Variant report

Variant	nsv603009
Chromosome Location	chr6:45530471-45543530
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:25)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:45529109..45532047-chr6:45550520..45552903,2	MCF-7	breast:
2	chr6:45521858..45524563-chr6:45528701..45531108,3	MCF-7	breast:
3	chr6:45533723..45535563-chr6:45552658..45554257,2	MCF-7	breast:
4	chr6:45538385..45540491-chr6:45545062..45546957,2	MCF-7	breast:
5	chr15:40509302..40509813-chr6:45530780..45531300,2	K562	blood:
6	chr6:45521600..45524007-chr6:45539938..45542034,2	MCF-7	breast:
7	chr6:45540470..45542325-chr6:45555218..45557403,2	MCF-7	breast:
8	chr6:45533105..45535281-chr6:45537536..45540429,2	MCF-7	breast:
9	chr6:45533105..45535281-chr6:45537536..45540429,2	MCF-7	breast:
10	chr6:45531563..45533620-chr6:45534711..45536211,2	MCF-7	breast:
11	chr6:45525346..45527240-chr6:45531716..45533270,2	MCF-7	breast:
12	chr6:45531563..45533620-chr6:45534711..45536211,2	MCF-7	breast:

(count:25 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SUPT3H-1	chr6:45541083-45541851	ENSG00000261080.1
2	lnc-SUPT3H-1	chr6:45535185-45535424	XLOC_005737
3	lnc-SUPT3H-1	chr6:45541116-45541851	XLOC_005737
4	lnc-SUPT3H-1	chr6:45541116-45542183	XLOC_005737
5	lnc-SUPT3H-1	chr6:45533780-45534135	XLOC_005737
6	lnc-SUPT3H-1	chr6:45535185-45535424	XLOC_005737
7	lnc-SUPT3H-1	chr6:45541116-45542183	XLOC_005737
8	lnc-SUPT3H-1	chr6:45541116-45542183	XLOC_005737
9	lnc-RUNX2-1	chr6:45540498-45543034	XLOC_005302
10	lnc-SUPT3H-1	chr6:45533740-45534135	XLOC_005737
11	lnc-SUPT3H-1	chr6:45541116-45541851	XLOC_005737
12	lnc-SUPT3H-1	chr6:45533740-45534135	XLOC_005737
13	lnc-SUPT3H-1	chr6:45533780-45534135	XLOC_005737
14	lnc-SUPT3H-1	chr6:45541083-45541851	NONHSAT112989
15	lnc-SUPT3H-1	chr6:45535185-45535428	XLOC_005737
16	lnc-SUPT3H-1	chr6:45534240-45535428	NONHSAT112988
17	lnc-SUPT3H-1	chr6:45533780-45534135	XLOC_005737
18	lnc-SUPT3H-1	chr6:45541116-45542183	XLOC_005737
19	lnc-SUPT3H-1	chr6:45539449-45540445	NONHSAT112989
20	lnc-SUPT3H-1	chr6:45539456-45540445	ENSG00000251681
21	lnc-SUPT3H-1	chr6:45535185-45535424	XLOC_005737
22	lnc-SUPT3H-1	chr6:45541083-45541851	ENSG00000251681
23	lnc-SUPT3H-1	chr6:45535185-45535424	XLOC_005737
24	lnc-SUPT3H-1	chr6:45541116-45541851	XLOC_005737
25	lnc-SUPT3H-1	chr6:45541116-45541851	NONHSAT112988

No data

Variant related genes	Relation type
ENSG00000259288	chromatin interactions
ENSG00000156970	chromatin interactions
TTLL3	miRNA target sites
LCA5	miRNA target sites

Extended variants
information (count: 491 )
Associated
traits (count: 91 )

Variant overlapped rSNPs/rCNVs (count:491 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs12202314	chr6:45530471-45530472	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs75419747	chr6:45530515-45530516	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs541672091	chr6:45530521-45530522	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs56297038	chr6:45530545-45530546	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs113056915	chr6:45530564-45530565	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs147768322	chr6:45530578-45530579	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs533696801	chr6:45530601-45530602	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
8	rs144936711	chr6:45530637-45530638	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
9	rs16873507	chr6:45530668-45530669	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs539429589	chr6:45530675-45530676	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
11	rs548956460	chr6:45530739-45530740	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
12	rs73737474	chr6:45530757-45530758	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs528544558	chr6:45530782-45530783	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs547584363	chr6:45530789-45530790	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs565696160	chr6:45530817-45530818	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs149051375	chr6:45530882-45530883	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs73450274	chr6:45530902-45530903	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs187431456	chr6:45530944-45530945	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs537075678	chr6:45530971-45530972	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs55784611	chr6:45531063-45531064	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs142068429	chr6:45531072-45531073	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs540737521	chr6:45531074-45531075	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs370187068	chr6:45531201-45531202	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs151131681	chr6:45531235-45531236	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs191261746	chr6:45531316-45531317	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs534478418	chr6:45531391-45531392	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs200346954	chr6:45531393-45531394	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs578077822	chr6:45531422-45531423	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs373646089	chr6:45531496-45531497	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs563867241	chr6:45531498-45531499	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs565970474	chr6:45531499-45531500	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs531096313	chr6:45531541-45531542	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs74901884	chr6:45531564-45531565	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs560911017	chr6:45531567-45531568	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs541953531	chr6:45531596-45531597	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs16873508	chr6:45531615-45531616	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs556935426	chr6:45531618-45531619	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs533017807	chr6:45531625-45531626	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs551534263	chr6:45531626-45531627	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs182669260	chr6:45531670-45531671	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs537311431	chr6:45531734-45531735	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs140716945	chr6:45531827-45531828	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs567232789	chr6:45531937-45531938	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs145893934	chr6:45531986-45531987	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs554757843	chr6:45531989-45531990	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs186960462	chr6:45532016-45532017	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs138445323	chr6:45532020-45532021	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs192225842	chr6:45532062-45532063	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs141340876	chr6:45532067-45532068	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs575556025	chr6:45532158-45532159	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:91)

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
Acute lymphoblastic leukemia	20435627	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	21858162	CNVD
Ewing''s sarcoma	17952124	CNVD
Autism	21448237	CNVD
Melanoma	18172304	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
Hepatocellular carcinoma	16750200	CNVD
Autism	22495311	CNVD
Cancer	16790693	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
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
Ovarian cancer	21720365	CNVD
Osteosarcoma	21197465	CNVD
Gastric cancer	24379144	CNVD
Neuroblastoma	18923191	CNVD
abnormal development	18461090	CNVD
Breast cancer	17603634	CNVD
Breast cancer	21364760	CNVD
Colorectal cancer	16790693	CNVD
Congenital adrenal hyperplasia	18478071	CNVD
Congenital anomalies of the kidney and urinary tract	18316590	CNVD
Systemic lupus erythematosus	19287148	CNVD
Colorectal cancer	19359472	CNVD
Multiple myeloma	16616336	CNVD
Chordoma	18071362	CNVD
Follicular lymphoma	16790693	CNVD
Osteosarcoma	19286668	CNVD
Neurocytoma	17123091	CNVD
lymphocytic leukemia	21291569	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Myelofibrosis	22110671	CNVD
Heart disease	21282601	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Breast cancer	16608533	CNVD
Glioblastoma multiforme	21510904	CNVD
Cleidocranial dysplasia	20014132	CNVD
Non-small cell lung cancer	17429853	CNVD
Breast cancer	22522925	CNVD
Cancer	20164919	CNVD
Pancreatic cancer	17952125	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:178 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45508200-45530600	Weak transcription	Psoas Muscle	Psoas
2	chr6:45519600-45532400	Weak transcription	Right Atrium	heart
3	chr6:45522000-45536800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr6:45522200-45533800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:45524800-45530600	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr6:45524800-45537000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:45525000-45532200	Weak transcription	Left Ventricle	heart
8	chr6:45525000-45533800	Weak transcription	HSMM	muscle
9	chr6:45525000-45534600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr6:45525200-45530600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:45525200-45530600	Weak transcription	Ovary	ovary
12	chr6:45528000-45530600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr6:45530600-45530800	Bivalent Enhancer	Fetal Muscle Leg	muscle
14	chr6:45530600-45531000	Enhancers	Ovary	ovary
15	chr6:45530600-45531000	Enhancers	Psoas Muscle	Psoas
16	chr6:45530600-45531200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:45530600-45531200	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr6:45530600-45531200	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr6:45530600-45531800	Enhancers	Fetal Stomach	stomach
20	chr6:45530800-45531000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:45530800-45531200	Enhancers	Fetal Muscle Leg	muscle
22	chr6:45530800-45531800	Enhancers	Fetal Lung	lung
23	chr6:45531000-45531400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:45531000-45536200	Weak transcription	Psoas Muscle	Psoas
25	chr6:45531000-45537000	Weak transcription	Ovary	ovary
26	chr6:45531000-45537200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:45531200-45531600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr6:45531200-45532200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr6:45531400-45532400	Enhancers	Fetal Heart	heart
30	chr6:45531600-45532600	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr6:45532200-45532400	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr6:45532200-45532400	Enhancers	HSMMtube	muscle
33	chr6:45532200-45532600	Enhancers	Left Ventricle	heart
34	chr6:45532400-45532800	Enhancers	Right Atrium	heart
35	chr6:45532400-45534200	Weak transcription	HSMMtube	muscle
36	chr6:45532400-45537000	Weak transcription	Fetal Heart	heart
37	chr6:45532600-45536200	Weak transcription	Left Ventricle	heart
38	chr6:45532800-45535600	Weak transcription	Right Atrium	heart
39	chr6:45533800-45534000	Enhancers	HSMM	muscle
40	chr6:45533800-45535000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:45533800-45535400	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr6:45533800-45537400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr6:45534000-45534400	Weak transcription	HSMM	muscle
44	chr6:45534000-45537600	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr6:45534200-45534400	Enhancers	HSMMtube	muscle
46	chr6:45534200-45534800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr6:45534200-45535400	Enhancers	HepG2	liver
48	chr6:45534200-45535400	Enhancers	NH-A	brain
49	chr6:45534200-45537800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr6:45534200-45538000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links