Variant report

Variant	nsv3255
Chromosome Location	chr20:1646524-1680522
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	BHLHE40	chr20:1647508-1647681	GM12878	blood:	n/a	n/a
2	BHLHE40	chr20:1674091-1674109	GM12878	blood:	n/a	n/a
3	CEBPB	chr20:1673568-1673647	A549	lung:	n/a	n/a
4	CTCF	chr20:1650010-1650203	Gliobla	brain:	n/a	n/a
5	CTCF	chr20:1657360-1657510	GM06990	blood:	n/a	n/a
6	CTCF	chr20:1649980-1650130	HBMEC	blood vessel:	n/a	n/a
7	CTCF	chr20:1650040-1650190	HBMEC	blood vessel:	n/a	n/a
8	CTCF	chr20:1650180-1650330	AG09309	skin:	n/a	n/a
9	CTCF	chr20:1650040-1650190	HCPEpiC	choroid plexus:	n/a	n/a
10	CTCF	chr20:1651131-1651163	GM10266	blood:	n/a	n/a
11	CTCF	chr20:1649980-1650130	Caco-2	colon:	n/a	n/a
12	CTCF	chr20:1650080-1650230	NHEK	skin:	n/a	n/a
13	CTCF	chr20:1650220-1650370	HFF-Myc	foreskin:	n/a	n/a
14	CTCF	chr20:1650080-1650131	MCF-7	breast:	n/a	n/a
15	CTCF	chr20:1653081-1653098	GM13976	blood:	n/a	n/a
16	CTCF	chr20:1650000-1650150	A549	lung:	n/a	n/a
17	CTCF	chr20:1650000-1650150	GM12864	blood:	n/a	n/a
18	CTCF	chr20:1650020-1650170	HEK293	kidney:	n/a	n/a
19	CTCF	chr20:1657900-1658050	HUVEC	blood vessel:	n/a	n/a
20	CTCF	chr20:1650000-1650150	RPTEC	kidney:	n/a	n/a
21	CTCF	chr20:1649940-1650090	HCPEpiC	choroid plexus:	n/a	n/a
22	CTCF	chr20:1650050-1650151	MCF-7	breast:	n/a	n/a
23	CTCF	chr20:1650020-1650170	HepG2	liver:	n/a	n/a
24	CTCF	chr20:1650160-1650310	RPTEC	kidney:	n/a	n/a
25	CTCF	chr20:1650020-1650170	HAc	cerebellar:	n/a	n/a
26	CTCF	chr20:1650080-1650230	BJ	skin:	n/a	n/a
27	CTCF	chr20:1668313-1668337	GM13976	blood:	n/a	n/a
28	CTCF	chr20:1649920-1650070	HCT-116	colon:	n/a	n/a
29	E2F4	chr20:1677085-1677206	MCF10A-Er-Src	breast:	n/a	n/a
30	EBF1	chr20:1671458-1671629	GM12878	blood:	n/a	n/a
31	ELF1	chr20:1655044-1655306	K562	blood:	n/a	chr20:1655166-1655179 chr20:1655182-1655195
32	ELF1	chr20:1655026-1655363	GM12878	blood:	n/a	chr20:1655166-1655179 chr20:1655182-1655195
33	EP300	chr20:1647530-1647736	GM12878	blood:	n/a	n/a
34	FOS	chr20:1650104-1650303	MCF10A-Er-Src	breast:	n/a	chr20:1650224-1650232
35	FOXM1	chr20:1652856-1653341	GM12878	blood:	n/a	n/a
36	GATA3	chr20:1663083-1663188	SH-SY5Y	brain:	n/a	n/a
37	GATA3	chr20:1652804-1652925	SH-SY5Y	brain:	n/a	n/a
38	MAFF	chr20:1679747-1679943	HepG2	liver:	n/a	n/a
39	MAFK	chr20:1679777-1679885	HepG2	liver:	n/a	n/a
40	MAFK	chr20:1674353-1674427	HepG2	liver:	n/a	n/a
41	MAFK	chr20:1658155-1658396	HepG2	liver:	n/a	n/a
42	MAFK	chr20:1669955-1670015	HepG2	liver:	n/a	n/a
43	MAFK	chr20:1679773-1679939	HepG2	liver:	n/a	n/a
44	MAX	chr20:1655340-1655417	HepG2	liver:	n/a	n/a
45	MAZ	chr20:1659011-1659028	HepG2	liver:	n/a	n/a
46	MYC	chr20:1669603-1669803	NB4	blood:	n/a	n/a
47	MYC	chr20:1679849-1679913	K562	blood:	n/a	n/a
48	MYC	chr20:1650580-1650688	H1-hESC	embryonic stem cell:	n/a	n/a
49	NFYB	chr20:1653138-1653338	GM12878	blood:	n/a	chr20:1653177-1653191 chr20:1653177-1653190 chr20:1653176-1653188
50	POLR2A	chr20:1662194-1662339	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
ENSG00000236550	TF binding region
RN7SL561P	TF binding region

Extended variants
information (count: 1537 )
Associated
traits (count: 64 )

Variant overlapped rSNPs/rCNVs (count:1537 , 50 per page) page: 1 2 3 4 5 6 7 ... 31

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs570155166	chr20:1646555-1646556	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs538162103	chr20:1646559-1646560	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs566533634	chr20:1646561-1646562	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs548555958	chr20:1646576-1646577	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs6080043	chr20:1646579-1646580	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs569489055	chr20:1646628-1646629	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs536819798	chr20:1646636-1646637	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs568639190	chr20:1646648-1646649	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs6074975	chr20:1646656-1646657	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs570612748	chr20:1646676-1646677	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs189780380	chr20:1646721-1646722	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs142459774	chr20:1646732-1646733	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs200835790	chr20:1646755-1646756	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs201897120	chr20:1646772-1646773	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs35015469	chr20:1646773-1646774	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs397781079	chr20:1646784-1646785	Weak transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs6080045	chr20:1646810-1646811	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs574926605	chr20:1646814-1646815	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs73604189	chr20:1646840-1646841	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs59129426	chr20:1646841-1646842	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs1022641	chr20:1646892-1646893	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs6074976	chr20:1646917-1646918	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs186172248	chr20:1646925-1646926	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs150894348	chr20:1646978-1646979	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs191824931	chr20:1647031-1647032	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
26	rs6135616	chr20:1647046-1647047	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
27	rs371321125	chr20:1647212-1647213	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
28	rs538717524	chr20:1647215-1647216	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
29	rs6074978	chr20:1647216-1647217	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs558909977	chr20:1647223-1647224	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
31	rs184064647	chr20:1647227-1647228	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
32	rs187360218	chr20:1647246-1647247	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
33	rs139715098	chr20:1647258-1647259	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
34	rs575279467	chr20:1647264-1647265	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
35	rs376384977	chr20:1647295-1647296	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs569375843	chr20:1647313-1647314	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs111348180	chr20:1647335-1647336	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs544528147	chr20:1647349-1647350	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs530638483	chr20:1647356-1647357	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs552038254	chr20:1647383-1647384	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs6043636	chr20:1647384-1647385	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs192267301	chr20:1647396-1647397	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs182480495	chr20:1647423-1647424	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs6110845	chr20:1647443-1647444	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
45	rs574666108	chr20:1647472-1647473	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs112490191	chr20:1647492-1647493	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs74990090	chr20:1647534-1647535	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs565553994	chr20:1647562-1647563	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs371275397	chr20:1647563-1647564	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs562955652	chr20:1647564-1647565	Weak transcription 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:363 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1638600-1649400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr20:1644000-1647200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr20:1644400-1648600	Enhancers	Fetal Thymus	thymus
4	chr20:1644800-1646600	Enhancers	GM12878-XiMat	blood
5	chr20:1644800-1646800	Flanking Active TSS	Primary T cells from cord blood	blood
6	chr20:1646000-1649400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr20:1646000-1652600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr20:1646200-1646600	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr20:1646200-1648000	Enhancers	Dnd41	blood
10	chr20:1646200-1648200	Weak transcription	Thymus	Thymus
11	chr20:1646200-1649800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr20:1646200-1649800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr20:1646200-1650200	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr20:1646200-1650600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr20:1646200-1653400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr20:1646200-1655200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr20:1646200-1655200	Weak transcription	Spleen	Spleen
18	chr20:1646200-1655400	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr20:1646200-1660200	Enhancers	Primary T cells fromperipheralblood	blood
20	chr20:1646400-1647600	Weak transcription	Primary B cells from peripheral blood	blood
21	chr20:1646400-1649400	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr20:1646600-1646800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr20:1646600-1647000	Weak transcription	GM12878-XiMat	blood
24	chr20:1646800-1649400	Enhancers	Primary T cells from cord blood	blood
25	chr20:1646800-1654400	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr20:1647000-1648600	Enhancers	GM12878-XiMat	blood
27	chr20:1647200-1652000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr20:1647600-1648400	Enhancers	Primary B cells from peripheral blood	blood
29	chr20:1648200-1648600	Enhancers	Thymus	Thymus
30	chr20:1648600-1651600	Weak transcription	Fetal Thymus	thymus
31	chr20:1649400-1649600	Enhancers	Brain Substantia Nigra	brain
32	chr20:1649400-1650000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr20:1649400-1650600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr20:1649400-1651000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr20:1649400-1652000	Genic enhancers	Primary T cells from cord blood	blood
36	chr20:1649600-1650600	Weak transcription	Brain Substantia Nigra	brain
37	chr20:1649800-1650200	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr20:1649800-1651400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr20:1649800-1652400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr20:1650000-1650200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr20:1650000-1650200	Bivalent Enhancer	Stomach Smooth Muscle	stomach
42	chr20:1650000-1650200	Bivalent Enhancer	A549	lung
43	chr20:1650000-1650400	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr20:1650200-1650400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr20:1650200-1650800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr20:1650200-1650800	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr20:1650200-1651200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr20:1650200-1651600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr20:1650400-1650600	Enhancers	Brain Hippocampus Middle	brain
50	chr20:1650600-1650800	Enhancers	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links