Variant report

Variant	nsv8563
Chromosome Location	chr9:115914276-115917151
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	chr9:115873156..115875899-chr9:115915858..115921312,4	MCF-7	breast:
2	chr9:115916182..115918262-chr9:115925062..115927268,3	MCF-7	breast:
3	chr9:115913111..115914699-chr9:115915133..115916997,2	K562	blood:
4	chr9:115916286..115919484-chr9:115921664..115924647,3	K562	blood:
5	chr9:115917061..115918640-chr9:115927400..115929607,2	MCF-7	breast:
6	chr9:115882894..115884462-chr9:115915677..115917990,2	MCF-7	breast:
7	chr9:115913327..115916086-chr9:115970304..115972231,2	MCF-7	breast:
8	chr9:115913631..115915237-chr9:115923889..115925758,2	K562	blood:
9	chr9:115913338..115915206-chr9:115920921..115923373,3	K562	blood:
10	chr9:115887611..115890231-chr9:115913519..115916345,2	MCF-7	breast:
11	chr9:115875175..115875677-chr9:115914252..115914851,2	MCF-7	breast:
12	chr9:115881515..115883241-chr9:115913395..115914943,2	MCF-7	breast:
13	chr9:115905644..115908349-chr9:115914691..115916468,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC31A1-4	chr9:115913931-115914596	NONHSAT134319

No data

Variant related genes	Relation type
ENSG00000231528	chromatin interactions
ENSG00000136867	chromatin interactions
ENSG00000225684	chromatin interactions

Extended variants
information (count: 106 )
Associated
traits (count: 54 )

Variant overlapped rSNPs/rCNVs (count:106 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs540465479	chr9:115914341-115914342	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
2	rs77532164	chr9:115914367-115914368	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
3	rs559678800	chr9:115914419-115914420	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
4	rs79492582	chr9:115914460-115914461	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
5	rs374186933	chr9:115914463-115914464	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
6	rs546084625	chr9:115914470-115914471	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
7	rs41280209	chr9:115914478-115914479	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs531296834	chr9:115914546-115914547	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
9	rs73655809	chr9:115914556-115914557	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
10	rs568196069	chr9:115914567-115914568	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
11	rs147707926	chr9:115914583-115914584	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
12	rs547620391	chr9:115914615-115914616	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs41280211	chr9:115914686-115914687	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs189175398	chr9:115914719-115914720	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs7851648	chr9:115914724-115914725	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs182218620	chr9:115914731-115914732	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs142656083	chr9:115914770-115914771	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs555472198	chr9:115914776-115914777	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs572528602	chr9:115914905-115914906	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs187269011	chr9:115914939-115914940	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs554024088	chr9:115914942-115914943	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs369898100	chr9:115914950-115914951	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs557448545	chr9:115914966-115914967	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs7852229	chr9:115915008-115915009	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs539706896	chr9:115915062-115915063	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	n/a	n/a	Overlapped CNVs	n/a
26	rs529555571	chr9:115915093-115915094	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	n/a	n/a	Overlapped CNVs	n/a
27	rs562842345	chr9:115915180-115915181	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs11794048	chr9:115915194-115915195	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
29	rs373586483	chr9:115915259-115915260	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs10981652	chr9:115915264-115915265	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs561512878	chr9:115915315-115915316	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs527398518	chr9:115915326-115915327	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs547063011	chr9:115915332-115915333	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs564346166	chr9:115915333-115915334	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs191720319	chr9:115915334-115915335	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs375393655	chr9:115915400-115915401	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs528433719	chr9:115915404-115915405	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs78877627	chr9:115915412-115915413	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs57402950	chr9:115915413-115915414	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs57917065	chr9:115915414-115915415	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs142439459	chr9:115915485-115915486	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs201939204	chr9:115915519-115915520	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs12342399	chr9:115915520-115915521	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs540127369	chr9:115915540-115915541	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs72756150	chr9:115915582-115915583	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs370370965	chr9:115915592-115915593	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs7027743	chr9:115915624-115915625	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
48	rs549390887	chr9:115915679-115915680	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs72756152	chr9:115915685-115915686	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs535144161	chr9:115915716-115915717	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:54)

Disease	PMID	Source
Acute lymphoblastic leukemia	22237106	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
Renal cell carcinoma	18592004	CNVD
Developmental delay	19490664	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
Medulloblastoma	21979893	CNVD
microdeletion syndrome	16199537	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Urothelial carcinoma	21177765	CNVD
Renal cell carcinoma	21668985	CNVD
Autism	22495311	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Cancer	16751803	CNVD
Myelofibrosis	22110671	CNVD
lymphocytic leukemia	21291569	CNVD
Leukemia	17361228	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Glioblastoma	16823260	CNVD
Non-small cell lung cancer	21044232	CNVD
Brain cancer	20823417	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Astrocytoma	17387387	CNVD
Glioblastoma multiforme	21080181	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Renal cell carcinoma	19461508	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Heart disease	21282601	CNVD
Lung cancer	18438408	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Breast cancer	17603634	CNVD
Acute myeloid leukemia	20729466	CNVD
Oral cancer	21386901	CNVD
Prostate cancer	18632612	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Gastric cancer	17908304	CNVD
small cell lung cancer	20016488	CNVD
Cardiac fibroma	18329553	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Testicular germ cell tumor	18059402	CNVD
Breast cancer	21364760	CNVD
Developmental delay	21147756	CNVD
Lung cancer	19147751	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Melanoma	18172304	CNVD
Colorectal cancer	16272173	CNVD
Bladder cancer	21909424	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:331 , 50 per page) page: 1 2 3 4 5 6 7

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115912600-115914400	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr9:115912600-115915000	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr9:115912800-115914400	Active TSS	Fetal Intestine Large	intestine
4	chr9:115912800-115914400	Active TSS	Ovary	ovary
5	chr9:115912800-115914800	Active TSS	Right Atrium	heart
6	chr9:115913000-115914400	Active TSS	Brain Hippocampus Middle	brain
7	chr9:115913000-115914400	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr9:115913000-115914400	Active TSS	Pancreas	Pancrea
9	chr9:115913000-115914400	Active TSS	HSMM	muscle
10	chr9:115913000-115914600	Active TSS	Brain Substantia Nigra	brain
11	chr9:115913000-115915000	Active TSS	Brain Cingulate Gyrus	brain
12	chr9:115913000-115915800	Active TSS	Brain Angular Gyrus	brain
13	chr9:115913000-115916600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr9:115913400-115914600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr9:115913400-115915000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr9:115913600-115915000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr9:115913800-115914400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr9:115913800-115914400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr9:115913800-115914400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
20	chr9:115913800-115914400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
21	chr9:115913800-115914400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
22	chr9:115913800-115914600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
23	chr9:115913800-115914800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
24	chr9:115913800-115915000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr9:115913800-115915000	Flanking Active TSS	Liver	Liver
26	chr9:115913800-115915000	Flanking Active TSS	Duodenum Mucosa	Duodenum
27	chr9:115913800-115915000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr9:115913800-115915400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr9:115913800-115915400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr9:115913800-115915400	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr9:115913800-115915800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
32	chr9:115913800-115918000	Weak transcription	Aorta	Aorta
33	chr9:115914000-115914400	Enhancers	Primary B cells from peripheral blood	blood
34	chr9:115914000-115914400	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr9:115914000-115914400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr9:115914000-115914400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr9:115914000-115914400	Flanking Active TSS	HepG2	liver
38	chr9:115914000-115914600	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr9:115914000-115914600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr9:115914000-115914600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr9:115914000-115914600	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr9:115914000-115914800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr9:115914000-115914800	Flanking Active TSS	Colonic Mucosa	Colon
44	chr9:115914000-115914800	Flanking Active TSS	Placenta	Placenta
45	chr9:115914000-115914800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
46	chr9:115914000-115914800	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr9:115914000-115914800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr9:115914000-115914800	Weak transcription	NH-A	brain
49	chr9:115914000-115915000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr9:115914000-115915000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast

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