapped rSNPs/rCNVs (count:71 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs545940463	chr21:40499098-40499099	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs2836899	chr21:40499101-40499102	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs909181	chr21:40499111-40499112	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs2836900	chr21:40499166-40499167	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs114909693	chr21:40499170-40499171	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs2836901	chr21:40499194-40499195	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs559211107	chr21:40499206-40499207	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs2178836	chr21:40499244-40499245	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
9	rs541691977	chr21:40499283-40499284	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs191252486	chr21:40499297-40499298	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs537325877	chr21:40499300-40499301	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs530040126	chr21:40499316-40499317	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs555574097	chr21:40499333-40499334	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs2142112	chr21:40499370-40499371	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
15	rs151091809	chr21:40499403-40499404	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs375936198	chr21:40499406-40499407	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs145268564	chr21:40499407-40499408	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs372856905	chr21:40499408-40499409	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs563395770	chr21:40499409-40499410	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs532380751	chr21:40499410-40499411	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs201031390	chr21:40499414-40499415	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs565157253	chr21:40499416-40499417	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs532563797	chr21:40499417-40499418	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs370924490	chr21:40499419-40499420	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs377691739	chr21:40499422-40499423	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs371295731	chr21:40499423-40499424	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs144601249	chr21:40499424-40499425	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs34160879	chr21:40499432-40499433	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs527616291	chr21:40499454-40499455	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs2836902	chr21:40499467-40499468	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
31	rs1882777	chr21:40499498-40499499	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
32	rs552358122	chr21:40499509-40499510	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
33	rs536422906	chr21:40499510-40499511	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
34	rs141199159	chr21:40499540-40499541	Weak transcription	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
35	rs1810383	chr21:40499541-40499542	Weak transcription	Chromatin interactive region lncRNA	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs2836903	chr21:40499556-40499557	Weak transcription	Chromatin interactive region lncRNA	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs368082470	chr21:40499577-40499578	Weak transcription	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
38	rs538117913	chr21:40499600-40499601	Weak transcription	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
39	rs73355803	chr21:40499620-40499621	Weak transcription	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
40	rs375464225	chr21:40499621-40499622	Weak transcription	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
41	rs184478356	chr21:40499632-40499633	Weak transcription	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
42	rs34912726	chr21:40499635-40499636	Weak transcription	Chromatin interactive region lncRNA	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs554817451	chr21:40499640-40499641	Weak transcription	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
44	rs574698964	chr21:40499716-40499717	Weak transcription	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
45	rs34989336	chr21:40499735-40499736	Weak transcription	Chromatin interactive region lncRNA	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs557123885	chr21:40499749-40499750	Weak transcription	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
47	rs112874741	chr21:40499750-40499751	Weak transcription	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
48	rs546258788	chr21:40499766-40499767	Weak transcription	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
49	rs190271563	chr21:40499773-40499774	Weak transcription	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
50	rs1810384	chr21:40499774-40499775	Weak transcription	Chromatin interactive region lncRNA	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	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
Breast cancer	21364760	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
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:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40497800-40506200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr21:40498000-40499200	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr21:40498000-40500200	Weak transcription	Right Atrium	heart
4	chr21:40498000-40503000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr21:40498000-40503000	Weak transcription	Esophagus	oesophagus
6	chr21:40498000-40503200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr21:40498000-40503200	Weak transcription	Psoas Muscle	Psoas
8	chr21:40499200-40500800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links