Variant report

Variant	nsv884061
Chromosome Location	chr6:30234627-30250450
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:13)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30247937..30250793-chr6:30252677..30256148,3	MCF-7	breast:
2	chr6:30233530..30235918-chr6:30253137..30255680,2	K562	blood:
3	chr6:30239562..30242228-chr6:30254581..30256565,2	K562	blood:
4	chr6:30233853..30235858-chr6:30238091..30240138,2	K562	blood:
5	chr6:30237407..30239197-chr6:30252856..30255574,2	K562	blood:
6	chr6:30233837..30236152-chr6:30240056..30242630,2	MCF-7	breast:
7	chr6:30235309..30237040-chr6:30295546..30298007,2	K562	blood:
8	chr6:30233837..30236152-chr6:30240056..30242630,2	MCF-7	breast:
9	chr6:30238831..30239507-chrX:112993035..112993630,2	MCF-7	breast:
10	chr6:30238145..30240956-chr6:30290362..30292756,2	MCF-7	breast:
11	chr6:30227118..30230021-chr6:30233412..30236216,2	MCF-7	breast:
12	chr6:30179598..30181245-chr6:30238787..30241131,2	MCF-7	breast:
13	chr6:30233853..30235858-chr6:30238091..30240138,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM39-2	chr6:30231053-30234728	NONHSAT108609

No data

Variant related genes	Relation type
ENSG00000243753	chromatin interactions
ENSG00000204599	chromatin interactions
ENSG00000234127	chromatin interactions
ENSG00000248167	chromatin interactions

Extended variants
information (count: 331 )
Associated
traits (count: 111 )

Variant overlapped rSNPs/rCNVs (count:331 , 50 per page) page: 1 2 3 4 5 6 7

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs3129831	chr6:30234627-30234628	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs534785923	chr6:30234638-30234639	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
3	rs3129832	chr6:30234657-30234658	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
4	rs2844764	chr6:30234668-30234669	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
5	rs3129704	chr6:30234700-30234701	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
6	rs3129705	chr6:30234721-30234722	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
7	rs188881664	chr6:30234785-30234786	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs543798092	chr6:30234864-30234865	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs138434744	chr6:30234865-30234866	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs141392491	chr6:30234883-30234884	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs3129706	chr6:30234931-30234932	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
12	rs3129835	chr6:30234934-30234935	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
13	rs3129836	chr6:30234945-30234946	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
14	rs28780092	chr6:30234991-30234992	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs150280062	chr6:30235020-30235021	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs2516696	chr6:30235046-30235047	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
17	rs556533104	chr6:30235151-30235152	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs576818361	chr6:30235171-30235172	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs2844763	chr6:30235184-30235185	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
20	rs3129707	chr6:30235204-30235205	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
21	rs137882881	chr6:30235230-30235231	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs535259884	chr6:30235274-30235275	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs534525424	chr6:30235291-30235292	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs546725141	chr6:30235299-30235300	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs541152615	chr6:30235315-30235316	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
26	rs193236952	chr6:30235316-30235317	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
27	rs149470733	chr6:30235380-30235381	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
28	rs73726146	chr6:30235412-30235413	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
29	rs190232731	chr6:30235443-30235444	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
30	rs75147689	chr6:30235445-30235446	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
31	rs548740121	chr6:30235460-30235461	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
32	rs75211427	chr6:30235474-30235475	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
33	rs62407489	chr6:30235607-30235608	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
34	rs551185976	chr6:30235648-30235649	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
35	rs374803830	chr6:30235682-30235683	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
36	rs536603084	chr6:30235739-30235740	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
37	rs191694673	chr6:30235740-30235741	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
38	rs536785168	chr6:30235759-30235760	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
39	rs183835647	chr6:30235781-30235782	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
40	rs536135579	chr6:30235809-30235810	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
41	rs556132986	chr6:30235963-30235964	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
42	rs572669546	chr6:30235984-30235985	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
43	rs548593361	chr6:30236002-30236003	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
44	rs3129708	chr6:30236038-30236039	Weak transcription	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
45	rs564376774	chr6:30236050-30236051	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
46	rs188226252	chr6:30236078-30236079	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
47	rs180749142	chr6:30236092-30236093	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
48	rs373050210	chr6:30236100-30236101	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
49	rs559003616	chr6:30236101-30236102	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
50	rs529277778	chr6:30236126-30236127	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:111)

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
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
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
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
Breast cancer	21364760	CNVD
Lung cancer	21569311	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30228200-30237400	Weak transcription	Aorta	Aorta
2	chr6:30228400-30236800	Weak transcription	Brain Hippocampus Middle	brain
3	chr6:30228400-30238000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr6:30228400-30238200	Weak transcription	Left Ventricle	heart
5	chr6:30228400-30239600	Weak transcription	HepG2	liver
6	chr6:30228400-30239800	Weak transcription	Colon Smooth Muscle	Colon
7	chr6:30228600-30236600	Weak transcription	Brain Substantia Nigra	brain
8	chr6:30229200-30235600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:30229400-30234800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr6:30229400-30235200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:30229400-30236400	Weak transcription	Fetal Muscle Leg	muscle
12	chr6:30229800-30235000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr6:30230800-30236200	Weak transcription	GM12878-XiMat	blood
14	chr6:30231000-30235000	Strong transcription	Primary B cells from cord blood	blood
15	chr6:30231600-30239600	Weak transcription	Brain Angular Gyrus	brain
16	chr6:30232200-30235200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:30232200-30235800	Weak transcription	Brain Anterior Caudate	brain
18	chr6:30232800-30235600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:30233000-30235200	Weak transcription	Primary T cells from cord blood	blood
20	chr6:30233200-30234800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr6:30233200-30235400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr6:30233200-30235800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:30233200-30243600	Weak transcription	HSMMtube	muscle
24	chr6:30233400-30235200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:30233400-30235200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:30233400-30235400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr6:30233400-30235600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:30233400-30236000	Weak transcription	Osteobl	bone
29	chr6:30233600-30235200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr6:30233800-30236200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr6:30233800-30241200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:30235000-30237400	Weak transcription	Primary B cells from cord blood	blood
33	chr6:30235600-30235800	Enhancers	Placenta Amnion	Placenta Amnion
34	chr6:30236800-30237000	Enhancers	Brain Hippocampus Middle	brain
35	chr6:30237200-30243400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr6:30239600-30240400	Enhancers	HepG2	liver
37	chr6:30239800-30240200	Enhancers	Colon Smooth Muscle	Colon
38	chr6:30241200-30241400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:30241200-30241800	Enhancers	Fetal Lung	lung
40	chr6:30241600-30241800	Bivalent Enhancer	HUVEC	blood vessel
41	chr6:30243800-30244000	Enhancers	HSMMtube	muscle
42	chr6:30247400-30253000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:30247600-30262400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr6:30247800-30249000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
45	chr6:30247800-30249600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
46	chr6:30248400-30251600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
47	chr6:30248400-30253400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr6:30248400-30255600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:30248600-30254000	ZNF genes & repeats	Liver	Liver
50	chr6:30248800-30251400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell

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