Variant report

Variant	nsv946496
Chromosome Location	chr1:169199774-169202986
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	GATA3	chr1:169202948-169202973	SH-SY5Y	brain:	n/a	n/a
2	POLR2A	chr1:169200340-169200381	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169201903..169204438-chr1:169206741..169208381,2	MCF-7	breast:

Variant related genes	Relation type
NME7	TF binding region

Extended variants
information (count: 133 )
Associated
traits (count: 93 )

Variant overlapped rSNPs/rCNVs (count:133 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs59028370	chr1:169199788-169199789	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs548789838	chr1:169199793-169199794	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs561570160	chr1:169199820-169199821	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs531808992	chr1:169199841-169199842	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs550356774	chr1:169199858-169199859	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs571985616	chr1:169199883-169199884	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs200432693	chr1:169199927-169199928	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs573370445	chr1:169199932-169199933	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs138530600	chr1:169199982-169199983	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs142020252	chr1:169200014-169200015	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs377259893	chr1:169200030-169200031	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs149843431	chr1:169200052-169200053	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs199706301	chr1:169200068-169200069	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs374288939	chr1:169200096-169200097	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs10800420	chr1:169200111-169200112	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
16	rs576433762	chr1:169200129-169200130	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs537662373	chr1:169200136-169200137	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs555907749	chr1:169200163-169200164	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs12410456	chr1:169200249-169200250	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
20	rs544882443	chr1:169200289-169200290	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs182195540	chr1:169200292-169200293	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs570287155	chr1:169200344-169200345	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs529466857	chr1:169200377-169200378	Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs150658072	chr1:169200389-169200390	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs139890188	chr1:169200417-169200418	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs35232870	chr1:169200462-169200463	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs550417976	chr1:169200488-169200489	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs565455605	chr1:169200497-169200498	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs61808865	chr1:169200510-169200511	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs2187963	chr1:169200540-169200541	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs566109445	chr1:169200553-169200554	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs536251414	chr1:169200582-169200583	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs12117362	chr1:169200600-169200601	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
34	rs570902236	chr1:169200601-169200602	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs536682045	chr1:169200620-169200621	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs570069228	chr1:169200649-169200650	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs12125057	chr1:169200670-169200671	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
38	rs187159917	chr1:169200826-169200827	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs577400958	chr1:169200829-169200830	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs538589413	chr1:169200849-169200850	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs12143790	chr1:169200872-169200873	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
42	rs572257350	chr1:169200887-169200888	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs149364336	chr1:169200888-169200889	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs190736115	chr1:169200995-169200996	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs183246163	chr1:169200999-169201000	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs543526328	chr1:169201001-169201002	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs186565780	chr1:169201021-169201022	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs146331441	chr1:169201027-169201028	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs541589819	chr1:169201074-169201075	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs77271624	chr1:169201091-169201092	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:93)

Disease	PMID	Source
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Autism	22495311	CNVD
Hepatocellular carcinoma	16750200	CNVD
Liposarcoma	21253554	CNVD
Burkitt''s lymphoma	18698080	CNVD
Melanoma	18172304	CNVD
Glioblastoma multiforme	21080181	CNVD
Cancer	21183584	CNVD
Multiple myeloma	16461302	CNVD
Rett syndrome	21593744	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Medulloblastoma	21979893	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	CNVD
Non-small cell lung cancer	21829676	CNVD
Carcinoma ex pleomorphic adenoma	18828159	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
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
Bladder cancer	19088036	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17002787	CNVD
Breast cancer	21858162	CNVD
Retinoblastoma	19183342	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
Chordoma	18071362	CNVD
Hepatocellular carcinoma	18803288	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Urothelial carcinoma	21177765	CNVD
Burkitt''s lymphoma	19759907	CNVD
Acute myeloid leukemia	21251322	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	21509527	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Testicular germ cell tumor	18059402	CNVD
Trisomy 5 syndrome	21098271	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Breast cancer	21611746	CNVD
Neuroblastoma	18923191	CNVD
Soft tissue tumor	16732325	CNVD
Cancer	17060936	CNVD
Lung cancer	16740712	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Ewing''s sarcoma	17952124	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Williams-beuren syndrome	16971481	CNVD
Developmental delay	21147756	CNVD
Burkitt''s lymphoma	20823134	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	21364760	CNVD
Myelofibrosis	22110671	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Lung cancer	18438408	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169172400-169207600	Weak transcription	Esophagus	oesophagus
2	chr1:169172600-169227000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:169173200-169202000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:169176600-169206200	Weak transcription	Aorta	Aorta
5	chr1:169177400-169207400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:169180000-169210000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:169180600-169206200	Weak transcription	Left Ventricle	heart
8	chr1:169182000-169201000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr1:169182800-169205400	Weak transcription	Adipose Nuclei	Adipose
10	chr1:169184400-169206200	Weak transcription	Lung	lung
11	chr1:169184600-169200600	Weak transcription	Fetal Stomach	stomach
12	chr1:169184800-169207400	Weak transcription	Ovary	ovary
13	chr1:169185000-169200800	Weak transcription	Fetal Intestine Small	intestine
14	chr1:169187600-169200200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr1:169187600-169207800	Weak transcription	Primary T cells from cord blood	blood
16	chr1:169187800-169211800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr1:169192200-169209600	Weak transcription	NHEK	skin
18	chr1:169192400-169210000	Weak transcription	Brain Hippocampus Middle	brain
19	chr1:169192600-169202800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:169194000-169210000	Weak transcription	NHDF-Ad	bronchial
21	chr1:169194800-169200600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:169194800-169207400	Weak transcription	Primary B cells from cord blood	blood
23	chr1:169194800-169214000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr1:169195200-169207600	Weak transcription	Fetal Lung	lung
25	chr1:169195400-169207600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:169197000-169200600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr1:169197000-169204600	Weak transcription	HUVEC	blood vessel
28	chr1:169197200-169206200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:169197200-169207600	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr1:169197200-169210200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:169197600-169200400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr1:169197600-169210200	Weak transcription	Brain Substantia Nigra	brain
33	chr1:169197800-169202200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr1:169198000-169209800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:169198400-169200600	Weak transcription	Colon Smooth Muscle	Colon
36	chr1:169198600-169205200	Weak transcription	Fetal Kidney	kidney
37	chr1:169199200-169205000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr1:169199200-169210200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr1:169199200-169211600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:169199600-169209800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:169200600-169200800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
42	chr1:169200600-169200800	Weak transcription	Psoas Muscle	Psoas
43	chr1:169200600-169201000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:169200600-169201200	Enhancers	Colon Smooth Muscle	Colon
45	chr1:169200600-169201200	Enhancers	Rectal Smooth Muscle	rectum
46	chr1:169200800-169201000	Enhancers	Psoas Muscle	Psoas
47	chr1:169200800-169204000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr1:169201000-169207800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:169201000-169212800	Weak transcription	Psoas Muscle	Psoas
50	chr1:169201200-169204600	Weak transcription	Rectal Smooth Muscle	rectum

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