Variant report

Variant	esv3349089
Chromosome Location	chr6:29957473-29963071
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr6:29960632-29960941	IMR90	lung:	n/a	n/a
2	CEBPB	chr6:29958470-29958501	K562	blood:	n/a	n/a
3	CTCF	chr6:29959140-29959222	GM20000	blood:	n/a	n/a
4	CTCF	chr6:29961220-29961370	GM12871	blood:	n/a	n/a
5	CTCF	chr6:29961440-29961590	HepG2	liver:	n/a	n/a
6	CTCF	chr6:29961520-29961547	MCF-7	breast:	n/a	n/a
7	CUX1	chr6:29957652-29957709	K562	blood:	n/a	n/a
8	FOS	chr6:29960566-29960988	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr6:29960506-29960978	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr6:29960604-29960913	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr6:29960551-29960976	MCF10A-Er-Src	breast:	n/a	n/a
12	FOSL1	chr6:29960548-29961113	HCT-116	colon:	n/a	n/a
13	FOSL1	chr6:29960453-29961105	HCT-116	colon:	n/a	n/a
14	FOSL2	chr6:29960551-29960899	SK-N-SH	brain:	n/a	n/a
15	GATA3	chr6:29956973-29957478	SK-N-SH	brain:	n/a	n/a
16	JUND	chr6:29960473-29961077	HCT-116	colon:	n/a	n/a
17	JUND	chr6:29962859-29962974	HepG2	liver:	n/a	n/a
18	MYC	chr6:29960665-29960913	MCF10A-Er-Src	breast:	n/a	n/a
19	MYC	chr6:29960604-29960952	MCF10A-Er-Src	breast:	n/a	n/a
20	RCOR1	chr6:29959157-29959188	GM12878	blood:	n/a	n/a
21	STAT3	chr6:29960547-29960967	MCF10A-Er-Src	breast:	n/a	n/a
22	STAT3	chr6:29960673-29960880	MCF10A-Er-Src	breast:	n/a	n/a
23	TCF12	chr6:29963022-29963700	SK-N-SH	brain:	n/a	n/a
24	USF1	chr6:29960638-29961036	HCT-116	colon:	n/a	n/a
25	USF2	chr6:29960642-29960948	Hela-S3	cervix:	n/a	chr6:29960822-29960833
26	USF2	chr6:29960702-29960922	HepG2	liver:	n/a	chr6:29960822-29960833

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:29958211..29960580-chr6:29962280..29965005,2	K562	blood:
2	chr6:29949567..29951883-chr6:29956360..29958897,2	K562	blood:
3	chr6:29955944..29957540-chr6:29961326..29963329,2	K562	blood:
4	chr6:29956108..29958898-chr6:29958953..29961030,2	K562	blood:
5	chr6:29949567..29952384-chr6:29955471..29958344,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HLA-A-6	chr6:29960986-29961108	NONHSAT108573
2	lnc-RNF39-7	chr6:29962214-29962378	NONHSAT108574
3	lnc-HLA-A-6	chr6:29961248-29961382	NONHSAT108573
4	lnc-RNF39-7	chr6:29962922-29963091	NONHSAT108574

No data

Variant related genes	Relation type
DDX39BP2	TF binding region
ENSG00000224312	chromatin interactions
ENSG00000238024	chromatin interactions

Extended variants
information (count: 367 )
Associated
traits (count: 120 )

Variant overlapped rSNPs/rCNVs (count:367 , 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	rs375686106	chr6:29957475-29957476	Weak transcription	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
2	rs557710231	chr6:29957485-29957486	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs61322523	chr6:29957495-29957496	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs9260931	chr6:29957508-29957509	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
5	rs530514082	chr6:29957528-29957529	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs199903096	chr6:29957529-29957530	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs550398606	chr6:29957532-29957533	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs570129342	chr6:29957558-29957559	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs372537614	chr6:29957573-29957574	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs535781019	chr6:29957580-29957581	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs569100183	chr6:29957595-29957596	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs374733537	chr6:29957619-29957620	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs116380157	chr6:29957632-29957633	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs76715340	chr6:29957633-29957634	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs75704588	chr6:29957636-29957637	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs199861540	chr6:29957668-29957669	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs566419378	chr6:29957669-29957670	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs113305417	chr6:29957681-29957682	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs77646702	chr6:29957685-29957686	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs73410541	chr6:29957708-29957709	Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs371590814	chr6:29957727-29957728	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs375277764	chr6:29957753-29957754	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs373525180	chr6:29957773-29957774	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs201881753	chr6:29957783-29957784	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs372796587	chr6:29957794-29957795	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs115658736	chr6:29957801-29957802	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs9260932	chr6:29957802-29957803	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
28	rs557151939	chr6:29957813-29957814	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs78396870	chr6:29957824-29957825	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs116591706	chr6:29957841-29957842	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs367848523	chr6:29957857-29957858	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs9260933	chr6:29957866-29957867	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
33	rs114717261	chr6:29957904-29957905	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs142409028	chr6:29957905-29957906	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs114205034	chr6:29957908-29957909	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs374601974	chr6:29957914-29957915	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs72843107	chr6:29957941-29957942	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs115868657	chr6:29957942-29957943	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs115443132	chr6:29957943-29957944	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs374229614	chr6:29957976-29957977	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs9260934	chr6:29957982-29957983	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
42	rs376992341	chr6:29958028-29958029	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs368162819	chr6:29958038-29958039	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs373566166	chr6:29958045-29958046	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs184179022	chr6:29958088-29958089	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs73410543	chr6:29958101-29958102	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs79304920	chr6:29958134-29958135	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs75954761	chr6:29958156-29958157	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs57927905	chr6:29958161-29958162	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
50	rs370110068	chr6:29958169-29958170	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:120)

Disease	PMID	Source
Acute lymphoblastic leukemia	22237106	CNVD
Follicular lymphoma	20505157	CNVD
Glioblastoma multiforme	21080181	CNVD
Ewing''s sarcoma	21437220	CNVD
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
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
Acute myeloid leukemia	20729466	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	21858162	CNVD
Lung cancer	18438408	CNVD
Ewing''s sarcoma	17952124	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Autism	21448237	CNVD
Cancer	20164919	CNVD
Melanoma	18172304	CNVD
Breast cancer	22844521	CNVD
HIV/AIDS	22844521	CNVD
Ovarian cancer	22844521	CNVD
Prostate cancer	22844521	CNVD
Psoriasis	22844521	CNVD
Rheumatoid arthritis	22844521	CNVD
Sclerosis systemic	22844521	CNVD
Systemic lupus erythematosus	22844521	CNVD
Breast cancer	22522925	CNVD
Ovarian cancer	21781307	CNVD
Breast cancer	21552322	CNVD
Immune disease	21076436	CNVD
Autoimmune disease	19135723	CNVD
Systemic lupus erythematosus	17953491	CNVD
Recurrent Infections	22737222	CNVD
Systemic lupus erythematosus	21904924	CNVD
Ependymoma	19289631	CNVD
Gestational infection	22844521	CNVD
Head circumference	22844521	CNVD
Infertility	22844521	CNVD
Recurrent birth weight diabetes	22844521	CNVD
Obesity	22844521	CNVD
Recurrent pregnancy loss	22844521	CNVD
Intellectual disability	21811512	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Congenital anomalies of the kidney and urinary tract	18694510	CNVD
Nasopharyngeal cancer	22815911	CNVD
Hepatocellular carcinoma	16750200	CNVD
Basal cell lymphoma	21115979	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	17133270	CNVD
Autism	22495311	CNVD
Cancer	16790693	CNVD
Cervical cancer	21062161	CNVD
Breast cancer	21785460	CNVD
Retinoblastoma	16790693	CNVD
Esophageal adenocarcinoma	18820669	CNVD
Systemic lupus erythematosus	17503323	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Urothelial carcinoma	18382360	CNVD
Cancer	21183584	CNVD
Hodgkin''s lymphoma	17606441	CNVD
small cell lung cancer	20016488	CNVD
Renal cell carcinoma	18765545	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Gastric cancer	17908304	CNVD
Metanephric adenoma	20802469	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Schizophrenia	19571809	CNVD
Schizophrenia	19571808	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Neuroblastoma	16790693	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
abnormal development	18461090	CNVD
Breast cancer	21509527	CNVD
Melanoma	17363583	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	16397240	CNVD
Retinoblastoma	22278416	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Systemic lupus erythematosus	20877625	CNVD
Cleidocranial dysplasia	18696259	CNVD
Holoprosencephaly	21359414	CNVD
Liposarcoma	21253554	CNVD
Uveal melanoma	20484589	CNVD
Fibroblasts	20926602	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Non-syndromic sensorineural hearing loss	17289997	CNVD
Pancreatic cancer	17952125	CNVD
Rett syndrome	21593744	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Congenital anomalies of the kidney and urinary tract	18316590	CNVD
Glioma	20126413	CNVD
Non-syndromic sensorineural hearing loss	19587683	CNVD
early-passage human iPS cells	21368824	CNVD
Oral cancer	21386901	CNVD

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29945600-29966400	Weak transcription	Pancreas	Pancrea
2	chr6:29957200-29960200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:29957200-29960400	Weak transcription	HMEC	breast
4	chr6:29957400-29957600	Weak transcription	NHEK	skin
5	chr6:29957400-29960400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:29960000-29961400	Enhancers	Fetal Intestine Large	intestine
7	chr6:29960000-29961600	Enhancers	NHDF-Ad	bronchial
8	chr6:29960200-29961400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:29960400-29961000	Enhancers	NHEK	skin
10	chr6:29960400-29961200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:29960400-29961200	Enhancers	HMEC	breast
12	chr6:29960400-29961400	Enhancers	Fetal Intestine Small	intestine
13	chr6:29960600-29960800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr6:29960600-29961000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr6:29960600-29961200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:29960800-29961200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:29961200-29963000	Weak transcription	HMEC	breast
18	chr6:29961400-29962400	Weak transcription	Fetal Intestine Large	intestine
19	chr6:29961400-29963800	Weak transcription	Fetal Intestine Small	intestine
20	chr6:29961600-29962400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr6:29961600-29963000	Weak transcription	NHDF-Ad	bronchial
22	chr6:29962400-29962600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr6:29962400-29962600	Enhancers	Fetal Intestine Large	intestine
24	chr6:29962400-29963000	Enhancers	Fetal Lung	lung
25	chr6:29962400-29968400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr6:29962600-29962800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr6:29962600-29963000	Weak transcription	Fetal Intestine Large	intestine
28	chr6:29962800-29963400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr6:29962800-29964200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:29963000-29963400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:29963000-29963400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr6:29963000-29963400	Enhancers	NHDF-Ad	bronchial
33	chr6:29963000-29963600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:29963000-29963600	Enhancers	HMEC	breast
35	chr6:29963000-29964200	Enhancers	Fetal Intestine Large	intestine
36	chr6:29963000-29964400	Enhancers	Hela-S3	cervix

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