Variant report

Variant	nsv978996
Chromosome Location	chr2:39037473-39038897
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:6)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:39038838-39038839	MCF-7	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:39036283..39037932-chr2:39043739..39045764,2	K562	blood:
2	chr2:38977082..38978650-chr2:39037995..39040389,2	K562	blood:
3	chr2:38975535..38978590-chr2:39035789..39038871,3	MCF-7	breast:
4	chr2:39004566..39006965-chr2:39038166..39040437,2	MCF-7	breast:
5	chr2:38977150..38978666-chr2:39038889..39040421,2	K562	blood:
6	chr2:38977053..38979638-chr2:39036320..39038717,3	K562	blood:

(count:6 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GEMIN6-1	chr2:39037948-39038059	NONHSAT070202
2	lnc-GEMIN6-1	chr2:39038701-39040716	predAs_engstrom06_BX108565_1
3	lnc-GEMIN6-1	chr2:39037948-39038059	NONHSAT070201
4	lnc-GEMIN6-1	chr2:39037899-39038059	NONHSAT070200
5	lnc-GEMIN6-1	chr2:39038728-39038917	NONHSAT070202
6	lnc-GEMIN6-1	chr2:39038728-39038917	NONHSAT070200

No data

Variant related genes	Relation type
ASS1P2	TF binding region
ENSG00000152147	chromatin interactions
ENSG00000115875	chromatin interactions

Extended variants
information (count: 72 )
Associated
traits (count: 59 )

Variant overlapped rSNPs/rCNVs (count:72 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs538764442	chr2:39037487-39037488	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs6753616	chr2:39037489-39037490	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs375614357	chr2:39037506-39037507	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs574715952	chr2:39037508-39037509	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs182206091	chr2:39037525-39037526	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs536403914	chr2:39037530-39037531	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs542186878	chr2:39037548-39037549	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs555283116	chr2:39037553-39037554	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs563569938	chr2:39037575-39037576	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs573572964	chr2:39037576-39037577	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs533797573	chr2:39037593-39037594	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs531019952	chr2:39037622-39037623	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs552752008	chr2:39037656-39037657	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs373272614	chr2:39037662-39037663	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs558569783	chr2:39037685-39037686	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs576870898	chr2:39037710-39037711	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs544302136	chr2:39037766-39037767	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs78599984	chr2:39037783-39037784	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs574618224	chr2:39037785-39037786	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs186854546	chr2:39037805-39037806	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs560044331	chr2:39037807-39037808	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs3112215	chr2:39037813-39037814	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
23	rs555812415	chr2:39037849-39037850	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs564960385	chr2:39037859-39037860	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs190359732	chr2:39037877-39037878	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs551062651	chr2:39037889-39037890	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs368576819	chr2:39037900-39037901	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
28	rs547281475	chr2:39037929-39037930	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
29	rs569240902	chr2:39037952-39037953	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
30	rs530363768	chr2:39037963-39037964	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
31	rs114274619	chr2:39037980-39037981	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
32	rs567204111	chr2:39037989-39037990	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
33	rs535799741	chr2:39037996-39037997	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
34	rs534508973	chr2:39038000-39038001	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
35	rs559251432	chr2:39038014-39038015	Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
36	rs550534081	chr2:39038033-39038034	Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
37	rs55809581	chr2:39038034-39038035	Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs556272191	chr2:39038043-39038044	Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
39	rs147037289	chr2:39038047-39038048	Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
40	rs112805353	chr2:39038055-39038056	Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
41	rs182649858	chr2:39038065-39038066	Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs116190771	chr2:39038099-39038100	Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs80298502	chr2:39038109-39038110	Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs545694792	chr2:39038122-39038123	Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs3099970	chr2:39038213-39038214	Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs34877549	chr2:39038222-39038223	Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs368059813	chr2:39038264-39038265	Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs138180075	chr2:39038270-39038271	Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs568800185	chr2:39038285-39038286	Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs115402513	chr2:39038309-39038310	Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:59)

Disease	PMID	Source
Breast cancer	17393978	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Breast cancer	17603634	CNVD
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17387387	CNVD
Neuroblastoma	17533364	CNVD
Neuroblastoma	18923191	CNVD
Endometrial cancer	22040021	CNVD
Adrenal tumor	17535989	CNVD
Breast cancer	21264507	CNVD
Basal cell lymphoma	17053054	CNVD
Medulloblastoma	17522785	CNVD
Cancer	23418310	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Bladder cancer	21909424	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Autism	22495311	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	19521722	CNVD
Autism	18522746	CNVD
Non-small cell lung cancer	18927303	CNVD
Breast cancer	21785460	CNVD
Lung cancer	18438408	CNVD
Prostate cancer	21965145	CNVD
Breast cancer	16397240	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21508638	CNVD
Neurodevelopmental disorder	22521361	CNVD
Neurocytoma	17123091	CNVD
small cell lung cancer	20016488	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
Breast cancer	21364760	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:222 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39006000-39037600	Weak transcription	Aorta	Aorta
2	chr2:39006000-39037600	Weak transcription	Gastric	stomach
3	chr2:39006400-39037800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr2:39006400-39045600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:39006400-39085600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:39006600-39038200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:39009200-39037600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr2:39009200-39037600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr2:39009200-39037600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:39009200-39037600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:39009200-39037600	Weak transcription	NHDF-Ad	bronchial
12	chr2:39009200-39037800	Weak transcription	NHEK	skin
13	chr2:39009200-39042600	Weak transcription	Fetal Kidney	kidney
14	chr2:39009200-39050000	Weak transcription	HMEC	breast
15	chr2:39009200-39052800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr2:39009400-39037600	Weak transcription	NHLF	lung
17	chr2:39009600-39037600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr2:39009600-39037600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr2:39012000-39037600	Weak transcription	Pancreas	Pancrea
20	chr2:39012200-39037600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr2:39017600-39042200	Weak transcription	Small Intestine	intestine
22	chr2:39018400-39037600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:39019000-39057800	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr2:39021400-39038000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr2:39021600-39038000	Weak transcription	Colonic Mucosa	Colon
26	chr2:39022000-39042600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr2:39022000-39066800	Weak transcription	Stomach Mucosa	stomach
28	chr2:39024000-39053000	Weak transcription	Psoas Muscle	Psoas
29	chr2:39025400-39038000	Weak transcription	HUVEC	blood vessel
30	chr2:39025600-39037600	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr2:39025600-39042400	Weak transcription	Hela-S3	cervix
32	chr2:39025600-39042400	Weak transcription	HSMM	muscle
33	chr2:39025800-39037800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr2:39026000-39037600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr2:39026600-39079800	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr2:39030000-39040800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr2:39030200-39037600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr2:39030600-39037600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr2:39030600-39037600	Weak transcription	Brain Hippocampus Middle	brain
40	chr2:39030600-39037600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr2:39030600-39088200	Weak transcription	Fetal Heart	heart
42	chr2:39032400-39037600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr2:39032600-39037600	Weak transcription	Right Ventricle	heart
44	chr2:39032800-39038200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr2:39032800-39072800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr2:39033000-39041400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr2:39033000-39053000	Weak transcription	Fetal Brain Male	brain
48	chr2:39033200-39037600	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr2:39033200-39037600	Weak transcription	HSMMtube	muscle
50	chr2:39033400-39037600	Weak transcription	Fetal Thymus	thymus

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