Variant report

Variant	nsv515808
Chromosome Location	chr6:53855489-53865667
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:50)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr6:53863712-53864591	HepG2	liver:	n/a	chr6:53864401-53864412 chr6:53864403-53864414
2	CEBPB	chr6:53863614-53863842	IMR90	lung:	n/a	n/a
3	CEBPB	chr6:53864048-53864525	IMR90	lung:	n/a	chr6:53864401-53864412 chr6:53864403-53864414
4	CTCF	chr6:53857434-53857602	MCF-7	breast:	n/a	n/a
5	CTCF	chr6:53857446-53857573	Hela-S3	cervix:	n/a	n/a
6	CTCF	chr6:53857460-53857610	HBMEC	blood vessel:	n/a	n/a
7	CTCF	chr6:53857420-53857570	Caco-2	colon:	n/a	n/a
8	CTCF	chr6:53857461-53857600	HepG2	liver:	n/a	n/a
9	CTCF	chr6:53857320-53857470	RPTEC	kidney:	n/a	n/a
10	CTCF	chr6:53857460-53857610	HCPEpiC	choroid plexus:	n/a	n/a
11	CTCF	chr6:53855641-53855723	GM13976	blood:	n/a	n/a
12	CTCF	chr6:53857397-53857665	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr6:53857260-53857410	HRE	kidney:	n/a	n/a
14	CTCF	chr6:53857480-53857630	RPTEC	kidney:	n/a	n/a
15	CTCF	chr6:53857500-53857650	HMF	breast:	n/a	n/a
16	CTCF	chr6:53857400-53857550	MCF-7	breast:	n/a	n/a
17	CTCF	chr6:53857420-53857570	HCM	heart:	n/a	n/a
18	CTCF	chr6:53857469-53857568	MCF-7	breast:	n/a	n/a
19	CTCF	chr6:53857460-53857610	WERI-Rb-1	eye:	n/a	n/a
20	CTCF	chr6:53857480-53857630	HAc	cerebellar:	n/a	n/a
21	CTCF	chr6:53857360-53857510	HCT-116	colon:	n/a	n/a
22	CTCF	chr6:53857400-53857550	HA-sp	spinal cord:	n/a	n/a
23	CTCF	chr6:53857400-53857550	HEK293	kidney:	n/a	n/a
24	CTCF	chr6:53857500-53857650	Hela-S3	cervix:	n/a	n/a
25	CTCF	chr6:53857476-53857594	HUVEC	blood vessel:	n/a	n/a
26	CTCF	chr6:53857460-53857610	AG04449	skin:	n/a	n/a
27	CTCF	chr6:53857400-53857550	HCPEpiC	choroid plexus:	n/a	n/a
28	CTCF	chr6:53863980-53864130	HepG2	liver:	n/a	n/a
29	CTCF	chr6:53857476-53857556	NHEK	skin:	n/a	n/a
30	CTCF	chr6:53857400-53857550	AoAF	blood vessel:	n/a	n/a
31	HEY1	chr6:53855706-53855969	K562	blood:	n/a	n/a
32	MAFF	chr6:53859026-53859365	HepG2	liver:	n/a	chr6:53859188-53859206
33	MAFF	chr6:53859088-53859300	K562	blood:	n/a	chr6:53859188-53859206
34	MAFK	chr6:53859036-53859375	IMR90	lung:	n/a	n/a
35	MAFK	chr6:53859043-53859339	HepG2	liver:	n/a	n/a
36	MAFK	chr6:53859032-53859376	HepG2	liver:	n/a	n/a
37	MAFK	chr6:53859088-53859312	K562	blood:	n/a	n/a
38	MAFK	chr6:53859127-53859314	H1-hESC	embryonic stem cell:	n/a	n/a
39	MAFK	chr6:53859055-53859350	Hela-S3	cervix:	n/a	n/a
40	PAX5	chr6:53855740-53856000	GM12878	blood:	n/a	n/a
41	POLR2A	chr6:53863527-53863616	MCF10A-Er-Src	breast:	n/a	n/a
42	POLR2A	chr6:53862744-53862869	MCF10A-Er-Src	breast:	n/a	n/a
43	RAD21	chr6:53857522-53857528	IMR90	lung:	n/a	n/a
44	RAD21	chr6:53857461-53857651	Hela-S3	cervix:	n/a	n/a
45	RAD21	chr6:53857400-53857659	HepG2	liver:	n/a	n/a
46	RAD21	chr6:53857273-53857758	H1-hESC	embryonic stem cell:	n/a	n/a
47	RAD21	chr6:53857391-53857652	H1-hESC	embryonic stem cell:	n/a	n/a
48	RAD21	chr6:53857375-53857666	HepG2	liver:	n/a	n/a
49	STAT3	chr6:53864792-53864947	MCF10A-Er-Src	breast:	n/a	n/a
50	TCF7L2	chr6:53861780-53862298	HEK293	kidney:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53857425..53857943-chr6:53933277..53933955,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRRC1-2	chr6:53863688-53863857	XLOC_005329
2	lnc-LRRC1-1	chr6:53859588-53859808	ENSG00000236740.2
3	lnc-LRRC1-1	chr6:53859762-53862465	ENSG00000236740.2
4	lnc-LRRC1-1	chr6:53859588-53859662	ENSG00000236740.2

No data

Variant related genes	Relation type
MLIP-IT1	TF binding region
GCH1	miRNA target sites

Extended variants
information (count: 379 )
Associated
traits (count: 79 )

Variant overlapped rSNPs/rCNVs (count:379 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1409107	chr6:53855489-53855490	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs529776206	chr6:53855490-53855491	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs150624532	chr6:53855497-53855498	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs76838518	chr6:53855504-53855505	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs532498669	chr6:53855529-53855530	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs115963770	chr6:53855549-53855550	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs114701200	chr6:53855550-53855551	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs372025132	chr6:53855565-53855566	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs202089182	chr6:53855567-53855568	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs189056894	chr6:53855593-53855594	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs552526571	chr6:53855614-53855615	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs550925763	chr6:53855629-53855630	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs567687350	chr6:53855635-53855636	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs140177145	chr6:53855662-53855663	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs564607038	chr6:53855677-53855678	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs553196986	chr6:53855714-53855715	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs376910816	chr6:53855716-53855717	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs573103549	chr6:53855729-53855730	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs538804123	chr6:53855736-53855737	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs535115278	chr6:53855750-53855751	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs180807431	chr6:53855751-53855752	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs543890981	chr6:53855768-53855769	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs554953932	chr6:53855787-53855788	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs184477117	chr6:53855879-53855880	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs143951829	chr6:53855914-53855915	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs11758570	chr6:53855947-53855948	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs532995098	chr6:53855954-53855955	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs560246054	chr6:53855976-53855977	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs532356983	chr6:53855977-53855978	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs552366567	chr6:53855980-53855981	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs577242543	chr6:53856010-53856011	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs562793113	chr6:53856043-53856044	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs537197699	chr6:53856045-53856046	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs374708149	chr6:53856046-53856047	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs531617154	chr6:53856120-53856121	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs568633468	chr6:53856122-53856123	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs9357782	chr6:53856128-53856129	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs200296253	chr6:53856146-53856147	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs146747692	chr6:53856150-53856151	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs201588936	chr6:53856151-53856152	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs201820405	chr6:53856155-53856156	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs539388334	chr6:53856181-53856182	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs372269909	chr6:53856278-53856279	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs545408311	chr6:53856305-53856306	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs377093954	chr6:53856310-53856311	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs536205251	chr6:53856325-53856326	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs188498255	chr6:53856332-53856333	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs146879723	chr6:53856390-53856391	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs181350763	chr6:53856403-53856404	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs552914103	chr6:53856417-53856418	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:79)

Disease	PMID	Source
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Leukemia	21518781	CNVD
Cancer	21637783	CNVD
Facial dysmorphism	22105932	CNVD
Medulloblastoma	21979893	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Endometrial cancer	22040021	CNVD
Acute myeloid leukemia	16864856	CNVD
Breast cancer	21264507	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Bladder cancer	19088036	CNVD
Wilms tumour	21544195	CNVD
Uveal melanoma	21693616	CNVD
Biliary cancer	19435499	CNVD
Malaria	21533027	CNVD
Retinoblastoma	19183342	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	21858162	CNVD
Ewing''s sarcoma	17952124	CNVD
Autism	21448237	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	21546498	CNVD
Autism	22495311	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Urothelial carcinoma	18382360	CNVD
Cancer	21183584	CNVD
Hodgkin''s lymphoma	17606441	CNVD
small cell lung cancer	20016488	CNVD
Gastric cancer	17908304	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Neuroblastoma	16790693	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Osteosarcoma	16790693	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Lung cancer	18438408	CNVD
Neuroblastoma	18923191	CNVD
Breast cancer	17603634	CNVD
Neurocytoma	17123091	CNVD
Systemic lupus erythematosus	17503323	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Breast cancer	16608533	CNVD
Melanoma	18172304	CNVD
Esophageal adenocarcinoma	18820669	CNVD
Neuroblastoma	19686582	CNVD
Neuroblastoma	17289879	CNVD
Breast cancer	17899364	CNVD
Breast cancer	17133270	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
Glioblastoma multiforme	22286061	CNVD
Colorectal cancer	16912164	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	21364760	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53852200-53861000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:53852400-53867800	Weak transcription	Fetal Heart	heart
3	chr6:53853400-53855600	Weak transcription	Psoas Muscle	Psoas
4	chr6:53855000-53855600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr6:53855600-53856000	Enhancers	Psoas Muscle	Psoas
6	chr6:53858200-53859200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:53860200-53861200	Enhancers	Fetal Brain Male	brain
8	chr6:53860800-53861000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:53860800-53861200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:53860800-53861200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:53860800-53861200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:53861000-53861200	Enhancers	NHEK	skin
13	chr6:53861000-53861400	Enhancers	Liver	Liver
14	chr6:53861000-53862600	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr6:53861000-53867200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr6:53861200-53861600	Enhancers	Fetal Brain Female	brain
17	chr6:53861200-53863400	Weak transcription	NHEK	skin
18	chr6:53861200-53863800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:53861200-53866200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:53861200-53866400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:53861400-53862800	Weak transcription	Liver	Liver
22	chr6:53861800-53862000	Enhancers	Aorta	Aorta
23	chr6:53862000-53870000	Weak transcription	Aorta	Aorta
24	chr6:53862200-53865600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr6:53862400-53863600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:53862600-53863200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr6:53862800-53863200	Enhancers	Liver	Liver
28	chr6:53862800-53864200	Enhancers	Fetal Intestine Large	intestine
29	chr6:53863000-53863200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:53863000-53863200	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr6:53863000-53863400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr6:53863000-53864200	Enhancers	Small Intestine	intestine
33	chr6:53863000-53864800	Enhancers	HepG2	liver
34	chr6:53863200-53863400	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr6:53863200-53863600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr6:53863200-53863600	Active TSS	Duodenum Mucosa	Duodenum
37	chr6:53863200-53863600	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr6:53863200-53864400	Flanking Active TSS	Liver	Liver
39	chr6:53863200-53864400	Enhancers	Placenta	Placenta
40	chr6:53863200-53864400	Enhancers	Left Ventricle	heart
41	chr6:53863200-53864400	Enhancers	Psoas Muscle	Psoas
42	chr6:53863200-53864400	Enhancers	Right Ventricle	heart
43	chr6:53863400-53864000	Enhancers	Placenta Amnion	Placenta Amnion
44	chr6:53863400-53864200	Enhancers	NHEK	skin
45	chr6:53863400-53866200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:53863600-53864000	Enhancers	Duodenum Mucosa	Duodenum
47	chr6:53863600-53864200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr6:53863600-53864200	Enhancers	Adipose Nuclei	Adipose
49	chr6:53863600-53864400	Enhancers	Fetal Intestine Small	intestine
50	chr6:53863600-53866400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links