Variant report

Variant	esv3489444
Chromosome Location	chr4:1366431-1366769
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:183)
Chromatin interactive
region (count:3)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:1366614-1366724	HUVEC	blood vessel:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:1366597-1366647	HCF	heart:	n/a
2	chr4:1366463-1366513	BJ	skin:	n/a
3	chr4:1366463-1366513	ECC-1	luminal epithelium:	n/a
4	chr4:1366662-1366712	SK-N-SH	brain:	n/a
5	chr4:1366662-1366712	BE2_C	brain:	n/a
6	chr4:1366597-1366647	SAEC	small airway:	n/a
7	chr4:1366597-1366647	HCM	heart:	n/a
8	chr4:1366597-1366647	GM12878	blood:	n/a
9	chr4:1366662-1366712	BJ	skin:	n/a
10	chr4:1366463-1366513	HUVEC	blood vessel:	n/a
11	chr4:1366463-1366513	SK-N-MC	brain:	n/a
12	chr4:1366463-1366513	PANC-1	pancreas:	n/a
13	chr4:1366662-1366712	NB4	blood:	n/a
14	chr4:1366597-1366647	NH-A	brain:	n/a
15	chr4:1366662-1366712	Hela-S3	cervix:	n/a
16	chr4:1366662-1366712	HepG2	liver:	n/a
17	chr4:1366662-1366712	AG04449	skin:	fetal
18	chr4:1366463-1366513	IMR90	lung:	fetal
19	chr4:1366463-1366513	HCT-116	colon:	n/a
20	chr4:1366597-1366647	GM19239	blood:	n/a
21	chr4:1366662-1366712	Jurkat	blood:	n/a
22	chr4:1366597-1366647	BJ	skin:	n/a
23	chr4:1366463-1366513	HNPCEpiC	eye:	n/a
24	chr4:1366662-1366712	U87	brain:	n/a
25	chr4:1366662-1366712	HIPEpiC	eye:	n/a
26	chr4:1366597-1366647	SKMC	muscle:	n/a
27	chr4:1366662-1366712	NHDF-neo	bronchial:	n/a
28	chr4:1366597-1366647	HNPCEpiC	eye:	n/a
29	chr4:1366597-1366647	AG09319	gingival:	n/a
30	chr4:1366463-1366513	HEK293	kidney:	embryo
31	chr4:1366597-1366647	HRCEpiC	kidney:	n/a
32	chr4:1366463-1366513	AG04450	lung:	fetal
33	chr4:1366662-1366712	AG09309	skin:	n/a
34	chr4:1366597-1366647	HRPEpiC	eye:	n/a
35	chr4:1366662-1366712	AoSMC	blood vessel:	n/a
36	chr4:1366463-1366513	HCF	heart:	n/a
37	chr4:1366662-1366712	HRPEpiC	eye:	n/a
38	chr4:1366597-1366647	U87	brain:	n/a
39	chr4:1366597-1366647	AG09309	skin:	n/a
40	chr4:1366597-1366647	ProgFib	skin:	n/a
41	chr4:1366597-1366647	SK-N-MC	brain:	n/a
42	chr4:1366662-1366712	Hepatocyte	liver:	n/a
43	chr4:1366463-1366513	HRE	kidney:	n/a
44	chr4:1366463-1366513	MCF10A-Er-Src	breast:	n/a
45	chr4:1366662-1366712	HCPEpiC	choroid plexus:	n/a
46	chr4:1366463-1366513	Hela-S3	cervix:	n/a
47	chr4:1366463-1366513	HMEC	breast:	n/a
48	chr4:1366597-1366647	HMEC	breast:	n/a
49	chr4:1366662-1366712	RPTEC	kidney:	n/a
50	chr4:1366463-1366513	BE2_C	brain:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:1366173..1368326-chr4:1369197..1371094,2	K562	blood:
2	chr4:1343113..1345553-chr4:1365278..1367179,2	K562	blood:
3	chr4:1344053..1346669-chr4:1364736..1366778,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NKX1-1-3	chr4:1366658-1366742	NONHSAT094704
2	lnc-NKX1-1-3	chr4:1365911-1366525	NONHSAT094704

No data

Variant related genes	Relation type
UVSSA	TF binding region
UVSSA	CpG island
ENSG00000163945	chromatin interactions

Extended variants
information (count: 57 )
Associated
traits (count: 63 )

Variant overlapped rSNPs/rCNVs (count:57 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs369271097	chr4:1366443-1366444	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
2	rs6856550	chr4:1366463-1366464	Weak transcription Strong transcription ZNF genes & repeats	CpG island Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
3	rs376572604	chr4:1366479-1366480	Weak transcription Strong transcription ZNF genes & repeats	CpG island Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
4	rs532001273	chr4:1366481-1366482	Weak transcription Strong transcription ZNF genes & repeats	CpG island Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
5	rs113062002	chr4:1366482-1366483	Weak transcription Strong transcription ZNF genes & repeats	CpG island Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
6	rs144409258	chr4:1366487-1366488	Weak transcription Strong transcription ZNF genes & repeats	CpG island Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
7	rs376610701	chr4:1366494-1366495	Weak transcription Strong transcription ZNF genes & repeats	CpG island Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
8	rs117937225	chr4:1366495-1366496	Weak transcription Strong transcription ZNF genes & repeats	CpG island Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
9	rs116776009	chr4:1366496-1366497	Weak transcription Strong transcription ZNF genes & repeats	CpG island Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
10	rs112635156	chr4:1366504-1366505	Weak transcription Strong transcription ZNF genes & repeats	CpG island Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
11	rs550267617	chr4:1366505-1366506	Weak transcription Strong transcription ZNF genes & repeats	CpG island Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
12	rs570333037	chr4:1366513-1366514	Weak transcription Strong transcription ZNF genes & repeats	CpG island Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
13	rs531157313	chr4:1366519-1366520	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
14	rs71168835	chr4:1366536-1366537	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs74536437	chr4:1366544-1366545	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs74662828	chr4:1366557-1366558	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs141008473	chr4:1366560-1366561	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs199622028	chr4:1366561-1366562	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs374537017	chr4:1366569-1366570	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs549644233	chr4:1366570-1366571	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs5015162	chr4:1366580-1366581	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs547736044	chr4:1366581-1366582	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs34798753	chr4:1366582-1366583	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs113733952	chr4:1366587-1366588	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs113033833	chr4:1366590-1366591	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs111425030	chr4:1366595-1366596	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs2336084	chr4:1366601-1366602	Weak transcription Strong transcription ZNF genes & repeats	CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs372763218	chr4:1366603-1366604	Weak transcription Strong transcription ZNF genes & repeats	CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs142178147	chr4:1366604-1366605	Weak transcription Strong transcription ZNF genes & repeats	CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs62284729	chr4:1366613-1366614	Weak transcription Strong transcription ZNF genes & repeats	CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs77387453	chr4:1366614-1366615	Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs62284730	chr4:1366618-1366619	Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs62284731	chr4:1366621-1366622	Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs62284732	chr4:1366622-1366623	Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs77405411	chr4:1366628-1366629	Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs77553344	chr4:1366636-1366637	Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs535211157	chr4:1366641-1366642	Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs553528509	chr4:1366645-1366646	Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs5015164	chr4:1366647-1366648	Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs6838590	chr4:1366654-1366655	Weak transcription Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs113063182	chr4:1366657-1366658	Weak transcription Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs113828343	chr4:1366662-1366663	Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
43	rs571732726	chr4:1366664-1366665	Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
44	rs540955915	chr4:1366676-1366677	Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
45	rs145842588	chr4:1366685-1366686	Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
46	rs539034692	chr4:1366687-1366688	Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
47	rs557029229	chr4:1366688-1366689	Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
48	rs575593443	chr4:1366693-1366694	Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
49	rs542597719	chr4:1366695-1366696	Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
50	rs554429243	chr4:1366696-1366697	Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:63)

Disease	PMID	Source
Myelofibrosis	22110671	CNVD
Wolf-Hirschhorn syndrome	21549014	CNVD
Breast cancer	21806811	CNVD
Wolf-Hirschhorn syndrome	22283845	CNVD
Wolf-Hirschhorn syndrome	16773131	CNVD
Mental retardation	16773131	CNVD
Wolf-Hirschhorn syndrome	22470819	CNVD
Wolf-Hirschhorn syndrome	18541967	CNVD
sporadic birth defects	19047251	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Retinitis pigmentosa	18421352	CNVD
Wolf-Hirschhorn syndrome	19259404	CNVD
Bladder cancer	19242612	CNVD
Breast cancer	19242612	CNVD
Congenital anomalies of the kidney and urinary tract	19242612	CNVD
abnormal development	18461090	CNVD
Olfactory neuroblastoma	18408657	CNVD
Wilms tumour	21544195	CNVD
Melanoma	20688739	CNVD
Colorectal cancer	16272173	CNVD
Non-syndromic sensorineural hearing loss	20606397	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17603634	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	17533364	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Cancer	21637783	CNVD
Melanoma	21693616	CNVD
Squamous cell cancer	21044232	CNVD
Colorectal cancer	20709793	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Non-small cell lung cancer	21044232	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	17387387	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Cervical cancer	21062161	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Neuroblastoma	18923191	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	17142309	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Developmental delay	21147756	CNVD
Urothelial carcinoma	21177765	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Lung cancer	18438408	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	20932292	CNVD
Breast cancer	22522925	CNVD
Type 2 diabetes	21754918	CNVD

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1341800-1387800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:1341800-1388800	Weak transcription	Small Intestine	intestine
3	chr4:1342200-1369800	Weak transcription	HSMMtube	muscle
4	chr4:1342200-1382600	Weak transcription	Primary B cells from cord blood	blood
5	chr4:1342400-1370000	Weak transcription	HSMM	muscle
6	chr4:1342400-1379800	Weak transcription	A549	lung
7	chr4:1342600-1367200	Weak transcription	Hela-S3	cervix
8	chr4:1342600-1385600	Weak transcription	Fetal Kidney	kidney
9	chr4:1342800-1379800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr4:1342800-1381200	Strong transcription	Fetal Intestine Small	intestine
11	chr4:1343400-1381200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr4:1346000-1386600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr4:1346000-1389200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr4:1346600-1369200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr4:1351800-1369400	Weak transcription	Colon Smooth Muscle	Colon
16	chr4:1352400-1369000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr4:1352600-1382000	Weak transcription	Fetal Brain Male	brain
18	chr4:1353200-1368800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr4:1353400-1369200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr4:1353400-1382000	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr4:1353600-1379600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr4:1353600-1382200	Weak transcription	Osteobl	bone
23	chr4:1353800-1380000	Weak transcription	GM12878-XiMat	blood
24	chr4:1355000-1368600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr4:1355000-1376800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr4:1355400-1380800	Strong transcription	Fetal Stomach	stomach
27	chr4:1357000-1367000	Weak transcription	Aorta	Aorta
28	chr4:1358400-1372200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:1358600-1371600	Strong transcription	Thymus	Thymus
30	chr4:1358600-1371800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:1358600-1381200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr4:1358800-1379400	Strong transcription	Spleen	Spleen
33	chr4:1359200-1368200	Weak transcription	Fetal Brain Female	brain
34	chr4:1359600-1375600	Strong transcription	Esophagus	oesophagus
35	chr4:1359800-1370800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:1360200-1371400	Strong transcription	Duodenum Mucosa	Duodenum
37	chr4:1360200-1371800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr4:1360400-1367800	Weak transcription	Fetal Thymus	thymus
39	chr4:1360800-1373200	Strong transcription	Placenta	Placenta
40	chr4:1360800-1389600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr4:1361000-1374400	Weak transcription	Psoas Muscle	Psoas
42	chr4:1362000-1369800	Weak transcription	Left Ventricle	heart
43	chr4:1362400-1367600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr4:1362600-1367600	Weak transcription	Brain Hippocampus Middle	brain
45	chr4:1362600-1368800	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr4:1362600-1368800	Weak transcription	Brain Substantia Nigra	brain
47	chr4:1362600-1369600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr4:1362600-1379400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr4:1363000-1380400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr4:1363000-1380800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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