Variant report

Variant	esv3424208
Chromosome Location	chr9:140385956-140388504
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:19)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:140366440..140369385-chr9:140386495..140388983,2	K562	blood:
2	chr9:140195173..140197851-chr9:140381665..140386088,4	MCF-7	breast:
3	chr9:140385602..140387946-chr9:140412336..140414686,2	K562	blood:
4	chr9:140386446..140388269-chr9:140413186..140415741,2	K562	blood:
5	chr9:140353788..140359040-chr9:140385385..140389520,8	K562	blood:
6	chr9:140189560..140193480-chr9:140384679..140388476,4	K562	blood:
7	chr9:140353655..140356104-chr9:140385846..140387400,2	MCF-7	breast:
8	chr9:140386948..140388697-chr9:140392621..140394758,2	K562	blood:
9	chr9:140385373..140390339-chr9:140393084..140398390,8	MCF-7	breast:
10	chr9:140355725..140357240-chr9:140385390..140388277,2	K562	blood:
11	chr9:140304848..140306360-chr9:140385866..140388682,2	K562	blood:
12	chr9:140209677..140212013-chr9:140385479..140387034,2	K562	blood:
13	chr9:140385694..140388620-chr9:140402959..140406743,3	K562	blood:
14	chr9:140347395..140351065-chr9:140385610..140390076,3	K562	blood:
15	chr9:140170582..140172704-chr9:140385378..140387482,2	K562	blood:
16	chr9:140192588..140195747-chr9:140385238..140387979,3	MCF-7	breast:
17	chr9:140385364..140389907-chr9:140391534..140397085,5	MCF-7	breast:
18	chr9:140347395..140349788-chr9:140384770..140388598,3	K562	blood:
19	chr9:140353512..140355543-chr9:140385777..140387498,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NELF-2	chr9:140385913-140386550	NONHSAT135731

No data

Variant related genes	Relation type
ENSG00000198113	chromatin interactions
ENSG00000198435	chromatin interactions
ENSG00000260996	chromatin interactions
ENSG00000165802	chromatin interactions

Extended variants
information (count: 82 )
Associated
traits (count: 20 )

Variant overlapped rSNPs/rCNVs (count:82 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs142071077	chr9:140385959-140385960	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
2	rs28562999	chr9:140385963-140385964	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
3	rs150851175	chr9:140385964-140385965	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
4	rs138174994	chr9:140385965-140385966	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
5	rs149552127	chr9:140386032-140386033	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
6	rs144612858	chr9:140386039-140386040	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
7	rs554329780	chr9:140386081-140386082	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	Chromatin interactive region lncRNA	4 gene(s)	Overlapped CNVs	n/a
8	rs571000914	chr9:140386158-140386159	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
9	rs564839689	chr9:140386182-140386183	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
10	rs116312326	chr9:140386196-140386197	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
11	rs558322536	chr9:140386215-140386216	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
12	rs139738293	chr9:140386256-140386257	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
13	rs550135061	chr9:140386263-140386264	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
14	rs182677222	chr9:140386269-140386270	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
15	rs371113318	chr9:140386284-140386285	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
16	rs574761961	chr9:140386291-140386292	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
17	rs185067556	chr9:140386370-140386371	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
18	rs560285730	chr9:140386392-140386393	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
19	rs145250299	chr9:140386401-140386402	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
20	rs545979360	chr9:140386409-140386410	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
21	rs562601077	chr9:140386410-140386411	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
22	rs531706456	chr9:140386422-140386423	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
23	rs76544955	chr9:140386429-140386430	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
24	rs140483151	chr9:140386466-140386467	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
25	rs563855910	chr9:140386474-140386475	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
26	rs142136906	chr9:140386487-140386488	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
27	rs571127227	chr9:140386597-140386598	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
28	rs539605748	chr9:140386658-140386659	Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
29	rs151166263	chr9:140386675-140386676	Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
30	rs189537485	chr9:140386691-140386692	Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
31	rs182615454	chr9:140386710-140386711	Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
32	rs140100176	chr9:140386741-140386742	Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
33	rs565660320	chr9:140386757-140386758	Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
34	rs560479602	chr9:140386763-140386764	Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
35	rs534091349	chr9:140386769-140386770	Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
36	rs374258450	chr9:140386802-140386803	Weak transcription Strong transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
37	rs188939971	chr9:140386828-140386829	Weak transcription Strong transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
38	rs149865530	chr9:140386829-140386830	Weak transcription Strong transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
39	rs545643203	chr9:140386926-140386927	Weak transcription Strong transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
40	rs566328040	chr9:140386960-140386961	Weak transcription Strong transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
41	rs562363413	chr9:140386981-140386982	Weak transcription Strong transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
42	rs576114622	chr9:140386982-140386983	Weak transcription Strong transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
43	rs541963308	chr9:140387143-140387144	Weak transcription Strong transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
44	rs561747174	chr9:140387385-140387386	Weak transcription Strong transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
45	rs527643585	chr9:140387401-140387402	Weak transcription Strong transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
46	rs547779251	chr9:140387414-140387415	Weak transcription Strong transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
47	rs368322846	chr9:140387415-140387416	Weak transcription Strong transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
48	rs193127488	chr9:140387455-140387456	Weak transcription Strong transcription Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
49	rs375258991	chr9:140387493-140387494	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs200763008	chr9:140387495-140387496	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:20)

Disease	PMID	Source
Leukemia	17361228	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Glioblastoma	16823260	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Cardiac fibroma	18329553	CNVD
Lung cancer	19147751	CNVD
Cervical cancer	17311676	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Gastric cancer	17908304	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Salivary gland adenoid cystic carcinoma	17545515	CNVD
Chordoma	18071362	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Sudden cardiac death	19188705	CNVD
Myoepithelioma	18604193	CNVD
Tuberous sclerosis	19566914	CNVD
Multiple myeloma	16616336	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Mantle cell lymphoma	19029149	CNVD
Breast cancer	21509527	CNVD

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:140373800-140396000	Weak transcription	Esophagus	oesophagus
2	chr9:140374000-140386200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:140375000-140392200	Weak transcription	Brain Angular Gyrus	brain
4	chr9:140375400-140386000	Weak transcription	Aorta	Aorta
5	chr9:140375400-140387600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr9:140376800-140444000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr9:140377000-140393400	Weak transcription	Brain Substantia Nigra	brain
8	chr9:140377000-140394400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr9:140377000-140437000	Weak transcription	Left Ventricle	heart
10	chr9:140377200-140386200	Weak transcription	Spleen	Spleen
11	chr9:140377200-140387600	Weak transcription	Right Ventricle	heart
12	chr9:140377200-140393800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:140377200-140420200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr9:140377400-140393200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr9:140379400-140389000	Weak transcription	Gastric	stomach
16	chr9:140380600-140386000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr9:140380800-140387600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr9:140381600-140386400	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr9:140381600-140386600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr9:140381600-140396600	Strong transcription	Liver	Liver
21	chr9:140381800-140386800	Strong transcription	Skeletal Muscle Male	skeletal muscle
22	chr9:140382400-140387600	Weak transcription	Fetal Stomach	stomach
23	chr9:140382400-140389400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr9:140382600-140397400	Weak transcription	Lung	lung
25	chr9:140382800-140387600	Weak transcription	Fetal Intestine Small	intestine
26	chr9:140382800-140387800	Weak transcription	Colonic Mucosa	Colon
27	chr9:140382800-140387800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr9:140383000-140386200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr9:140383000-140387600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr9:140383000-140388800	Weak transcription	Stomach Mucosa	stomach
31	chr9:140383200-140386000	Strong transcription	Primary B cells from cord blood	blood
32	chr9:140383400-140386400	Strong transcription	Adipose Nuclei	Adipose
33	chr9:140383400-140388000	Weak transcription	Pancreas	Pancrea
34	chr9:140383600-140386000	Enhancers	K562	blood
35	chr9:140384400-140391200	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr9:140384600-140386600	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr9:140384600-140397600	Strong transcription	Ovary	ovary
38	chr9:140385200-140386000	Weak transcription	Fetal Muscle Leg	muscle
39	chr9:140385600-140386600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr9:140385600-140386600	Strong transcription	Brain Anterior Caudate	brain
41	chr9:140385800-140386400	Strong transcription	Primary B cells from peripheral blood	blood
42	chr9:140385800-140386400	Strong transcription	Brain Hippocampus Middle	brain
43	chr9:140385800-140386800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr9:140386000-140386400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr9:140386000-140386600	Strong transcription	Aorta	Aorta
46	chr9:140386000-140386600	Strong transcription	Fetal Muscle Leg	muscle
47	chr9:140386000-140386800	Flanking Active TSS	K562	blood
48	chr9:140386000-140393000	Weak transcription	Primary B cells from cord blood	blood
49	chr9:140386200-140386400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr9:140386200-140386400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell

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