Variant report

Variant	esv3321965
Chromosome Location	chr1:211571888-211574349
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:211554866..211557592-chr1:211571886..211574017,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRAF5-1	chr1:211571378-211572206	NONHSAT009291
2	lnc-TRAF5-1	chr1:211572502-211572779	NONHSAT009292
3	lnc-RD3-5	chr1:211572618-211572779	NONHSAT009295

Variant related genes	Relation type
ENSG00000153363	chromatin interactions
MSN	miRNA target sites

Extended variants
information (count: 93 )
Associated
traits (count: 89 )

Variant overlapped rSNPs/rCNVs (count:93 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs577527449	chr1:211571954-211571955	Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
2	rs563923523	chr1:211571962-211571963	Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
3	rs116563998	chr1:211571987-211571988	Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
4	rs544993638	chr1:211571992-211571993	Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
5	rs563209898	chr1:211571994-211571995	Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
6	rs573963027	chr1:211572046-211572047	Active TSS Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
7	rs147278992	chr1:211572091-211572092	Active TSS Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
8	rs531668716	chr1:211572110-211572111	Active TSS Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
9	rs553195904	chr1:211572139-211572140	Active TSS Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
10	rs542831167	chr1:211572140-211572141	Active TSS Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
11	rs190460219	chr1:211572141-211572142	Active TSS Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
12	rs528394775	chr1:211572142-211572143	Active TSS Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
13	rs140783282	chr1:211572158-211572159	Active TSS Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
14	rs570514758	chr1:211572160-211572161	Active TSS Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
15	rs539664500	chr1:211572162-211572163	Active TSS Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
16	rs571519362	chr1:211572206-211572207	Active TSS Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
17	rs533144484	chr1:211572338-211572339	Active TSS Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs551764721	chr1:211572368-211572369	Active TSS Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs570033210	chr1:211572369-211572370	Active TSS Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs142166445	chr1:211572441-211572442	Active TSS Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs555537250	chr1:211572462-211572463	Active TSS Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs201598373	chr1:211572508-211572509	Active TSS Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
23	rs1084977	chr1:211572519-211572520	Active TSS Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs553344531	chr1:211572533-211572534	Active TSS Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
25	rs578213588	chr1:211572543-211572544	Active TSS Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
26	rs180868079	chr1:211572544-211572545	Active TSS Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
27	rs556954584	chr1:211572613-211572614	Active TSS Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
28	rs575391907	chr1:211572621-211572622	Active TSS Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
29	rs542792518	chr1:211572652-211572653	Active TSS Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
30	rs561055613	chr1:211572660-211572661	Active TSS Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
31	rs566803841	chr1:211572722-211572723	Active TSS Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
32	rs573025304	chr1:211572740-211572741	Active TSS Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
33	rs540452175	chr1:211572754-211572755	Active TSS Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
34	rs564996649	chr1:211572758-211572759	Active TSS Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
35	rs532469045	chr1:211572770-211572771	Active TSS Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
36	rs140413679	chr1:211572777-211572778	Active TSS Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
37	rs184668103	chr1:211572892-211572893	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs530901492	chr1:211572914-211572915	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs549024057	chr1:211573009-211573010	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs375271251	chr1:211573049-211573050	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs567425264	chr1:211573109-211573110	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs535417495	chr1:211573118-211573119	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs189129081	chr1:211573184-211573185	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs575327698	chr1:211573235-211573236	Active TSS Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs181382674	chr1:211573276-211573277	Active TSS Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs146056323	chr1:211573282-211573283	Active TSS Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs112996368	chr1:211573283-211573284	Active TSS Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs185597488	chr1:211573326-211573327	Active TSS Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs190702811	chr1:211573337-211573338	Active TSS Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs181468656	chr1:211573355-211573356	Active TSS Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:89)

Disease	PMID	Source
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Autism	22495311	CNVD
Liposarcoma	21253554	CNVD
Burkitt''s lymphoma	18698080	CNVD
Melanoma	18172304	CNVD
Rett syndrome	21593744	CNVD
Medulloblastoma	21979893	CNVD
Cancer	20164919	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	CNVD
Non-small cell lung cancer	21044232	CNVD
Cervical cancer	21063398	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	20632083	CNVD
Endometrial cancer	22040021	CNVD
Ewing''s sarcoma	21437220	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Medulloblastoma	21292688	CNVD
Phyllodes tumor	17334353	CNVD
Breast cancer	21264507	CNVD
Multiple myeloma	21628407	CNVD
Cancer	16751803	CNVD
Prostate cancer	16705090	CNVD
Neuroblastoma	19435921	CNVD
Breast cancer	17850661	CNVD
Breast cancer	16461572	CNVD
Intracranial tumor	16823260	CNVD
Medulloblastoma	18056178	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Colorectal cancer	16272173	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Neuroblastoma	21899760	CNVD
Glioblastoma multiforme	17002787	CNVD
Breast cancer	21858162	CNVD
Non-small cell lung cancer	21385341	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	16608533	CNVD
Ewing''s sarcoma	22429812	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Acute myeloid leukemia	21251322	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Testicular germ cell tumor	18059402	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Breast cancer	21509527	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	17393978	CNVD
Hepatocellular carcinoma	16750200	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Trisomy 5 syndrome	21098271	CNVD
Urothelial carcinoma	21177765	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Chordoma	18071362	CNVD
Macular degeneration	22558131	CNVD
Alzheimer''s disease	21403675	CNVD
Multiple myeloma	16461302	CNVD
van der Woude syndrome	22470819	CNVD
van der Woude syndrome	20818247	CNVD
T-cell lymphomas	19863542	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Cancer	17060936	CNVD
Atypical hemolytic uremic syndrome	19861685	CNVD
Hepatocellular carcinoma	18803288	CNVD
Urothelial tumor	18831757	CNVD
Lung cancer	18438408	CNVD
Ovarian cancer	21720365	CNVD
Breast cancer	21364760	CNVD
small cell lung cancer	20016488	CNVD
Ovarian clear cell carcinoma	19293255	CNVD
Medulloblastoma	16783165	CNVD

Chromatin state (count:129 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211556800-211585800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:211556800-211589800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:211557000-211572400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:211557000-211573200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:211557000-211575000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr1:211557000-211576600	Weak transcription	Left Ventricle	heart
7	chr1:211557000-211580600	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr1:211557000-211581000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:211557000-211581800	Weak transcription	Fetal Kidney	kidney
10	chr1:211557200-211572800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr1:211557200-211573400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:211557400-211572800	Weak transcription	Fetal Intestine Large	intestine
13	chr1:211557400-211572800	Weak transcription	K562	blood
14	chr1:211557400-211574400	Weak transcription	Brain Substantia Nigra	brain
15	chr1:211557400-211574400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr1:211557400-211575600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:211557400-211576000	Weak transcription	Fetal Intestine Small	intestine
18	chr1:211557600-211573400	Weak transcription	GM12878-XiMat	blood
19	chr1:211557600-211573400	Weak transcription	Hela-S3	cervix
20	chr1:211557600-211576200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:211561600-211573000	Weak transcription	Right Ventricle	heart
22	chr1:211563400-211572000	Weak transcription	Primary T cells from cord blood	blood
23	chr1:211565200-211573000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr1:211565600-211574000	Strong transcription	Liver	Liver
25	chr1:211566200-211572800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr1:211566800-211572000	Weak transcription	Colonic Mucosa	Colon
27	chr1:211566800-211574600	Weak transcription	Pancreas	Pancrea
28	chr1:211566800-211574800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:211566800-211576800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr1:211567000-211574600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:211567000-211581600	Weak transcription	Gastric	stomach
32	chr1:211568200-211573400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr1:211568200-211575000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:211568400-211572000	Weak transcription	Fetal Stomach	stomach
35	chr1:211568400-211573000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:211568600-211573600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr1:211568800-211572200	Weak transcription	Fetal Muscle Trunk	muscle
38	chr1:211569000-211572000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:211569000-211576600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr1:211569600-211572600	Weak transcription	Placenta	Placenta
41	chr1:211569800-211573600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr1:211570000-211572800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:211570000-211573000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:211570000-211573200	Weak transcription	Ovary	ovary
45	chr1:211570000-211574800	Weak transcription	Adipose Nuclei	Adipose
46	chr1:211570000-211575000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:211570200-211574800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:211570800-211581000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:211571400-211572000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:211571400-211572000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell

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