Variant report

Variant	esv3439264
Chromosome Location	chr5:37910413-37927801
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	chr5:37915417-37915488	GM12878	blood:	n/a	n/a
2	CEBPB	chr5:37913841-37914136	HepG2	liver:	n/a	n/a
3	CEBPB	chr5:37913889-37914065	K562	blood:	n/a	n/a
4	CTCF	chr5:37926980-37927038	LNCaP	prostate:	n/a	chr5:37926996-37927014
5	CTCF	chr5:37926991-37927025	HepG2	liver:	n/a	chr5:37926996-37927014
6	CTCF	chr5:37926960-37927110	AG04449	skin:	n/a	chr5:37926996-37927014
7	CTCF	chr5:37926876-37927120	Medullo	brain:	n/a	chr5:37926996-37927014
8	CTCF	chr5:37926880-37927030	AG04450	lung:	n/a	chr5:37926996-37927014
9	CTCF	chr5:37926920-37927070	HA-sp	spinal cord:	n/a	chr5:37926996-37927014
10	CTCF	chr5:37926900-37927050	NHDF-neo	bronchial:	n/a	chr5:37926996-37927014
11	CTCF	chr5:37926920-37927070	HVMF	connective:	n/a	chr5:37926996-37927014
12	CTCF	chr5:37926880-37927030	BJ	skin:	n/a	chr5:37926996-37927014
13	CTCF	chr5:37926980-37927130	SAEC	small airway:	n/a	chr5:37926996-37927014
14	CTCF	chr5:37926900-37927050	AG10803	skin:	n/a	chr5:37926996-37927014
15	CTCF	chr5:37926980-37927130	AG09319	gingival:	n/a	chr5:37926996-37927014
16	CTCF	chr5:37926920-37927070	HFF	foreskin:	n/a	chr5:37926996-37927014
17	CTCF	chr5:37926914-37927051	HepG2	liver:	n/a	chr5:37926996-37927014
18	CTCF	chr5:37926839-37927140	IMR90	lung:	n/a	chr5:37926996-37927014
19	CTCF	chr5:37926940-37927090	HCPEpiC	choroid plexus:	n/a	chr5:37926996-37927014
20	CTCF	chr5:37926969-37927065	GM12878	blood:	n/a	chr5:37926996-37927014
21	CTCF	chr5:37926940-37927090	NHEK	skin:	n/a	chr5:37926996-37927014
22	CTCF	chr5:37926940-37927090	AG04449	skin:	n/a	chr5:37926996-37927014
23	CTCF	chr5:37927000-37927150	MCF-7	breast:	n/a	n/a
24	CTCF	chr5:37926820-37926970	HFF-Myc	foreskin:	n/a	n/a
25	CTCF	chr5:37926860-37927010	AG09309	skin:	n/a	n/a
26	CTCF	chr5:37926908-37927119	MCF-7	breast:	n/a	chr5:37926996-37927014
27	CTCF	chr5:37926800-37926950	HVMF	connective:	n/a	n/a
28	CTCF	chr5:37926997-37927017	ProgFib	skin:	n/a	n/a
29	CTCF	chr5:37926960-37927110	HCPEpiC	choroid plexus:	n/a	chr5:37926996-37927014
30	CTCF	chr5:37926900-37927050	HMEC	breast:	n/a	chr5:37926996-37927014
31	CTCF	chr5:37926920-37927070	WERI-Rb-1	eye:	n/a	chr5:37926996-37927014
32	CTCF	chr5:37926940-37927090	AG04450	lung:	n/a	chr5:37926996-37927014
33	CTCF	chr5:37926880-37927030	HBMEC	blood vessel:	n/a	chr5:37926996-37927014
34	CTCF	chr5:37918280-37918430	BE2_C	brain:	n/a	n/a
35	CTCF	chr5:37926910-37927154	GM12878	blood:	n/a	chr5:37926996-37927014
36	CTCF	chr5:37926930-37927078	MCF-7	breast:	n/a	chr5:37926996-37927014
37	CTCF	chr5:37926880-37927030	AoAF	blood vessel:	n/a	chr5:37926996-37927014
38	CTCF	chr5:37926980-37927130	HAc	cerebellar:	n/a	chr5:37926996-37927014
39	CTCF	chr5:37926940-37927090	SAEC	small airway:	n/a	chr5:37926996-37927014
40	CTCF	chr5:37926980-37927130	NHLF	lung:	n/a	chr5:37926996-37927014
41	CTCF	chr5:37926920-37927070	NHDF-neo	bronchial:	n/a	chr5:37926996-37927014
42	CTCF	chr5:37926957-37927020	Pancreas_OC	pancreas:	n/a	chr5:37926996-37927014
43	CTCF	chr5:37926880-37927030	HEEpiC	esophagus:	n/a	chr5:37926996-37927014
44	CTCF	chr5:37926960-37927110	MCF-7	breast:	n/a	chr5:37926996-37927014
45	CTCF	chr5:37926940-37927090	AG09309	skin:	n/a	chr5:37926996-37927014
46	CTCF	chr5:37926880-37927138	NHEK	skin:	n/a	chr5:37926996-37927014
47	CTCF	chr5:37914389-37914471	Spleen_OC	spleen:	n/a	n/a
48	CTCF	chr5:37926940-37927090	HEEpiC	esophagus:	n/a	chr5:37926996-37927014
49	CTCF	chr5:37926940-37927090	BJ	skin:	n/a	chr5:37926996-37927014
50	CTCF	chr5:37926940-37927090	AG09319	gingival:	n/a	chr5:37926996-37927014

No.	Distal block	Cell Line	Cell type
1	chr5:37923679..37926090-chr5:37927944..37930176,2	K562	blood:
2	chr5:37917797..37919563-chr5:37921139..37923191,2	MCF-7	breast:
3	chr5:37412825..37413381-chr5:37926629..37927147,2	MCF-7	breast:
4	chr5:37912263..37916512-chr5:37918512..37922383,4	K562	blood:
5	chr5:37923033..37924657-chr5:37948116..37950668,2	K562	blood:
6	chr5:37847283..37849747-chr5:37922255..37924001,2	MCF-7	breast:
7	chr5:37913319..37915798-chr5:37919046..37921083,2	K562	blood:
8	chr5:37907286..37908926-chr5:37910657..37912434,2	K562	blood:
9	chr5:37917797..37919563-chr5:37921139..37923191,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GDNF-1	chr5:37920056-37920148	NONHSAT101075
2	lnc-GDNF-1	chr5:37920056-37920199	XLOC_004788
3	lnc-GDNF-1	chr5:37920933-37920971	XLOC_004788
4	lnc-GDNF-1	chr5:37919842-37919892	NONHSAT101075
5	lnc-GDNF-1	chr5:37918311-37918924	NONHSAT101075
6	lnc-GDNF-1	chr5:37919842-37919892	XLOC_004788

Variant related genes	Relation type
ENSG00000248539	TF binding region
ENSG00000251518	chromatin interactions
ENSG00000248539	chromatin interactions

Extended variants
information (count: 703 )
Associated
traits (count: 98 )

Variant overlapped rSNPs/rCNVs (count:703 , 50 per page) page: 1 2 3 4 5 6 7 ... 15

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs569788255	chr5:37910430-37910431	Enhancers Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
2	rs537020504	chr5:37910432-37910433	Enhancers Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
3	rs549031550	chr5:37910443-37910444	Enhancers Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
4	rs2366835	chr5:37910484-37910485	Enhancers Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
5	rs146967664	chr5:37910490-37910491	Enhancers Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
6	rs3096142	chr5:37910506-37910507	Enhancers Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
7	rs137995033	chr5:37910515-37910516	Enhancers Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs2366836	chr5:37910520-37910521	Enhancers Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs557015410	chr5:37910621-37910622	Enhancers Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
10	rs34584420	chr5:37910633-37910634	Enhancers Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
11	rs575368290	chr5:37910660-37910661	Enhancers Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
12	rs554793521	chr5:37910720-37910721	Enhancers Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
13	rs191322829	chr5:37910773-37910774	Enhancers Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs566224931	chr5:37910796-37910797	Enhancers Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs185654923	chr5:37910802-37910803	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
16	rs370141738	chr5:37910886-37910887	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
17	rs561173342	chr5:37910904-37910905	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
18	rs573197104	chr5:37910908-37910909	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
19	rs144710099	chr5:37910992-37910993	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
20	rs185317810	chr5:37912263-37912264	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs566984673	chr5:37912282-37912283	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs10075194	chr5:37912283-37912284	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs148515189	chr5:37912319-37912320	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs577607150	chr5:37912326-37912327	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs544870843	chr5:37912342-37912343	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs556905924	chr5:37912385-37912386	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs2910728	chr5:37912474-37912475	Inactive region	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs62360408	chr5:37912505-37912506	Inactive region	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs189144247	chr5:37912507-37912508	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs114295450	chr5:37912577-37912578	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs139593072	chr5:37912583-37912584	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs144211319	chr5:37912584-37912585	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs114484651	chr5:37912652-37912653	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs34393966	chr5:37912718-37912719	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs556472155	chr5:37912719-37912720	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs397997430	chr5:37912731-37912732	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs550429694	chr5:37912734-37912735	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs11958863	chr5:37912743-37912744	Inactive region	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs529830337	chr5:37912792-37912793	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs528028449	chr5:37912794-37912795	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs574235628	chr5:37912799-37912800	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs548397834	chr5:37912800-37912801	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs533677870	chr5:37912830-37912831	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs146535117	chr5:37912851-37912852	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs534347011	chr5:37912919-37912920	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs559095093	chr5:37912976-37912977	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs34462076	chr5:37912979-37912980	Inactive region	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs11959616	chr5:37912995-37912996	Inactive region	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
49	rs35038886	chr5:37913046-37913047	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs181169124	chr5:37913086-37913087	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:98)

Disease	PMID	Source
Myofibroblastic sarcoma	19369631	CNVD
Cervical squamous cell carcinoma	21590768	CNVD
Non-small cell lung cancer	20864512	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	21080181	CNVD
Medulloblastoma	16783165	CNVD
Thyroid cancer	19087340	CNVD
Liposarcoma	21253554	CNVD
Pancreatic endocrine tumor	17639061	CNVD
Cervical Cancer	21857958	CNVD
Cervical cancer	21062161	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	19960244	CNVD
Oral cancer	21386901	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Ewing''s sarcoma	17952124	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Cervical cancer	18559093	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Metanephric adenoma	20802469	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Medulloblastoma	21979893	CNVD
Phyllodes tumor	17334353	CNVD
Malaria	21533027	CNVD
Renal cell carcinoma	19461508	CNVD
Colorectal cancer	21645411	CNVD
Gastric cancer	22152101	CNVD
Oesophago-gastric ulcer	22152101	CNVD
Ovarian cancer	21781307	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Cancer	20164919	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Multiple myeloma	17550852	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Bladder cancer	21909424	CNVD
DNA damage stimulus	22844521	CNVD
DNA repair	22844521	CNVD
Breast cancer	21785460	CNVD
Spinal muscular atrophy	22422766	CNVD
Spinal muscular atrophy	22558076	CNVD
Spinal muscular atrophy	21320981	CNVD
Spinal muscular atrophy	21762474	CNVD
Breast cancer	21858162	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Cancer	16751803	CNVD
Breast cancer	16608533	CNVD
Autism	22495311	CNVD
Melanoma	18172304	CNVD
Non-syndromic sensorineural hearing loss	20606397	CNVD
Intellectual disability	22102821	CNVD
Prostate cancer	21965145	CNVD
Cancer	21183584	CNVD
Ovarian cancer	20844748	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Breast cancer	17603634	CNVD
Non-small cell lung cancer	19010865	CNVD
Glioblastoma multiforme	22286061	CNVD
Ovarian cancer	21720365	CNVD
Lung cancer	18438408	CNVD
Glioma	20126413	CNVD
Non-small cell lung cancer	21829676	CNVD
Breast cancer	22032731	CNVD
Esophageal cancer	20955586	CNVD
Prostate cancer	18632612	CNVD
Medulloblastoma	19270706	CNVD
Breast cancer	19553991	CNVD
Lung cancer	19553991	CNVD
Melanoma	19553991	CNVD
Ovarian cancer	19553991	CNVD
Prostate cancer	19553991	CNVD
Non-small cell lung cancer	17156491	CNVD
Breast cancer	17133270	CNVD
Congenital anomalies of the kidney and urinary tract	18694510	CNVD
Breast cancer	17393978	CNVD
Pleomorphic liposarcoma	18784837	CNVD
Acute lymphoblastic leukemia	17640729	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Lung cancer	19153074	CNVD
Cornelia de Lange syndrome	21085971	CNVD
Autism	21701786	CNVD
Cervical cancer	16585170	CNVD
Ovarian clear cell carcinoma	19293255	CNVD
Hodgkin''s lymphoma	17606441	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	21364760	CNVD
Schizophrenia	19197363	CNVD

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:37909800-37910800	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr5:37909800-37910800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr5:37909800-37910800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr5:37910400-37910800	Flanking Active TSS	GM12878-XiMat	blood
5	chr5:37910600-37910800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
6	chr5:37910800-37911000	Bivalent Enhancer	GM12878-XiMat	blood
7	chr5:37913000-37913600	Enhancers	Ovary	ovary
8	chr5:37913600-37916000	Weak transcription	Ovary	ovary
9	chr5:37914800-37915400	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr5:37914800-37915400	Enhancers	NHEK	skin
11	chr5:37914800-37915600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:37915000-37915600	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr5:37915200-37915400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:37915200-37915400	Bivalent/Poised TSS	NHDF-Ad	bronchial
15	chr5:37915400-37915800	Bivalent Enhancer	NHDF-Ad	bronchial
16	chr5:37915400-37916000	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr5:37915400-37916800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr5:37915400-37926400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr5:37915600-37915800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr5:37915600-37916000	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr5:37915600-37916000	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:37915600-37916600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:37916000-37916400	Enhancers	Ovary	ovary
24	chr5:37916200-37917800	Enhancers	HMEC	breast
25	chr5:37916400-37919400	Weak transcription	Ovary	ovary
26	chr5:37916600-37916800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr5:37916600-37917000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr5:37917600-37919000	Enhancers	Fetal Heart	heart
29	chr5:37917800-37918200	Weak transcription	HMEC	breast
30	chr5:37918200-37918400	Enhancers	HMEC	breast
31	chr5:37918200-37919400	Enhancers	Colon Smooth Muscle	Colon
32	chr5:37918400-37919000	Enhancers	Rectal Smooth Muscle	rectum
33	chr5:37918400-37926400	Weak transcription	HMEC	breast
34	chr5:37919000-37919200	Flanking Active TSS	Fetal Heart	heart
35	chr5:37919200-37919400	Enhancers	Fetal Heart	heart
36	chr5:37919400-37919600	Flanking Active TSS	Fetal Heart	heart
37	chr5:37919400-37919800	Enhancers	Ovary	ovary
38	chr5:37919400-37919800	Enhancers	Pancreas	Pancrea
39	chr5:37920600-37921000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr5:37920800-37921600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr5:37921400-37921600	Enhancers	Fetal Heart	heart
42	chr5:37926400-37927000	Enhancers	NHEK	skin
43	chr5:37926400-37927600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr5:37926400-37927600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr5:37926400-37927600	Enhancers	HMEC	breast
46	chr5:37926800-37927400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr5:37926800-37927600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr5:37927000-37927200	Flanking Active TSS	NHEK	skin
49	chr5:37927000-37927400	Enhancers	Spleen	Spleen
50	chr5:37927200-37927400	Enhancers	NHEK	skin

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