Variant report

Variant	esv3501550
Chromosome Location	chr20:1645258-1649732
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	ATF2	chr20:1645577-1645900	GM12878	blood:	n/a	n/a
2	ATF2	chr20:1645510-1646022	GM12878	blood:	n/a	n/a
3	BCL11A	chr20:1645573-1645931	GM12878	blood:	n/a	chr20:1645725-1645734 chr20:1645691-1645700
4	BCL3	chr20:1645525-1645977	GM12878	blood:	n/a	chr20:1645725-1645734 chr20:1645691-1645700
5	BCLAF1	chr20:1645421-1645899	GM12878	blood:	n/a	chr20:1645725-1645734 chr20:1645691-1645700
6	BHLHE40	chr20:1647508-1647681	GM12878	blood:	n/a	n/a
7	CEBPB	chr20:1645595-1646101	GM12878	blood:	n/a	n/a
8	EBF1	chr20:1645541-1645950	GM12878	blood:	n/a	chr20:1645785-1645796
9	EBF1	chr20:1645480-1646075	GM12878	blood:	n/a	chr20:1645785-1645796
10	EBF1	chr20:1645579-1645953	GM12878	blood:	n/a	chr20:1645785-1645796
11	EGR1	chr20:1645589-1645839	GM12878	blood:	n/a	chr20:1645725-1645734 chr20:1645745-1645754
12	EGR1	chr20:1645593-1645835	GM12878	blood:	n/a	chr20:1645725-1645734 chr20:1645745-1645754
13	ELF1	chr20:1645239-1646153	GM12878	blood:	n/a	n/a
14	ELF1	chr20:1645526-1645982	GM12878	blood:	n/a	n/a
15	EP300	chr20:1647530-1647736	GM12878	blood:	n/a	n/a
16	ETS1	chr20:1645528-1645861	GM12878	blood:	n/a	chr20:1645742-1645753 chr20:1645722-1645735 chr20:1645720-1645734 chr20:1645723-1645734 chr20:1645740-1645754 chr20:1645722-1645733
17	FOXM1	chr20:1645456-1646041	GM12878	blood:	n/a	n/a
18	IKZF1	chr20:1645603-1645946	GM12878	blood:	n/a	n/a
19	MAX	chr20:1645205-1645972	NB4	blood:	n/a	n/a
20	MAZ	chr20:1645575-1645900	GM12878	blood:	n/a	n/a
21	MTA3	chr20:1645489-1645914	GM12878	blood:	n/a	n/a
22	MTA3	chr20:1645339-1645957	GM12878	blood:	n/a	n/a
23	MYC	chr20:1645578-1645984	NB4	blood:	n/a	n/a
24	NFIC	chr20:1645335-1646181	GM12878	blood:	n/a	n/a
25	NFIC	chr20:1645509-1645902	GM12878	blood:	n/a	n/a
26	PAX5	chr20:1645525-1646006	GM12878	blood:	n/a	chr20:1645725-1645734
27	PML	chr20:1645471-1646074	GM12878	blood:	n/a	n/a
28	POLR2A	chr20:1645597-1646020	GM12878	blood:	n/a	n/a
29	POU2F2	chr20:1648190-1648655	GM12891	blood:	n/a	n/a
30	RAD21	chr20:1645595-1645944	GM12878	blood:	n/a	n/a
31	REST	chr20:1645663-1645820	GM12878	blood:	n/a	chr20:1645691-1645700
32	RUNX3	chr20:1645438-1646133	GM12878	blood:	n/a	n/a
33	RUNX3	chr20:1647387-1647852	GM12878	blood:	n/a	n/a
34	RUNX3	chr20:1647514-1647823	GM12878	blood:	n/a	n/a
35	RUNX3	chr20:1645438-1646007	GM12878	blood:	n/a	n/a
36	SP1	chr20:1645484-1645923	GM12878	blood:	n/a	n/a
37	SP1	chr20:1645574-1645933	GM12878	blood:	n/a	n/a
38	STAT3	chr20:1648039-1648200	MCF10A-Er-Src	breast:	n/a	n/a
39	STAT5A	chr20:1645546-1646072	GM12878	blood:	n/a	n/a
40	STAT5A	chr20:1645476-1646212	GM12878	blood:	n/a	n/a
41	TBL1XR1	chr20:1648330-1648332	GM12878	blood:	n/a	n/a
42	WRNIP1	chr20:1645666-1645837	GM12878	blood:	n/a	n/a
43	YY1	chr20:1645598-1645955	GM12878	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SIRPA-5	chr20:1647006-1647284	NONHSAT078126

Variant related genes	Relation type
RN7SL561P	TF binding region

Extended variants
information (count: 217 )
Associated
traits (count: 64 )

Variant overlapped rSNPs/rCNVs (count:217 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs185923772	chr20:1645267-1645268	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs567764137	chr20:1645360-1645361	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs575887425	chr20:1645419-1645420	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs543362393	chr20:1645483-1645484	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs6110838	chr20:1645502-1645503	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
6	rs11394821	chr20:1645571-1645572	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs72543558	chr20:1645573-1645574	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs397691226	chr20:1645574-1645575	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs552749687	chr20:1645583-1645584	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs73572933	chr20:1645631-1645632	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs559558557	chr20:1645655-1645656	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs530231051	chr20:1645670-1645671	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs548757813	chr20:1645782-1645783	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs576555485	chr20:1645794-1645795	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs563874238	chr20:1645803-1645804	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs201292543	chr20:1645809-1645810	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs2273334	chr20:1645830-1645831	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
18	rs552635221	chr20:1645866-1645867	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs143454553	chr20:1645869-1645870	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs538229417	chr20:1645886-1645887	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs143868411	chr20:1645950-1645951	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs564860780	chr20:1645976-1645977	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs2246123	chr20:1645982-1645983	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs532239751	chr20:1645991-1645992	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs181261953	chr20:1646026-1646027	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs111754131	chr20:1646043-1646044	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs2273333	chr20:1646052-1646053	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs35550744	chr20:1646088-1646089	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs369984749	chr20:1646106-1646107	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs536928801	chr20:1646133-1646134	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs561153861	chr20:1646182-1646183	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs529809971	chr20:1646202-1646203	Weak transcription Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs558604977	chr20:1646237-1646238	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
34	rs577087900	chr20:1646240-1646241	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
35	rs55827782	chr20:1646266-1646267	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs117617521	chr20:1646277-1646278	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
37	rs116934924	chr20:1646301-1646302	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
38	rs542389027	chr20:1646333-1646334	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
39	rs563862101	chr20:1646338-1646339	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
40	rs532453752	chr20:1646340-1646341	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
41	rs148810060	chr20:1646351-1646352	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
42	rs546399981	chr20:1646355-1646356	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
43	rs6074973	chr20:1646391-1646392	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs528793267	chr20:1646429-1646430	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs34530824	chr20:1646444-1646445	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs369740937	chr20:1646445-1646446	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs185852444	chr20:1646500-1646501	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs117726277	chr20:1646513-1646514	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs551928833	chr20:1646523-1646524	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs570155166	chr20:1646555-1646556	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:64)

Disease	PMID	Source
Hodgkin''s lymphoma	18641027	CNVD
Myelofibrosis	22110671	CNVD
Intellectual disability	22045946	CNVD
Glioblastoma multiforme	22286061	CNVD
Hepatocellular carcinoma	22174799	CNVD
Colorectal cancer	19455253	CNVD
Ovarian cancer	20844748	CNVD
Breast cancer	17603634	CNVD
Colorectal cancer	19359472	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Intracranial aneurysm	16715129	CNVD
Colorectal cancer	16774939	CNVD
Autism	18414403	CNVD
Neurocytoma	17123091	CNVD
Medulloblastoma	21979893	CNVD
Breast cancer	16397240	CNVD
abortions and stillbirths	19751515	CNVD
Wilms tumour	21544195	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	16272173	CNVD
Melanoma	18172304	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Oral cancer	19627613	CNVD
colon cancer	17210682	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	21080181	CNVD
Thyroid cancer	19087340	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Human rectal carcinomas	16397240	CNVD
Olfactory neuroblastoma	18408657	CNVD
Central neurocytomas	17123091	CNVD
Colorectal cancer	16272173	CNVD
Gastric cancer	17908304	CNVD
Urothelial carcinoma	21177765	CNVD
lymphocytic leukemia	21291569	CNVD
Acute myeloid leukemia	20729466	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
Ewing''s sarcoma	17952124	CNVD
Oral cancer	21386901	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Colorectal cancer	21645411	CNVD
small cell lung cancer	20016488	CNVD
Melanoma	17363583	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Lung cancer	18438408	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1638600-1645400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
2	chr20:1638600-1649400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr20:1639000-1645400	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr20:1639000-1645400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr20:1639000-1645800	Enhancers	Primary T cells fromperipheralblood	blood
6	chr20:1639200-1645400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr20:1640600-1645400	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr20:1642800-1645800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr20:1644000-1647200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr20:1644200-1645800	Enhancers	Dnd41	blood
11	chr20:1644200-1646000	Enhancers	HMEC	breast
12	chr20:1644200-1646000	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr20:1644400-1645400	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr20:1644400-1645400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr20:1644400-1646000	Enhancers	Primary hematopoietic stem cells	blood
16	chr20:1644400-1646200	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr20:1644400-1646200	Enhancers	Spleen	Spleen
18	chr20:1644400-1646400	Enhancers	Primary B cells from cord blood	blood
19	chr20:1644400-1646400	Enhancers	Primary B cells from peripheral blood	blood
20	chr20:1644400-1648600	Enhancers	Fetal Thymus	thymus
21	chr20:1644600-1646200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
22	chr20:1644800-1645400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
23	chr20:1644800-1646200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr20:1644800-1646600	Enhancers	GM12878-XiMat	blood
25	chr20:1644800-1646800	Flanking Active TSS	Primary T cells from cord blood	blood
26	chr20:1645000-1645800	Enhancers	Thymus	Thymus
27	chr20:1645200-1646000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
28	chr20:1645200-1646000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr20:1645200-1646200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr20:1645200-1646400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr20:1645400-1645800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr20:1645400-1646000	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr20:1645400-1646200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr20:1645400-1646200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr20:1645400-1646200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr20:1645400-1646200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
37	chr20:1645600-1645800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr20:1645600-1646000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr20:1645800-1646000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
40	chr20:1645800-1646200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
41	chr20:1645800-1646200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr20:1645800-1646200	Flanking Active TSS	Thymus	Thymus
43	chr20:1645800-1646200	Flanking Active TSS	Dnd41	blood
44	chr20:1646000-1649400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr20:1646000-1652600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr20:1646200-1646600	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr20:1646200-1648000	Enhancers	Dnd41	blood
48	chr20:1646200-1648200	Weak transcription	Thymus	Thymus
49	chr20:1646200-1649800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr20:1646200-1649800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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