Variant report

Variant	esv3501609
Chromosome Location	chr1:211964429-211966827
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:211965100-211965250	BE2_C	brain:	n/a	n/a
2	CTCF	chr1:211965120-211965270	GM12872	blood:	n/a	n/a
3	CTCF	chr1:211965060-211965210	GM12873	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NEK2-3	chr1:211965455-211965748	NONHSAT009327

Variant related genes	Relation type
RN7SL344P	TF binding region
LPGAT1	TF binding region

Extended variants
information (count: 94 )
Associated
traits (count: 89 )

Variant overlapped rSNPs/rCNVs (count:94 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs111375861	chr1:211964456-211964457	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs113885358	chr1:211964457-211964458	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs113081127	chr1:211964460-211964461	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs67423377	chr1:211964461-211964462	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs535965684	chr1:211964597-211964598	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs190793644	chr1:211964628-211964629	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs572964765	chr1:211964681-211964682	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs77554650	chr1:211964763-211964764	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs558914462	chr1:211964769-211964770	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs149398810	chr1:211964781-211964782	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs577175219	chr1:211964794-211964795	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs545454048	chr1:211964818-211964819	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs563529290	chr1:211964873-211964874	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs182220822	chr1:211964918-211964919	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs542764997	chr1:211964950-211964951	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs561385726	chr1:211964992-211964993	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs184926608	chr1:211965011-211965012	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs546753560	chr1:211965016-211965017	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs190998721	chr1:211965031-211965032	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs573870649	chr1:211965056-211965057	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs532643667	chr1:211965062-211965063	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs550210788	chr1:211965100-211965101	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs4951428	chr1:211965103-211965104	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs568753054	chr1:211965104-211965105	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs375507441	chr1:211965108-211965109	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs371457864	chr1:211965112-211965113	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs374360790	chr1:211965116-211965117	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs368287761	chr1:211965120-211965121	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs78791498	chr1:211965127-211965128	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs372450624	chr1:211965203-211965204	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs376740778	chr1:211965221-211965222	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs369213019	chr1:211965257-211965258	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs141541372	chr1:211965336-211965337	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs547986029	chr1:211965373-211965374	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs566533636	chr1:211965434-211965435	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
36	rs113393076	chr1:211965460-211965461	Weak transcription Strong transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
37	rs533992999	chr1:211965461-211965462	Weak transcription Strong transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
38	rs541619402	chr1:211965476-211965477	Weak transcription Strong transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
39	rs558771224	chr1:211965541-211965542	Weak transcription Strong transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
40	rs75683854	chr1:211965580-211965581	Weak transcription Strong transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
41	rs61828468	chr1:211965605-211965606	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
42	rs373979073	chr1:211965711-211965712	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
43	rs188180018	chr1:211965713-211965714	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
44	rs146040144	chr1:211965730-211965731	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
45	rs398103662	chr1:211965732-211965733	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
46	rs575551715	chr1:211965738-211965739	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
47	rs542977362	chr1:211965752-211965753	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs561238868	chr1:211965757-211965758	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs192971916	chr1:211965808-211965809	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs9887808	chr1:211965814-211965815	Weak transcription Strong transcription	n/a	n/a	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:221 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211912600-211964600	Weak transcription	NHEK	skin
2	chr1:211912800-211970200	Weak transcription	HMEC	breast
3	chr1:211913800-211967800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr1:211913800-211968800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr1:211913800-211969600	Weak transcription	Small Intestine	intestine
6	chr1:211914000-211965400	Weak transcription	Thymus	Thymus
7	chr1:211914000-211973600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:211915800-211991800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr1:211916200-211965400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:211916800-211994200	Weak transcription	Fetal Brain Male	brain
11	chr1:211917000-211970400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr1:211919200-212001200	Weak transcription	Gastric	stomach
13	chr1:211922600-211965600	Weak transcription	Osteobl	bone
14	chr1:211922800-211964800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:211922800-211965400	Weak transcription	Right Ventricle	heart
16	chr1:211923000-211967200	Weak transcription	Colonic Mucosa	Colon
17	chr1:211923000-211991800	Weak transcription	HSMM	muscle
18	chr1:211923200-211967200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr1:211924000-212002400	Weak transcription	NHLF	lung
20	chr1:211931600-211964800	Weak transcription	Fetal Kidney	kidney
21	chr1:211935800-211969000	Weak transcription	Fetal Heart	heart
22	chr1:211936000-211966800	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr1:211936400-211968200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:211938200-211999400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:211939600-211978200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr1:211939600-211992600	Weak transcription	Esophagus	oesophagus
27	chr1:211939800-212002400	Weak transcription	HSMMtube	muscle
28	chr1:211940000-211965200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr1:211940000-212000600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:211940200-211964600	Weak transcription	Lung	lung
31	chr1:211940800-211964800	Weak transcription	Aorta	Aorta
32	chr1:211943200-211971200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:211943400-211972000	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr1:211945800-211979000	Weak transcription	Colon Smooth Muscle	Colon
35	chr1:211946200-211984200	Weak transcription	NH-A	brain
36	chr1:211946800-211966600	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr1:211947400-212002400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:211950000-211987000	Weak transcription	Fetal Thymus	thymus
39	chr1:211950600-211971800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr1:211950800-211971200	Weak transcription	Placenta	Placenta
41	chr1:211951400-211965200	Weak transcription	Fetal Brain Female	brain
42	chr1:211951400-211965400	Weak transcription	Primary T cells from cord blood	blood
43	chr1:211951400-211966200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:211951400-211978800	Weak transcription	Fetal Lung	lung
45	chr1:211951400-211992600	Weak transcription	Ovary	ovary
46	chr1:211952200-212003000	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr1:211952400-211964600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr1:211952600-211965400	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr1:211955200-211969400	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr1:211957400-211965400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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